diff --git a/modelling/build_promod_models.py b/modelling/build_promod_models.py
index f51cf0717ede4fac08a801bd1ec6b53b23edcaa8..03d8fd7f98cb46ff7808fa8dfe4fd252922e1d80 100644
--- a/modelling/build_promod_models.py
+++ b/modelling/build_promod_models.py
@@ -19,6 +19,9 @@ for t in targets:
os.path.exists(prof_path):
cmd = ['pm', 'build-model', '-p', tpl_path, '-f', aln_path,
'-s', prof_path, '-o', out_path]
- subprocess.run(cmd)
+ p = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ print(p.stdout.decode())
+ print(p.stderr.decode())
print("full modelling time: ", time.time() - start_time)
+
diff --git a/other/README.md b/other/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..037bab916b9c0c449ee0139045b62db8647757b1
--- /dev/null
+++ b/other/README.md
@@ -0,0 +1,25 @@
+Scripts and data to reproduce various plots / table from the Supporting
+information
+
+1. S1 Fig: Length of modelled loops
+2. S1 Table: Structural coverage in default StructureDB
+
+
+S1 Fig: Length of modelled loops
+--------------------------------
+
+- fetch the stdout of running build_promod_models.py in the modelling
+ benchmark by executing
+ `pm build_promod_models.py > promod3_modelling_out.txt`
+- copy promod3_modelling_out.txt in the same directory as
+ cameo_benchmark_loop_lengths.py
+- execute `pm cameo_benchmark_loop_length.py` which creates
+ cameo_benchmark_loop_lengths.png and spits out some numbers
+
+S1 Table: Structural coverage in default StructureDB
+----------------------------------------------------
+
+- execute `pm structural_coverage_in_StructureDB.py` to get the values that are
+ displayed in S1 Table. Be aware: the table reports the average values over 3
+ runs of this script.
+
diff --git a/other/cameo_benchmark_loop_lengths.png b/other/cameo_benchmark_loop_lengths.png
new file mode 100644
index 0000000000000000000000000000000000000000..393a9ea3896259d77b7671c2a149d6e0fe0a6cf0
Binary files /dev/null and b/other/cameo_benchmark_loop_lengths.png differ
diff --git a/other/cameo_benchmark_loop_lengths.py b/other/cameo_benchmark_loop_lengths.py
new file mode 100644
index 0000000000000000000000000000000000000000..f3536151c5937b870996a575ea5ce813ec750fcd
--- /dev/null
+++ b/other/cameo_benchmark_loop_lengths.py
@@ -0,0 +1,73 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+with open('promod3_modelling_out.txt', 'r') as fh:
+ modelling_out = fh.readlines()
+
+n_deletions_relaxed = 0
+initial_loop_lengths = list()
+resolved_loop_lengths = list()
+
+for line in modelling_out:
+ if line.startswith('Resolved'):
+ loop_string_initial = line.split()[1]
+ loop_string_resolved = line.split()[4]
+ loop_seq_initial = loop_string_initial.split('-')[1].strip('()')
+ loop_seq_resolved = loop_string_resolved.split('-')[1].strip('()')
+ initial_loop_lengths.append(len(loop_seq_initial))
+ resolved_loop_lengths.append(len(loop_seq_resolved))
+ if line.startswith('Closed') and 'relaxing' in line:
+ n_deletions_relaxed += 1
+
+initial_histogram = [0] * 26
+resolved_histogram = [0] * 26
+initial_n_above = 0
+resolved_n_above = 0
+
+for l in initial_loop_lengths:
+ if l > 25:
+ initial_n_above += 1
+ else:
+ initial_histogram[l] += 1
+
+
+for l in resolved_loop_lengths:
+ if l > 25:
+ resolved_n_above += 1
+ else:
+ resolved_histogram[l] += 1
+
+n_resolved_12 = sum(resolved_histogram[:13])
+n_resolved_total = sum(resolved_histogram) + resolved_n_above
+
+print('total:', n_resolved_total)
+print('resolved fraction <= 12:', float(n_resolved_12)/(n_resolved_total))
+print('initial above 25:', initial_n_above)
+print('resolved above 25:', resolved_n_above)
+print('relaxed deletions that didnt enter loop modelling', n_deletions_relaxed)
+
+x_initial = np.linspace(0, 25, 26) - 0.2
+x_resolved = x_initial + 0.4
+
+cred = (128.0/255,0.0,0.0)
+cblue = (102.0/255,153.0/255,204.0/255)
+
+# do the barplots representing the length histograms
+plt.bar(x_initial, initial_histogram, width=0.4, color=cred, align='center',
+ linewidth=1.5, label='initial length', edgecolor='k')
+plt.bar(x_resolved, resolved_histogram, width=0.4, color=cblue, align='center',
+ linewidth=1.5, label='resolved length', edgecolor='k')
+
+# do the vertical line representing the cutoff for database approach /
+# Monte Carlo fallback
+plt.axvline(12.5, linewidth = 2.0, color='k', linestyle='dashed')
+
+plt.legend(frameon=False, fontsize='x-large')
+plt.xlim((-0.4, 25.4))
+plt.xticks([0, 5, 10, 12, 15, 20, 25],['0', '5', '10', '12', '15', '20', '25'])
+plt.tick_params(axis ='both', which ='both', length = 0)
+plt.xlabel('Loop Length', fontsize='x-large')
+plt.ylabel('N', fontsize='x-large')
+
+plt.savefig('cameo_benchmark_loop_lengths.png')
+
diff --git a/other/promod3_modelling_out.txt b/other/promod3_modelling_out.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7cb47f5885ada994d6eb2356c9bf2b0f6714d7a
--- /dev/null
+++ b/other/promod3_modelling_out.txt
@@ -0,0 +1,7601 @@
+
+Build model with the following alignment:
+target MHHHHHHSSGVDLGTENLYFQSMKWDMPMAYAATNFHSEHGVIFADKVKAYTGGKLEITT
+pdb_id=2pfz, cha... ----------------------TKWDLPTAYPASNLHVENLTQFVKDVDSLSGGKLKITL
+
+target HPGGSLFKGGEIKRAVQTGQAPIGERFMSAHANEAPLLGWDNLPFLATSYEDNDKLWAAA
+pdb_id=2pfz, cha... HNNASLYKAPEIKRAVQGNQAQIGEILLTNFANEDPVYELDGLPFLATGYDASFKLYQAQ
+
+target KDKVNAQLADLNLVALYTCPWPGQGFYFKKEVTSSADTQGIKFRSYNSATATFAKELGML
+pdb_id=2pfz, cha... KPFLEKKLASQGMMLLYSVAWPPQGIFANRDIKQVSDMKGLKWRAYSPVTAKIAELVGAQ
+
+target PVQVEAAELSQALATGVAEAFISSGSTGYDRKVWEHLSHYYKVNAWLPRNYVIINKGIYE
+pdb_id=2pfz, cha... PVTVQQAELAQAMATGVIDSYMSSGSTGFDTKTYEYIKKFYDTEAWLPKNAVLVNKKAFD
+
+target GLSDDIRSALHKAADETGAACAAKSAELANWYFEQLEANGMKVEDAGPAFLKELKSIGAK
+pdb_id=2pfz, cha... ALDPATQQALKKAGAQAEERGWKLSQEKNSWYKEQLAKNGMAIIAPTAELKSGLTEVGKR
+
+target MQADWLASVGADGQAIVDAYKKM
+pdb_id=2pfz, cha... MLDDWLKKAGADGQAMIDAYRK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.80271e+12)
+Perform energy minimization (iteration 2, energy: 25920.1)
+No more stereo-chemical problems -> final energy: 23536.8
+
+
+Build model with the following alignment:
+target QVQLQESGGGSVQAGGSLRLSCVASGSIFSINAMDWYRQAPGKQRELVAGITSGGSTNYG
+pdb_id=6mxt, cha... QVQLQESGGGLVQPGGSLRLSCAASGFAFSSYELRWYRQAPGKQHELVAGITTGGNTYYA
+
+target DFVKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAAEVGGWGPPRPDYWGHGTQVTVSS
+pdb_id=6mxt, cha... DSVKGRFTISRDNAKNTVYLQMSNLRPEDTAVYACNANWD-L---LSDYWGQGTQVTVSS
+
+target GSLEVLFQ
+pdb_id=6mxt, cha... H-------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Merged gap A.GLY100-(G)-A.TRP102 and A.TRP102-(GPP)-A.ARG106 into A.GLY100-(GWGPP)-A.ARG106
+Trying to fill 1 gap(s) by database.
+Resolved A.GLY100-(GWGPP)-A.ARG106 by filling A.VAL99-(GGWGPPR)-A.PRO107 (51 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.24144e+10)
+No more stereo-chemical problems -> final energy: 5365.27
+
+
+Build model with the following alignment:
+target MAHHHHHHMTAATDPLISLSHYYLPVYKPRQVVLERGQGARVWDSQGREFIDLAAGIAVC
+pdb_id=4e3r, cha... -----------------------------GTVVVTHGEGPYIVDVNGRRYLDANSGLFNM
+
+target GLGHNDPDLVAALVEQAGKLWHTSN--VFYSAPPLHLAEELVKASR-FAERVFLCNSGAE
+pdb_id=4e3r, cha... VAGFDHKGLIDAAKAQYERFPGYHAAFGKMSDQTVMLSEKLVEVSPFDSGRVFYTNSGSE
+
+target ANEVAIKMVRKWASSQGRPADKRVIITFRGSFHGRTMGAVTATAQPKYQEGYEPLPGGFR
+pdb_id=4e3r, cha... ANDTMVKMLWFLHAAEGKP-QKRKILTRWNAYHGATAVSASMTGFPY-NSVFGLPLPGFV
+
+target YID----F-----ND---------EVQLETAMAA---GDVAAVMLEPIQGEGGVMPAKSG
+pdb_id=4e3r, cha... HLTCPHYWRYGEEGETEEQFVARLARELEETIQREGADTIAGFFAEPVMGAGGVIPPAKG
+
+target FLKRVRELCDQHDALLVLDEIQAGMGRTGTLFAHWQDDVVPDMVTLAKALGGG-FPIGAM
+pdb_id=4e3r, cha... YFQAILPILRKYDIPVISDEVVCGFGRTGNTWGCVTYDFTPDAIISSKNLTAGFFPMGAV
+
+target LAGPKVAETMQFG-------AHGTTFGGNPLAAAVARVALRKLASSEIAANVSRQSKALR
+pdb_id=4e3r, cha... ILGPELSKRLETAIEAIEEFPHGFTASGHPVGCAIALKAIDVVMNEGLAENVRRLAPRFE
+
+target DGFARINEEFGVFSEVRGRGLMLGAVLSKDF----A--G-QA--GAILDHAAGQGLLTLQ
+pdb_id=4e3r, cha... ERLKHIA-ERPNIGEYRGIGFMWALEAVKDKASKTPFDGNLSVSERIANTCTDLGLICFP
+
+target AGPDVLRFVPSLNITDEEVAEGLKRLRAAIAAFIAAR
+pdb_id=4e3r, cha... L-GQSVVLCPPFILTEAQMDEMFDKLEKALDKVFA--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 16).
+Initialized default backbone scoring for modelling.
+Closed: A.ARG104-()-A.PHE105 by relaxing A.ALA102-(SR)-A.PHE105
+Closed: A.ALA193-()-A.GLY194 by relaxing A.ALA193-(GDV)-A.ALA197
+Closed: A.GLY269-()-A.PHE270 by relaxing A.GLY269-(F)-A.PRO271
+Closed: A.GLY361-()-A.GLN362 by relaxing A.GLY361-(Q)-A.ALA363
+Closed: A.ALA363-()-A.GLY364 by relaxing A.ALA363-(GA)-A.ILE366
+Trying to merge 11 gap(s) with distance 0.
+Merged gap A.ASP180-()-A.PHE181 and A.PHE181-()-A.ASN182 into A.ASP180-(F)-A.ASN182
+Merged gap A.PHE359-()-A.ALA360 and A.ALA360-()-A.GLY361 into A.PHE359-(A)-A.GLY361
+Trying to fill 9 gap(s) by database.
+Resolved A.ASN85-()-A.VAL86 by filling A.SER84-(NVF)-A.TYR88 (92 candidates, BB_DB)
+Resolved A.PRO136-(A)-A.ASP138 by filling A.PRO136-(ADKR)-A.VAL141 (130 candidates, BB_DB)
+Resolved A.LYS164-(Y)-A.GLN166 by filling A.ALA161-(QPKY)-A.GLN166 (69 candidates, BB_DB)
+Resolved A.ASP180-(F)-A.ASN182 by filling A.ILE179-(DFND)-A.GLU184 (72 candidates, BB_DB)
+Resolved A.GLY288-()-A.ALA289 by filling A.MET285-(QFGAH)-A.GLY291 (85 candidates, BB_DB)
+Resolved A.ASN335-(E)-A.GLU337 by filling A.ASN335-(EEF)-A.GLY339 (103 candidates, BB_DB)
+Resolved A.PHE359-(A)-A.GLY361 by filling A.LEU355-(SKDFA)-A.GLY361 (45 candidates, BB_DB)
+Resolved A.ALA380-(G)-A.PRO382 by filling A.GLN379-(AGPD)-A.VAL384 (87 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.95994e+11)
+No more stereo-chemical problems -> final energy: 12756.9
+
+
+Build model with the following alignment:
+target GSMRGKVSLEEAFELPKFAAQTKEK-------A--------ELYIAPNNRDRYFEEILNP
+pdb_id=4qrn, cha... -GYL-RIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDL
+
+target CGNRLELSNKHGIGYTIYSIYSPGPQGWTERAECEEYARECNDYISGEIANHKDRMGAFA
+pdb_id=4qrn, cha... GERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMG
+
+target ALSMHDPKQASEELTRCVKELGFLGALVNDVQHAGPEGETHIFYDQPEWDIFWQTCVDLD
+pdb_id=4qrn, cha... TVAPQDPEWSAREIHRGARELGFKGIQINSHTQG-------RYLDEEFFDPIFRALVEVD
+
+target VPFYLHPEPPFGSYLRNQYEGRKYLIGPPVSFANGVSLHVLGMIVNGVFDRFPKLKVILG
+pdb_id=4qrn, cha... QPLYIHPATSPDSMI-DPM-LEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVG
+
+target HLGEHIPGDFWRIEHWFEHCSRP----LAKSRGDVFAEKPLLHYFRNNIWLTTSGNFSTE
+pdb_id=4qrn, cha... HMGEALPYWLYRLDYMHQAGVRSQRYERMK-----PLKKTIEGYLKSNVLVTNSGVAWEP
+
+target TLKFCVEHVGAERILFSVDSPYEHIDVGCGWYDDNAKAIMEAVGGEKAYKDIGRDNAKKL
+pdb_id=4qrn, cha... AIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMD--M-SA--QT--KKKFFQTNAEKW
+
+target FKLGKFYDSEA
+pdb_id=4qrn, cha... FKL--------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Trying to merge 12 gap(s) with distance 0.
+Merged gap A.LYS25-()-A.ALA26 and A.ALA26-()-A.GLU27 into A.LYS25-(A)-A.GLU27
+Merged gap A.ALA317-(KA)-A.ILE320 and A.ILE320-(M)-A.GLU322 into A.ALA317-(KAIM)-A.GLU322
+Trying to fill 10 gap(s) by database.
+Resolved A.ARG4-(G)-A.LYS6 by filling A.SER2-(MRGK)-A.VAL7 (68 candidates, BB_DB)
+Resolved A.LYS25-(A)-A.GLU27 by filling A.THR22-(KEKA)-A.GLU27 (74 candidates, BB_DB)
+Resolved A.ALA139-(GPEGETH)-A.ILE147 by filling A.GLN137-(HAGPEGETH)-A.ILE147 (869 candidates, BB_DB)
+Resolved A.LEU180-(R)-A.ASN182 by filling A.GLY177-(SYLR)-A.ASN182 (49 candidates, BB_DB)
+Resolved A.TYR184-(E)-A.GLY186 by filling A.TYR184-(EGRKY)-A.LEU190 (52 candidates, BB_DB)
+Resolved A.PRO248-()-A.LEU249 by filling A.CYS245-(SRP)-A.LEU249 (40 candidates, BB_DB)
+Resolved A.LYS251-(SRGDV)-A.PHE257 by filling A.ALA250-(KSRGDVF)-A.ALA258 (65 candidates, BB_DB)
+Resolved A.ALA317-(KAIM)-A.GLU322 by filling A.ASP315-(NAKAIM)-A.GLU322 (150 candidates, BB_DB)
+Resolved A.ALA323-(VG)-A.GLY326 by filling A.ALA319-(IMEAVG)-A.GLY326 (91 candidates, BB_DB)
+Resolved A.GLU327-(KA)-A.TYR330 by filling A.ALA323-(VGGEKA)-A.TYR330 (46 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.89497e+21)
+No more stereo-chemical problems -> final energy: 21458.6
+
+
+Build model with the following alignment:
+target GHMMVKIMPNLPGLYFLQAYPSEEIWRLFVDGRFWSKENGWRGYESREPGSLNAALESLC
+pdb_id=4bet, cha... -------MPNLPGLYFLQAYPSEEIWRLFVDGRFWSKENGWRGYESREPGCLNAALESLC
+
+target SIALQVEKSGEEFELSVDLIKRIHKKSGKKVEELQEKNPGELRTDEPVSFCIPAGRASIK
+pdb_id=4bet, cha... SIALQVEKSGEEFELSVDLIKRIHKKCGKKVEELQEKNPGELRTDEPVSFGIPAGRASIK
+
+target GIEEFLSLVFLTEGGAEFGPGKAGPFGPRFDKNYFKNLNPEQIPDLAKQIYFDMSKYGHS
+pdb_id=4bet, cha... GIEEFLSLVFLTEGGAEFGPGKAGPFGPRFDKNYFKNLNPEQIPDLAKQIYFDMCKYGHS
+
+target NTNHFYLAVMKNVDVYLEKITQSYNKEIKTAETLDEKLKIIVKHIRMYEVLHPFRDANGR
+pdb_id=4bet, cha... NTNHFYLAVMKNVDVYLEKITQSYNKEIKTAETLDEKLKIIVKHIRMYEVLAPFRDANGR
+
+target TFVNNLLNILLMQQGLPPATFYEPNVFDLYSAEELVVVVKEAIFNTVEII--------EQ
+pdb_id=4bet, cha... TFVNNLLNIPLMQQGLPPATFYEPNVFDLYSAEE--------LVVVVKEAIFNTVEIIEQ
+
+target SKRKTPITLYGYHSSLEEQTKFRDMLDSPSYEKIKHMDFSDLNPEKLHLKTQKCLSSLNE
+pdb_id=4bet, cha... SKRKTPITLYGYHSSLEEQTKFRDMLDSPSYEKIKHMDFSDLNPEKLHLKTQKCLSSLNE
+
+target QYPLHRGAIYLSDPGEIKLLLSNRNESQINQQIEQGAPPIYVGKTPAHLAVISGNMAMLD
+pdb_id=4bet, cha... QYPLHRGAIYLSDPGEIKLLLSNRNESQINQQIEQGAPPIYVGKTPAHLAVISGNMAMLD
+
+target ELIAKKADLSLQDYDGKTALHYAAECGNMQIMGKILKVVLSQEDAIKVLNIKDNHGKTAF
+pdb_id=4bet, cha... ELIAKKADLSLQDYDGKTALHYAAECGNMQIMGKILKVVLSQEDAIKVLNIKDNHGKTAF
+
+target HYAAEFGTPELISALTTTEVIQINEPDNSGSSAITLAYKNHKLKIFDELLNSGADISDEL
+pdb_id=4bet, cha... HYAAEFGTPELISAL---------------------------------------------
+
+target LDAIWARKDKETLGKIIAKNEKILLNKEAFRIAISLGSVSLVKKFLRAGVDIDIPLTKDK
+pdb_id=4bet, cha... ------------------------------------------------------------
+
+target ATPLMLSINSGNPKLVSYLLKKGANTRLTDTSGNSVLHYVFYSKAENREALANIITEKDK
+pdb_id=4bet, cha... ------------------------------------------------------------
+
+target KLINQPNANGNPPLYNAVVVNDLKMATILLEMGARVDFEDRLGNNILHSAMRRCDLPIIL
+pdb_id=4bet, cha... ------------------------------------------------------------
+
+target DIVKKDSTLLHKRNSERRNPFHQALHEMHTFPSSKETEEIHFMNLSDLLLKEGVDLNKKD
+pdb_id=4bet, cha... ------------------------------------------------------------
+
+target IKGKTILDIALSKQYFHLCVKLMKAGAHTNI
+pdb_id=4bet, cha... -------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLU274-(LVVVVKEA)-A.ILE283), only 31 candidates
+Resolved A.ILE290-()-A.GLU291 by filling A.ILE289-(IEQSKR)-A.LYS296 (61 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLU274-(LVVVVKEA)-A.ILE283), only 31 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLU274-(LVVVVKEA)-A.ILE283), only 31 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLU274-(LVVVVKEA)-A.ILE283), only 31 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLU274-(LVVVVKEA)-A.ILE283), only 31 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.GLU274-(LVVVVKEA)-A.ILE283 by filling A.SER271-(AEELVVVVKEA)-A.ILE283 (49 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.06821e+18)
+No more stereo-chemical problems -> final energy: 30215.6
+
+
+Build model with the following alignment:
+target MSKTIT-YYN-SGA-VPLINA-SELPYDVVNLAFLSSSSNNP-FNLVLSGAIAATESSFT
+pdb_id=3hu7, cha... --LDIAVYWGQNFDERSLEATCDTGNYAYVIIGFLNTFGGGQTPALDISGH----S----
+
+target T-NTIEAIKVMQHKGQKVLISFGGGTMGSNAYRSLSEDTAKLADSLA------------S
+pdb_id=3hu7, cha... PSGLEPQIKHCQSKNVKVLLSIGGPKGPY-SL-DSRSDANDLAVYLFNNFLLPPGHSENR
+
+target FVKNNQLDGVDIDYEDTAAFTGQAGYDGAQFLISLTQELRKRLP-SPDYIISHAPQPPYL
+pdb_id=3hu7, cha... PFGNAVLDGIDFHIEHGGP----------SQYQLLANILSSFRLAGTEFALTAAPQCVYP
+
+target EQGGYMAGYVEVVELVGQEIDWLNVQFYNNPPWSA---NPDQIVSSYLNYTKLPNMSPEK
+pdb_id=3hu7, cha... DP------NLGTVIN-SATFDAIWVQFYNNPQCSYSSGNAEALMNAWREWS--MKARTKK
+
+target VIAGFPVTQNDAGSGYMPVQTIINEVIKPIQQQSSLGGIMNWQFSSDHNGDWIKAIAQSL
+pdb_id=3hu7, cha... VFLGFPAHPDAAGSGYMPPEKVKFHVFPAAKKSYKFGGIMLWDSYWDTVSNFSSKILGE-
+
+target NSLEHHHHHH
+pdb_id=3hu7, cha... ----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 17).
+Initialized default backbone scoring for modelling.
+Closed: A.ASN9-()-A.SER10 by relaxing A.TYR8-(NS)-A.GLY11
+Closed: A.ALA12-()-A.VAL13 by relaxing A.SER10-(GAV)-A.PRO14
+Closed: A.ALA18-()-A.SER19 by relaxing A.ASN17-(AS)-A.GLU20
+Closed: A.PRO146-()-A.SER147 by relaxing A.LEU145-(PS)-A.PRO148
+Trying to merge 13 gap(s) with distance 0.
+Merged gap A.ALA46-(IAAT)-A.GLU51 and A.GLU51-(SSFT)-A.THR56 into A.ALA46-(IAATESSFT)-A.THR56
+Merged gap A.ALA46-(IAATESSFT)-A.THR56 and A.THR56-()-A.ASN57 into A.ALA46-(IAATESSFTT)-A.ASN57
+Trying to fill 11 gap(s) by database.
+Resolved A.THR6-()-A.TYR7 by filling A.THR6-(YYNSGA)-A.VAL13 (99 candidates, BB_DB)
+Resolved A.PRO38-()-A.PHE39 by filling A.SER35-(NNP)-A.PHE39 (43 candidates, BB_DB)
+Resolved A.ALA46-(IAATESSFTT)-A.ASN57 by filling A.ALA46-(IAATESSFTTN)-A.THR58 (71 candidates, BB_DB)
+Resolved A.SER83-(N)-A.ALA85 by filling A.GLY79-(TMGSN)-A.ALA85 (46 candidates, BB_DB)
+Resolved A.TYR86-(R)-A.SER88 by filling A.TYR86-(RSL)-A.SER90 (49 candidates, BB_DB)
+Resolved A.ALA101-()-A.SER102 by filling A.ALA101-(SFVKN)-A.ASN107 (84 candidates, BB_DB)
+Failed at loop insertion (A.ALA121-(FTGQAGYDGA)-A.GLN132), only 11 candidates
+Resolved A.GLN163-(GGYMAG)-A.TYR170 by filling A.TYR160-(LEQGGYMAGY)-A.VAL171 (59 candidates, BB_DB)
+Resolved A.LEU176-(V)-A.GLY178 by filling A.LEU176-(VGQE)-A.ILE181 (104 candidates, BB_DB)
+Resolved A.ALA196-()-A.ASN197 by filling A.ASN191-(PPWSA)-A.ASN197 (40 candidates, BB_DB)
+Resolved A.THR209-(KL)-A.PRO212 by filling A.THR209-(KLPNM)-A.SER215 (46 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ALA121-(FTGQAGYDGA)-A.GLN132), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ALA121-(FTGQAGYDGA)-A.GLN132), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ALA121-(FTGQAGYDGA)-A.GLN132), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ALA121-(FTGQAGYDGA)-A.GLN132), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.ALA121-(FTGQAGYDGA)-A.GLN132 by filling A.THR119-(AAFTGQAGYDGA)-A.GLN132 (68 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.00794e+12)
+No more stereo-chemical problems -> final energy: 29955.2
+
+
+Build model with the following alignment:
+target MTAVEFIEPLTHEEGVSQATKLFVDTYGAAPEGVWAAPGRVNLIGEHTDYNAGLCLPIAL
+pdb_id=2aj4, cha... --------------KCPSIIKKFISAYDAKPDFVARSPGRVNLIGEHIDYCDFSVLPLAI
+
+target PHRTFIALKPREDTK--VRVVSGVAPDKVAEADLDG------LKARGVDGWSAYPTGV--
+pdb_id=2aj4, cha... DFDMLCAVKVLNEKNPSITLINADPKFAQRKFDLPLDGSYVTID-PSVSDWSNYFKCGLH
+
+target --AWALRQA---GFD--KVKGFDAAFVSCVPLGSGLSSSAAMTCSTALALDDVYGLG---
+pdb_id=2aj4, cha... VAHSFLKKLAPERFASAPLAGLQVFCEGDVPTGSGLSSSAAFICAVALAVVKANMGPGYH
+
+target YGDSDAGRVTLINAAIKSENEMAGASTGGLDQNASMRCTEGHALLLDCRPELTPLENVSQ
+pdb_id=2aj4, cha... M-----SKQNLMRITVVAEH-YVGVNNGGMDQAASVCGEEDHALYVEFKP----QLKATP
+
+target QEFDLDKY-NLELLVVDTQAPHQL---NDGQYAQRRATCEEAAKILG----VA-------
+pdb_id=2aj4, cha... FKFPQLKNHEISFVIANTLVVSNKFETAPTNYNLRVVEVTTAANVLAATYGVVLL-----
+
+target ------NLRVTADGISK----------------ADDQFQALKETLDALPD----------
+pdb_id=2aj4, cha... ---NKGNLRDFMNVYYARYHNISTPWNGDIESGIERLTKMLVLVEESLANKKQGFSVDDV
+
+target -------------------E------TMKKRVRHVVTEIERVRSFVRAFAQ-----GD--
+pdb_id=2aj4, cha... AQSLNCSREEFTRDYLTTSPVRFQVLKLYQRAKHVYSESLRVLKAVKLMTT--FTADEDF
+
+target IKAAGRLFNASHDSLAADYEVTVPELDIAVDVARKNGAYGARMTGGGFGGSIIALVDK--
+pdb_id=2aj4, cha... FKQFGALMNESQASCDKLYECSCPEIDKICSIALSNGSYGSRLTGAGWGGCTVHLVPGGP
+
+target -GQGHEIAQKIADRFEKEGFN-------APRALPAFAAASASREAKLAAALEHHHHHH
+pdb_id=2aj4, cha... NGNIEKVKEALANEFYKVKYPKITDAELENAIIVSKPALGSCLY--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 21).
+Initialized default backbone scoring for modelling.
+Trying to merge 21 gap(s) with distance 0.
+Merged gap A.GLY160-()-A.TYR161 and A.TYR161-(GDSDA)-A.GLY167 into A.GLY160-(YGDSDA)-A.GLY167
+Merged gap A.ASP293-()-A.GLU294 and A.GLU294-()-A.THR295 into A.ASP293-(E)-A.THR295
+Trying to fill 19 gap(s) by database.
+Resolved A.LYS75-()-A.VAL76 by filling A.PRO70-(REDTK)-A.VAL76 (66 candidates, BB_DB)
+Resolved A.GLY94-()-A.LEU95 by filling A.ALA90-(DLDG)-A.LEU95 (57 candidates, BB_DB)
+Resolved A.LYS96-(A)-A.ARG98 by filling A.LYS96-(ARG)-A.VAL100 (86 candidates, BB_DB)
+Resolved A.VAL110-()-A.ALA111 by filling A.PRO107-(TGV)-A.ALA111 (113 candidates, BB_DB)
+Resolved A.ALA117-()-A.GLY118 by filling A.ALA117-(GFDKV)-A.LYS123 (251 candidates, BB_DB)
+Resolved A.GLY160-(YGDSDA)-A.GLY167 by filling A.GLY160-(YGDSDA)-A.GLY167 (184 candidates, BB_DB)
+Resolved A.ASN180-(E)-A.MET182 by filling A.ASN180-(EMAGA)-A.SER186 (121 candidates, BB_DB)
+Resolved A.PRO210-(ELTP)-A.LEU215 by filling A.ARG209-(PELTPL)-A.GLU216 (42 candidates, BB_DB)
+Resolved A.TYR228-()-A.ASN229 by filling A.LEU225-(DKY)-A.ASN229 (47 candidates, BB_DB)
+Resolved A.LEU243-()-A.ASN244 by filling A.LEU243-(NDGQ)-A.TYR248 (75 candidates, BB_DB)
+Resolved A.GLY263-()-A.VAL264 by filling A.ILE261-(LGVAN)-A.LEU267 (83 candidates, BB_DB)
+Resolved A.LYS276-()-A.ALA277 by filling A.ALA271-(DGISK)-A.ALA277 (143 candidates, BB_DB)
+Resolved A.ASP293-(E)-A.THR295 by filling A.LEU291-(PDET)-A.MET296 (49 candidates, BB_DB)
+Resolved A.GLN319-()-A.GLY320 by filling A.ALA316-(FAQGD)-A.ILE322 (98 candidates, BB_DB)
+Resolved A.LYS379-()-A.GLY380 by filling A.ASP378-(KGQ)-A.GLY382 (52 candidates, BB_DB)
+Resolved A.ASN399-()-A.ALA400 by filling A.GLU394-(KEGFN)-A.ALA400 (99 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.03913e+17)
+Perform energy minimization (iteration 2, energy: 19876.9)
+Perform energy minimization (iteration 3, energy: 14656.3)
+Perform energy minimization (iteration 4, energy: 12708.1)
+No more stereo-chemical problems -> final energy: 11707.8
+
+
+Build model with the following alignment:
+target GSGSGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVA
+pdb_id=3a1m, cha... -----------EGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVA
+
+target GTVDWDVGGDWTEKMASMSSKGNVTHEGNYNQLGNYTVQGNVGIQGAFSQFGGAGSVEGG
+pdb_id=3a1m, cha... GTVDWDVGGDWTEKMASMSSISS-------------------------------------
+
+target WTIDNIRYLGHRHGGVQSGGSKTDTPSA
+pdb_id=3a1m, cha... ----------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 17360.7)
+No more stereo-chemical problems -> final energy: 9023.14
+
+
+Build model with the following alignment:
+target MAHHHHHHMFRTHTNGELSLKNLNEEVTLSGWVQTIRDKGFMIWIDLRDRYGITQLVFDQ
+pdb_id=4rmf, cha... -------------AAGSLRPADAGQTVTLAGWVARRRDHGGVIFIDLRDASGVSQVVFRE
+
+target DRSSAALLEEAKKLGREFVIQVSGKVIERASK--NPKIPTGEIEILVEKLTILNNSELPP
+pdb_id=4rmf, cha... G----DVLAAAHRLRAEFCVAVTGVVEVRPEGNENPEIPTGQIEVNATELTVLGESAPLP
+
+target FTIEDETDGGEELRMKYRYLDIRRNPVKEKLIFRHKIAQKVRNYLSDQGFIEVETPVLIK
+pdb_id=4rmf, cha... FQLDEQ--AGEEARLKYRYLDLRREGPGNALRLRSKVNAAARSVLAEHDFVEIETPTLTR
+
+target STPEGARDFVVPSRMNPGQFYALPQSPQTFKQLLMVGGMDKYFQIVKCFRDEDLRADRQP
+pdb_id=4rmf, cha... STPEGARDFLVPARLQPGSFYALPQSPQLFKQLLMVAGMERYYQIARCYRDEDFRADRQP
+
+target EFTQIDCEMAFVEQEDVMNIFEGLTQNLLKDIAGQEFGK-FPRMTFAEAMKKYGNDKPDI
+pdb_id=4rmf, cha... EFTQLDMEMSFVEADDVIAISEQVLKAVWATI-GYDLPLPLPRISYEEAMRRFGSDKPDL
+
+target RFGMEFHELNDLVKGKDFKIFDEAELVVGINVEGCAEYTRKQIDELTDWIKRPQIGATGM
+pdb_id=4rmf, cha... RFGIELVECTEYFKDTTFRVFQA-PYVGAVVMPGGASQPRRTLDGWQEFAKQ--RGHKGL
+
+target VWIKYQADGIVTSSVNKFYNEEDLKKIAEEFGAKPGDLMLVLSGNENKVRAQLSALRMEL
+pdb_id=4rmf, cha... AYVLVGEDGTLGGPVAKNLSDAERDGLVAHVGANPGDCIFFAAGPAKGARALLGATRIEI
+
+target GNRLGLRKGNEFAPLWVIDFPLLEWDEDT----------QRYHAMHHPFTSPKPEDIHLL
+pdb_id=4rmf, cha... AKRLDLIDPNAWAFTWVVDFPMFEAADEATAAGDVAVGSGAWTAMHHAFTAPKPDSVDTF
+
+target ENEAGKARANAYDLVINGNEIGGGSIRIFDKDLQAQMFSLLGFTPEEAEAQFGFLMNAFK
+pdb_id=4rmf, cha... DSDPGNALSDAYDIVCNGNEIGGGSIRIHRRDIQERVFAMMGIDHDEAQEKFGFLLDAFS
+
+target YGAPPHGGLAFGFDRLVAVLDGNEVIRDYIAFPKNNSGRDVMIDAPASIANEQLDELALT
+pdb_id=4rmf, cha... YGAPPHGGIAFGWDRITALLAGVDSIREVIAFPKSGGGVDPLTDAPAPITPQQRKESG--
+
+target ININE
+pdb_id=4rmf, cha... -----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 8).
+Initialized default backbone scoring for modelling.
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.ASP61-(RSSA)-A.ALA66 by filling A.ASP59-(QDRSSA)-A.ALA66 (94 candidates, BB_DB)
+Resolved A.LYS92-()-A.ASN93 by filling A.GLU88-(RASK)-A.ASN93 (119 candidates, BB_DB)
+Resolved A.GLU124-(TD)-A.GLY127 by filling A.GLU122-(DETD)-A.GLY127 (66 candidates, BB_DB)
+Resolved A.ILE270-(A)-A.GLY272 by filling A.LYS268-(DIAG)-A.GLN273 (78 candidates, BB_DB)
+Resolved A.LYS277-()-A.PHE278 by filling A.PHE275-(GKF)-A.PRO279 (51 candidates, BB_DB)
+Resolved A.GLU320-(A)-A.GLU322 by filling A.PHE318-(DEAE)-A.LEU323 (187 candidates, BB_DB)
+Resolved A.ARG349-(PQ)-A.ILE352 by filling A.ARG349-(PQIGA)-A.THR355 (40 candidates, BB_DB)
+Resolved A.THR446-()-A.GLN447 by filling A.TRP442-(DEDT)-A.GLN447 (71 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.84798e+12)
+Perform energy minimization (iteration 2, energy: 21361.8)
+No more stereo-chemical problems -> final energy: 17003.6
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMATKSVKRGVAYDVASPADLSALSTGMSWWYNWSPKPHDR
+pdb_id=5u22, cha... ------------------------------------------------------------
+
+target LAAYDYAGQYNVDFVPMVWNANLDDGQLKLYLLAHPGIRYLLVINEPNLVDQANMTPQAA
+pdb_id=5u22, cha... ---------------------------------------GNEIWNEPDVTWK--DSNGLS
+
+target -AQLWPRLEQISAQ--TGVKLVGPAMNWGTMTGYGDPVAWLDAFYAAYASAHQGRDPQID
+pdb_id=5u22, cha... FNQMWKQTYDLLRQIDPNEKIIGPSFSW-----Y--EENKMKNFLQFSKQ----NNCLPD
+
+target YLAFHWYDY--GLSSMLDRL----SRYG---KPFWVTEFANWHTLDDGLQIDSLEKQKQQ
+pdb_id=5u22, cha... IIAWHELSGIDGVSSHFRSYRNLEKSLGISERPITINEYCDENHDL----EGQPGSSARF
+
+target MAEMVTMLERRSDV-FRYAWFTGRMTPDPHFSSLLDAEGRLTELGQYYLSLPYSE
+pdb_id=5u22, cha... IGR----FERYKVDSGMITWWFVP-HPGR-LGSLLASDTQKGAGWYFY-------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 14).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA120-()-A.ALA121 by relaxing A.ALA120-(A)-A.GLN122
+Closed: A.TYR186-()-A.GLY187 by relaxing A.TRP183-(YDY)-A.GLY187
+Trying to merge 12 gap(s) with distance 0.
+Merged gap A.TRP145-(GTMTG)-A.TYR151 and A.TYR151-(GD)-A.PRO154 into A.TRP145-(GTMTGYGD)-A.PRO154
+Trying to fill 11 gap(s) by database.
+Resolved A.GLN112-(AN)-A.MET115 by filling A.LEU109-(VDQAN)-A.MET115 (170 candidates, BB_DB)
+Resolved A.GLN133-()-A.THR134 by filling A.GLN133-(TGVKL)-A.VAL139 (111 candidates, BB_DB)
+Resolved A.TRP145-(GTMTGYGD)-A.PRO154 by filling A.ASN144-(WGTMTGYGDP)-A.VAL155 (52 candidates, BB_DB)
+Resolved A.SER167-(AHQG)-A.ARG172 by filling A.SER167-(AHQGRD)-A.PRO174 (59 candidates, BB_DB)
+Resolved A.LEU195-()-A.SER196 by filling A.LEU195-(SRY)-A.GLY199 (42 candidates, BB_DB)
+Resolved A.GLY199-()-A.LYS200 by filling A.LEU195-(SRYG)-A.LYS200 (41 candidates, BB_DB)
+Resolved A.ASP214-(DGLQ)-A.ILE219 by filling A.LEU213-(DDGLQIDS)-A.LEU222 (148 candidates, BB_DB)
+Resolved A.GLU231-(MVTM)-A.LEU236 by filling A.GLU231-(MVTMLER)-A.ARG239 (41 candidates, BB_DB)
+Resolved A.VAL242-()-A.PHE243 by filling A.GLU237-(RRSDV)-A.PHE243 (42 candidates, BB_DB)
+Resolved A.ARG251-(M)-A.THR253 by filling A.PHE248-(TGRM)-A.THR253 (42 candidates, BB_DB)
+Resolved A.PRO256-(H)-A.PHE258 by filling A.THR253-(PDPH)-A.PHE258 (40 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8.81665e+13)
+Perform energy minimization (iteration 2, energy: 12675.2)
+No more stereo-chemical problems -> final energy: 10253.3
+
+
+Build model with the following alignment:
+target GAMAESFFSDFGLLWYLKELRKEEFWKFKELLKQPLEKFELKPIPWAELKKASKEDVAKL
+pdb_id=4n1k, cha... -----SFFPDFGLLLYLEELNKEELNTFKLFLKETMEPEH-GLTPWNEVKKARREDLANL
+
+target LDKHYPGKQAWEVTLNLFLQINRKDLWTKAQEEMRNKLN
+pdb_id=4n1k, cha... MKKYYPGEKAWSVSLKIFGKMNLKVLCERAKE-------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.GLU40-(L)-A.LYS42 by filling A.GLU40-(LKPI)-A.PRO45 (58 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 135452)
+No more stereo-chemical problems -> final energy: 8102.49
+
+
+Build model with the following alignment:
+target QGTGCSVEIINSNQVSVGSGCARINSVTNIGDNQGRRWGVLANSSCGLST-TQNLPSGWS
+pdb_id=2mm0, cha... ----CVANILNINEAVIATGCVPAGGELRIFVGSSHSYLIKATSSCGLSLTNQVFINGES
+
+target LRQTGFCNA
+pdb_id=2mm0, cha... VQSGGRC--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Closed: A.THR50-()-A.THR51 by relaxing A.THR50-(T)-A.GLN52
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.51763e+07)
+No more stereo-chemical problems -> final energy: 2148.45
+
+
+Build model with the following alignment:
+target GPGSDAEQRAVAKALFDAVNKHLS--NPFIEVEMRLGQFKVEED----------------
+pdb_id=3kyh, cha... ----DDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTE
+
+target --ANFTACVSTEDYERIKTYLMTEME------NSSMTRSVTHDVSLR---------GWRH
+pdb_id=3kyh, cha... LDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVG-----PRFLRM
+
+target TYATDENGNPTRCVSIVRKKRLFVKNIVVPLGAYNLRFAVSTETPGDLRFSGA---GPRA
+pdb_id=3kyh, cha... STDI----KTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSP
+
+target GHTRLKDRLSITDG--MFRYDMTQVTEKGV--------LMHEVEIEGVFSS--H--EKQL
+pdb_id=3kyh, cha... ISERTKDRVSYIHNDSCTRIDITKVENH--------SETTHEVELEINTPALLNAFDNIT
+
+target TE-SWLEELLRRAMRLATLRTN
+pdb_id=3kyh, cha... NDSKEYASLIRTFLNNGT----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.GLU190-()-A.SER191 by relaxing A.GLU190-(S)-A.TRP192
+Trying to merge 10 gap(s) with distance 0.
+Merged gap A.SER183-()-A.HIS184 and A.HIS184-()-A.GLU185 into A.SER183-(H)-A.GLU185
+Trying to fill 9 gap(s) by database.
+Resolved A.SER24-()-A.ASN25 by filling A.LYS21-(HLS)-A.ASN25 (64 candidates, BB_DB)
+Resolved A.ASP42-()-A.ALA43 by filling A.LYS38-(VEED)-A.ALA43 (44 candidates, BB_DB)
+Resolved A.GLU66-()-A.ASN67 by filling A.MET65-(ENSS)-A.MET70 (82 candidates, BB_DB)
+Resolved A.ARG81-()-A.GLY82 by filling A.VAL78-(SLRG)-A.TRP83 (89 candidates, BB_DB)
+Resolved A.THR89-(DENG)-A.ASN94 by filling A.THR89-(DENGNPTR)-A.CYS98 (249 candidates, BB_DB)
+Resolved A.ALA138-()-A.GLY139 by filling A.ALA138-(GPRA)-A.GLY143 (109 candidates, BB_DB)
+Resolved A.GLY156-()-A.MET157 by filling A.THR154-(DGM)-A.PHE158 (62 candidates, BB_DB)
+Resolved A.LYS168-(GV)-A.LEU171 by filling A.THR166-(EKGV)-A.LEU171 (43 candidates, BB_DB)
+Resolved A.SER183-(H)-A.GLU185 by filling A.SER183-(HEKQ)-A.LEU188 (138 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.4402e+10)
+No more stereo-chemical problems -> final energy: 1128.7
+
+
+Build model with the following alignment:
+target MKLGVCYYPEHWPKSRWVEDAQHMRRIGIQYVRVGEFSWSTIEPTPGELHWEWLDESLDI
+pdb_id=1kwk, cha... -MLGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIAT
+
+target LHSQGLKVILGTPTATPPKWLVDRHPSMLAKDEAGRVRGFGSRRHYTFASLEYREECRRM
+pdb_id=1kwk, cha... LAAEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRI
+
+target VTMMAERYGHHPAVASWQTDNEYGCHDTVLSYAEADLAAFRLWLAEKYGTVEALNKAWGN
+pdb_id=1kwk, cha... VTLLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGT
+
+target VFWSMDYRSFDEIELPNLTVTEANPSHRLDFQRCCSDQVVAFNKLQVDILREHSAGRDLV
+pdb_id=1kwk, cha... AFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVT
+
+target HNYMGFFTAFDHHKVGQDLDVASWDSYPLGSLDKEPLYTEDEKHTYLRVGHPDAGAFHHD
+pdb_id=1kwk, cha... HNFMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMP-LPPEEKLRYARTGHPDVAAFHHD
+
+target LYRGCGNGRLWIMEQQPGPVNWAPHNPTPADGAVRLWTWEAFSHGAELVSYFRWRQAPFG
+pdb_id=1kwk, cha... LYRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFA
+
+target QEQMHAGLLRPDAQEAEAAKEATLVAQEVKVLAESIGLDADELMSLPSAGKVALMFDYDA
+pdb_id=1kwk, cha... QEQMHAGLHRPDSAPDQGFFEAKRVAEELAAL----------ALPPVAQAPVALVFDYEA
+
+target CWSLDIQPQSRAYRYFFWCYRMYEAMRELGLSVDIVPSNAPLDMYELLVLPAQAHITPEL
+pdb_id=1kwk, cha... AWIYEVQPQGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEA
+
+target QNRLNSY-QGVLLAGPRTGSKTETYQIPENLAPGPLASLLPLTVERVDALPEHTQPAVSG
+pdb_id=1kwk, cha... LEAF-REAEGPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAE-
+
+target RW-GAGKLKHWHEQIKTEL-PCLLKDDGGNPVLMGEGRHYYLGSCIDNTLLKASLAKLSE
+pdb_id=1kwk, cha... GALGRFPLGLWREWV-EAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAA
+
+target VAGLSTYYLPKGVRVRERGNVIFAFNYSSNTVVFEPQ-NAELVIGSMCLGAADVAIWKKQ
+pdb_id=1kwk, cha... EAGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVWE--
+
+target HHHHHH
+pdb_id=1kwk, cha... ------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.TYR487-()-A.GLN488 by relaxing A.TYR487-(QG)-A.VAL490
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.PRO276-(L)-A.TYR278 by filling A.GLU275-(PLY)-A.THR279 (52 candidates, BB_DB)
+Failed at loop insertion (A.LEU392-(AESIGLDADE)-A.LEU403), only 26 candidates
+Resolved A.LEU484-(N)-A.SER486 by filling A.LEU484-(NSYQG)-A.VAL490 (124 candidates, BB_DB)
+Resolved A.SER538-(G)-A.ARG540 by filling A.SER538-(GRW)-A.GLY542 (63 candidates, BB_DB)
+Resolved A.ILE553-(K)-A.THR555 by filling A.ILE553-(KTEL)-A.PRO558 (85 candidates, BB_DB)
+Resolved A.GLN634-()-A.ASN635 by filling A.PRO633-(QNA)-A.GLU637 (41 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU392-(AESIGLDADE)-A.LEU403), only 26 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU392-(AESIGLDADE)-A.LEU403), only 26 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU392-(AESIGLDADE)-A.LEU403), only 26 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU392-(AESIGLDADE)-A.LEU403), only 26 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.LEU392-(AESIGLDADE)-A.LEU403 by filling A.VAL391-(LAESIGLDADEL)-A.MET404 (48 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.83643e+11)
+Perform energy minimization (iteration 2, energy: 19587.9)
+No more stereo-chemical problems -> final energy: 14801.9
+
+
+Build model with the following alignment:
+target GPLGSLAQFFLLNEDDDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRK
+pdb_id=5zbu, cha... --------------------NRLRKDQLKKLPVHKFKKGDEYDVCAICLDEYEDGDKLRI
+
+target LPCSHEYHVHCIDRWLSE-NSTCPICRRAVLASGNRESVV
+pdb_id=5zbu, cha... LPCSHAYHCKCVDPWLTKTKKTCPVCKQKVV---------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.GLU78-()-A.ASN79 by filling A.LEU76-(SEN)-A.SER80 (79 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 10618.1)
+No more stereo-chemical problems -> final energy: 109.582
+
+
+Build model with the following alignment:
+target AASSPLLIGDSVMVDIGNVFTKKIPNAQIDGKVGRQLVDATPIVKSQYKDYAKKGQKVVV
+pdb_id=5ug1, cha... -ADGTMLIGDSVALRANTALQTALPGAQINAQVSVTTKTANEIML-NNSQNKFLPKTVVI
+
+target ELGTN-GAFTKDQLNELLDSFG-KADIYLVSIRVPRDYE------GRINKLIYEAAAARS
+pdb_id=5ug1, cha... ATGVNNPENYKDDWDSIVKNLPKGHHMILVTPYEGDKTKETYAIVEKAAAYMRELAEKTP
+
+target NVHLVDWYKASAGHPE-YFAYDGIHLEYA------GSKALTDLIVKTMETHATN
+pdb_id=5ug1, cha... YITIADWNQVAKEHPEIWAGTDQVHFGSESSTIEAGAKLYADTIATALQTAQD-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.ASN65-()-A.GLY66 by relaxing A.THR64-(NG)-A.ALA67
+Closed: A.GLY81-()-A.LYS82 by relaxing A.SER79-(FGKA)-A.ASP84
+Closed: A.GLU128-()-A.TYR129 by relaxing A.PRO127-(EY)-A.PHE130
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.LYS45-(S)-A.GLN47 by filling A.VAL44-(KSQ)-A.TYR48 (72 candidates, BB_DB)
+Resolved A.GLU97-()-A.GLY98 by filling A.VAL92-(PRDYE)-A.GLY98 (215 candidates, BB_DB)
+Resolved A.ALA140-()-A.GLY141 by filling A.ILE135-(HLEYA)-A.GLY141 (41 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.36639e+15)
+Perform energy minimization (iteration 2, energy: 14410.2)
+No more stereo-chemical problems -> final energy: 12049
+
+
+Build model with the following alignment:
+target MIICSVDIGIKNPAYAIFNYDNTSNTIKLIAIEKSDWTKNWERSVARDLTRYNPDVVILE
+pdb_id=5e6f, cha... TIICSVDIGIKNPAYTIFRYEDS--KVSLIAIEKSDWSDNWEYNVTKDLTKYNPDIIVLE
+
+target KQGFKSPNSKIIYFIKGFFYNSNTKVIVRNPTFKGGSYRNRKKQSIDVFIQKISEYTDYK
+pdb_id=5e6f, cha... KQGYRSPNAKIIYFIKGFFYNTNTSVIVRNPTFQGGSYSDRKKQSVITFMDKLS------
+
+target NDILNKYTKLDDIANSFNLGLSYMESLLK
+pdb_id=5e6f, cha... --------KLDDIADSFNLGIAYIES---
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.THR23-(SN)-A.THR26 by filling A.TYR20-(DNTSN)-A.THR26 (149 candidates, BB_DB)
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER114-(EYTDYKNDILNKYT)-A.LYS129), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.SER114-(EYTDYKNDILNKYT)-A.LYS129 by filling A.SER114-(EYTDYKNDILNKYT)-A.LYS129 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.39902e+14)
+No more stereo-chemical problems -> final energy: 8229.76
+
+
+Build model with the following alignment:
+target MKIVSWNINGIRATR----VGLKETLDSLDADIICLQETKVTRDLLD--EPSAIVEGYNS
+pdb_id=2j63, cha... YKFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSF
+
+target YFSFSRVRSGYSGVATFCKSSTT--PQAA--EEGLSGVFCNRTGSVGCYGNTEQFLEEEL
+pdb_id=2j63, cha... VDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSE-----------L------VE
+
+target QSLDQEGRAVLTQHRILNCED-KEETLTVINVYCPRADPEKPERKTYKLR-FYHLLQTRA
+pdb_id=2j63, cha... GAGDEEGRVLTTFLSPDPD----SSRIALVNTYVANSG-MGLTRLPYRVQSFDPSMREYL
+
+target EAILQN------------------GGHVIILGDVNTSHRPLDHCD---PTDL--ETFEEN
+pdb_id=2j63, cha... HRLDTWATENAA----------SSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAP
+
+target PGRQWLNQFLGDPIPSQKGDSETVMPPSAGSGLFYDSFRYFHPTQKNAFTCWCSASGARQ
+pdb_id=2j63, cha... EERMSFRETM-----Q--------------RTNSVDIFRQLYPQAGPVYSFWSQRINGRP
+
+target TNYGTRIDYILGNRELVESEFLDSVIMPEVEGSDHCPVKAFMKCQPIAANKCPPLCTKYL
+pdb_id=2j63, cha... RNLGWRLDYFVVSSRLA-SYVVDCFPMPTVMGSDHCPFQMWMRH----------------
+
+target PEFAGRQQKLLQFLVKKENTLGNTTEESSE
+pdb_id=2j63, cha... ------------------------------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Closed: A.ARG159-()-A.PHE160 by relaxing A.LEU158-(RF)-A.TYR161
+Trying to merge 14 gap(s) with distance 0.
+Merged gap A.CYS90-(NRTGSVGCYGN)-A.THR102 and A.THR102-(EQFLEE)-A.GLU109 into A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109
+Merged gap A.LEU215-(GDPIP)-A.SER221 and A.SER221-(QKGDSETVMPPSAG)-A.SER236 into A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236
+Trying to fill 12 gap(s) by database.
+Resolved A.ARG15-()-A.VAL16 by filling A.THR14-(RVGL)-A.LYS19 (66 candidates, BB_DB)
+Resolved A.ASP43-()-A.GLU44 by filling A.ASP43-(EPSA)-A.ILE48 (90 candidates, BB_DB)
+Resolved A.THR77-()-A.PRO78 by filling A.THR77-(PQAA)-A.GLU82 (57 candidates, BB_DB)
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Resolved A.CYS129-(EDK)-A.GLU133 by filling A.CYS129-(EDKE)-A.GLU134 (46 candidates, BB_DB)
+Resolved A.ASP147-(P)-A.GLU149 by filling A.PRO144-(RADP)-A.GLU149 (41 candidates, BB_DB)
+Resolved A.ASN174-()-A.GLY175 by filling A.ASN174-(GGHV)-A.ILE179 (41 candidates, BB_DB)
+Resolved A.ASP195-()-A.PRO196 by filling A.ARG189-(PLDHCD)-A.PRO196 (47 candidates, BB_DB)
+Resolved A.LEU199-()-A.GLU200 by filling A.LEU199-(ETFE)-A.GLU204 (80 candidates, BB_DB)
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Resolved A.VAL282-(E)-A.SER284 by filling A.LEU281-(VES)-A.GLU285 (90 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109), only 0 candidates
+Failed at loop insertion (A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.CYS90-(NRTGSVGCYGNTEQFLEE)-A.GLU109 by filling A.CYS90-(NRTGSVGCYGNTEQFLEEE)-A.LEU110 (6 candidates, BB)
+Resolved A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236 by filling A.LEU215-(GDPIPSQKGDSETVMPPSAG)-A.SER236 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8.31872e+16)
+Perform energy minimization (iteration 2, energy: 13810.9)
+No more stereo-chemical problems -> final energy: 10923.7
+
+
+Build model with the following alignment:
+target VQLAETGGGLAQAGGSLRLSCAASGSIFSINAMGWYRQAPGKERELVADISGSGRTNYAD
+pdb_id=5f7l, cha... VQLQESGGGLVQPGGSLRLSCAASGSIYSLIAMGWYRQAPGKEHELVATISSGSTTYYAD
+
+target SVKGRFTISRDNAKNTVSLQMNSLKPEDTAVYYCNVVG---GSYYYDEYNYWGQGTQVTV
+pdb_id=5f7l, cha... SVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAYSDRLTDCSNCEADYWGQGTQVTV
+
+target SSEP
+pdb_id=5f7l, cha... ----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.GLY98-()-A.GLY99 by filling A.GLY98-(GSYYY)-A.ASP104 (98 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 60978.3)
+Perform energy minimization (iteration 2, energy: 4616.96)
+Perform energy minimization (iteration 3, energy: 3965.27)
+Perform energy minimization (iteration 4, energy: 3620.18)
+Perform energy minimization (iteration 5, energy: 3334.43)
+No more stereo-chemical problems -> final energy: 3186.06
+
+
+Build model with the following alignment:
+target MSYYHHHHHHDYDIPTTENLYFQGAMDPEFASLDRVKVLVLGDSGVGKSSLVHLLCHNQV
+pdb_id=5u4v, cha... ---------------------------------DKVNLFILGKDGLAQ-----ELANE-I
+
+target LGNPSWTVGCSVDIRVHDYKEGTPEEKTYYIELWDVGGSVGSASSVKSTRAVFYN----S
+pdb_id=5u4v, cha... R--TQST-DDEYA-----L-----DGKIYELDLRPVDA----------------------
+
+target VNGIILVHDLTNKKSSQNLYRWSLEVLN-RDAVPTGVLVTNGDYDREQFADNQIPL-LVI
+pdb_id=5u4v, cha... PHGCFCVFN--SIESLSFIGEFIGKIRTEASQI-----------------MANLPFTLIL
+
+target GTKLDQIHETKRHEVLIRTAFLAEDFNAEEINLDCTNPRSSAAGSSN---A---VKLSRF
+pdb_id=5u4v, cha... AN--------NLPILRHQGQQLANKLQCP--FVDVP-------------RKFNETQIKQA
+
+target FDKVIEKRYFFREGNQI
+pdb_id=5u4v, cha... LRGVLESVKH-------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Trying to merge 15 gap(s) with distance 0.
+Merged gap A.ASP73-(IRVHD)-A.TYR79 and A.TYR79-(KEGTP)-A.GLU85 into A.ASP73-(IRVHDYKEGTP)-A.GLU85
+Merged gap A.THR210-(NPRSSAAGSSN)-A.ALA222 and A.ALA222-()-A.VAL223 into A.THR210-(NPRSSAAGSSNA)-A.VAL223
+Trying to fill 13 gap(s) by database.
+Resolved A.LYS48-(SSLVH)-A.LEU54 by filling A.SER44-(GVGKSSLVH)-A.LEU54 (67 candidates, BB_DB)
+Resolved A.ASN58-(Q)-A.VAL60 by filling A.LEU55-(CHNQ)-A.VAL60 (42 candidates, BB_DB)
+Resolved A.LEU61-(GN)-A.PRO64 by filling A.VAL60-(LGNPSW)-A.THR67 (89 candidates, BB_DB)
+Resolved A.THR67-(V)-A.GLY69 by filling A.PRO64-(SWTV)-A.GLY69 (98 candidates, BB_DB)
+Failed at loop insertion (A.ASP73-(IRVHDYKEGTP)-A.GLU85), only 3 candidates
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Resolved A.ASP125-(LT)-A.ASN128 by filling A.HIS124-(DLTN)-A.LYS129 (50 candidates, BB_DB)
+Resolved A.ASN144-()-A.ARG145 by filling A.LEU143-(NRDA)-A.VAL148 (128 candidates, BB_DB)
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Resolved A.LEU171-()-A.LEU172 by filling A.ASN167-(QIPL)-A.LEU172 (60 candidates, BB_DB)
+Resolved A.THR176-(KLDQIHET)-A.LYS185 by filling A.THR176-(KLDQIHET)-A.LYS185 (159 candidates, BB_DB)
+Resolved A.GLU203-(EI)-A.ASN206 by filling A.PHE200-(NAEEI)-A.ASN206 (64 candidates, BB_DB)
+Resolved A.THR210-(NPRSSAAGSSNA)-A.VAL223 by filling A.THR210-(NPRSSAAGSSNA)-A.VAL223 (131 candidates, BB_DB)
+Trying to merge 3 gap(s) with distance 1.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.ASP73-(IRVHDYKEGTP)-A.GLU85), only 3 candidates
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Trying to merge 3 gap(s) with distance 2.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.ASP73-(IRVHDYKEGTP)-A.GLU85), only 3 candidates
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Trying to merge 3 gap(s) with distance 3.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.ASP73-(IRVHDYKEGTP)-A.GLU85), only 3 candidates
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.ASP73-(IRVHDYKEGTP)-A.GLU85), only 3 candidates
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Resolved A.ASP73-(IRVHDYKEGTP)-A.GLU85 by filling A.ASP73-(IRVHDYKEGTPE)-A.GLU86 (32 candidates, BB_DB)
+Failed at loop insertion (A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117), only 0 candidates
+Failed at loop insertion (A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117 by filling A.GLY98-(SVGSASSVKSTRAVFYNS)-A.VAL117 (6 candidates, BB)
+Resolved A.VAL148-(PTGVLVTNGDYDREQFA)-A.ASP166 by filling A.VAL148-(PTGVLVTNGDYDREQFAD)-A.ASN167 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.23913e+13)
+No more stereo-chemical problems -> final energy: 12048.1
+
+
+Build model with the following alignment:
+target MNHKVHHHHHHLQENLYFQGMGAEPQQLHVVFFPIMAHGHMIPTLDIARLFAA-RNVRAT
+pdb_id=6jtd, cha... -------------------------SKPHVFLLASPGMGHLIPFLELSKRLVTLNTLQVT
+
+target IITTP-L-N---AHTFTKAIEMGKKNGSPTIHLELFKFPAQDVGLPEGCENLEQALGSSL
+pdb_id=6jtd, cha... LFIVSNEATKARSHLMESSNN-----FHPDLELVDLTPA----NLSELLST--D---ATV
+
+target IEKFFKGVGLLREQLEAYLEKT--RPNCLVADMFFPWATDSAAKFNIPRLVFHGTSFFSL
+pdb_id=6jtd, cha... FKRIFLITQAAIKDLESRISSMSTPPAALIVDVFSMDAFPVADRFGIKKYVFVTLNAWFL
+
+target CALEVVRLYEP-HK-NVSSDEELFSLPLFPHDIKMMRLQLPEDVWKHEKAEGKTRLKLIK
+pdb_id=6jtd, cha... ALTTYVRTLDREIEGEYVDLPEPIAIPGCKP---LRPEDVFDPMLSRSSDGYRPYL-GMS
+
+target ESELKSYGVIVNSFYELEPNYAEFFRKEL------GRRAWNIGPVSLCNRSTEDKAQRGK
+pdb_id=6jtd, cha... ERLTKADGLLLNTWEALEPVSLKALRENEKLNQIMTPPLYPVGPVARTTV---Q------
+
+target QTSIDEHECLKWLNSKKKNSVIYICFGSTAHQIAPQLYEIAMALEASGQEFIWVVRNNN-
+pdb_id=6jtd, cha... --EVVGNECLDWLSKQPTESVLYVALGSGGIISYKQMTELAWGLEMSRQRFIWVVRLPTM
+
+target ---N-----NDD-D-DDDSWLPRGFEQRVEGKGLIIRGWAPQVLILEHEAIGAFVTHCGW
+pdb_id=6jtd, cha... EKDGACRFFSDVNVKGPLEYLPEGFLDRNKELGMVLPNWGPQDAILAHPSTGGFLSHCGW
+
+target NSTLEGITAGVPMVTWPIFAEQFYNEKLVNQILKIGVPVGANKWSRETSIEDVIKKDAIE
+pdb_id=6jtd, cha... NSSLESIVNGVPVIAWPLYAEQKMNATLLTEELGVAVRPEVLPT------KAVVSRDEIE
+
+target KALREIMVGDEAEERRSRAKKLKEMAWKAVEEGGSSYSDLSALIEELRGYHA
+pdb_id=6jtd, cha... KMVRRVIESKEGKMKRNRARSVQSDALKAIEKGGSSYNTLIEVAKEFEKNH-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 21).
+Initialized default backbone scoring for modelling.
+Closed: A.THR136-()-A.ARG137 by relaxing A.GLU134-(KTR)-A.PRO138
+Closed: A.PRO183-()-A.HIS184 by relaxing A.GLU182-(PH)-A.LYS185
+Closed: A.LYS185-()-A.ASN186 by relaxing A.HIS184-(KN)-A.VAL187
+Trying to merge 18 gap(s) with distance 0.
+Merged gap A.PRO64-()-A.LEU65 and A.LEU65-()-A.ASN66 into A.PRO64-(L)-A.ASN66
+Merged gap A.PRO64-(L)-A.ASN66 and A.ASN66-()-A.ALA67 into A.PRO64-(LN)-A.ALA67
+Merged gap A.ASN105-(LE)-A.GLN108 and A.GLN108-(ALG)-A.SER112 into A.ASN105-(LEQALG)-A.SER112
+Merged gap A.ARG274-(STE)-A.ASP278 and A.ASP278-(KAQRGKQT)-A.SER287 into A.ARG274-(STEDKAQRGKQT)-A.SER287
+Merged gap A.ASN343-()-A.ASN344 and A.ASN344-()-A.ASN345 into A.ASN343-(N)-A.ASN345
+Merged gap A.ASP347-()-A.ASP348 and A.ASP348-()-A.ASP349 into A.ASP347-(D)-A.ASP349
+Trying to fill 12 gap(s) by database.
+Resolved A.ALA53-()-A.ARG54 by filling A.ALA53-(RNVR)-A.ALA58 (60 candidates, BB_DB)
+Resolved A.PRO64-(LN)-A.ALA67 by filling A.ILE61-(TTPLN)-A.ALA67 (62 candidates, BB_DB)
+Resolved A.GLU75-(MGKKN)-A.GLY81 by filling A.GLU75-(MGKKNGSPT)-A.ILE85 (41 candidates, BB_DB)
+Resolved A.PRO93-(AQDV)-A.GLY98 by filling A.PRO93-(AQDVGL)-A.PRO100 (200 candidates, BB_DB)
+Resolved A.ASN105-(LEQALG)-A.SER112 by filling A.ASN105-(LEQALGS)-A.SER113 (48 candidates, BB_DB)
+Resolved A.HIS201-(DIK)-A.MET205 by filling A.LEU198-(FPHDIK)-A.MET205 (59 candidates, BB_DB)
+Resolved A.LEU226-(K)-A.LEU228 by filling A.LEU226-(KLI)-A.LYS230 (41 candidates, BB_DB)
+Resolved A.LEU259-()-A.GLY260 by filling A.GLU258-(LGRRA)-A.TRP264 (52 candidates, BB_DB)
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Resolved A.ASN343-(N)-A.ASN345 by filling A.VAL339-(RNNNN)-A.ASN345 (62 candidates, BB_DB)
+Resolved A.ASP347-(D)-A.ASP349 by filling A.ASN345-(DDDD)-A.ASP350 (188 candidates, BB_DB)
+Resolved A.TRP437-(SRETSI)-A.GLU444 by filling A.ALA434-(NKWSRETSI)-A.GLU444 (41 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG274-(STEDKAQRGKQT)-A.SER287), only 1 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.ARG274-(STEDKAQRGKQT)-A.SER287 by filling A.ARG274-(STEDKAQRGKQTS)-A.ILE288 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.44107e+13)
+Perform energy minimization (iteration 2, energy: 26761.7)
+No more stereo-chemical problems -> final energy: 21660
+
+
+Build model with the following alignment:
+target NTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLQEHKGKKARLDWN
+pdb_id=6nyb, cha... ------------------------------------------------------------
+
+target TDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEH
+pdb_id=6nyb, cha... ---------------------TTHNFVRKTFFTLAFCDFCRKLLFQGFRCQTCGYKFHQR
+
+target CSTKVPTMCVDW
+pdb_id=6nyb, cha... CSTEVPLMCV--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 11960.5)
+No more stereo-chemical problems -> final energy: 4175.88
+
+
+Build model with the following alignment:
+target GAMGIELFVKAGIDGESIGNCPFSQRLFMILWLKGVVFNVTTVDLKRKPADLHNLAPGTH
+pdb_id=6erz, cha... ----ITLFVKAGYDGESIGNCPFSQRLFMILWLKGVIFNVTTVDL-------------TN
+
+target PPFLTFNGDVKTDVNKIEEFLEETLTPEKYPKLAAKHRESNTAGIDIFSKFSAYIKNTKQ
+pdb_id=6erz, cha... PPFMTFDGEVKTDVNKIEEFLEEKLVPPRYPKLGTQHPESNSAGNDVFAKFSAFIKNTKK
+
+target QNNAALERGLTKALKKLDDYLNTPLPEEIDANTCGEDKGSRRKFLDGDELTLADCNLLPK
+pdb_id=6erz, cha... DANEIYEKNLLRALKKLDSYLNSPLPDEIDADSSEDVTVSQRKFLDGDELTLADCNLLPK
+
+target LHVVKIVAKKYRNYDIPAEMTGLWRYLKNAYARDEFTNTCAADSEIELAYADVAKRLSRS
+pdb_id=6erz, cha... LHIIKIVAKKYRDFEFPSEMTGIWRYLNNAYARDEFTNTCPADREIEHAYSDAAKRMK--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU45-(KRKPADLHNLAPG)-A.THR59), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.LEU45-(KRKPADLHNLAPG)-A.THR59 by filling A.ASP44-(LKRKPADLHNLAPG)-A.THR59 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 305550)
+No more stereo-chemical problems -> final energy: 8961.06
+
+
+Build model with the following alignment:
+target ADTLDNVNLVSSPVHSGFLVSFMVDARGGSMRGSRHHGMRIIIPPRKCTAPTRITCRLVK
+pdb_id=4d8o, cha... ---------------SGFLVSFMVDARGGAMRGCRHNGLRIIIPPRKCTAPTRVTCRLVK
+
+target RHKLANPPPMVEGEGLASRLVEMGPAGAQFLGPVIVEIPHFGSMRGKERELIVLRSENGE
+pdb_id=4d8o, cha... RHRLATMPPMVEGEGLASRLIEVGPSGAQFLGPVIVEIPHFAALRGKERELVVLRSENGD
+
+target TWKEHQFDSKNEDLSELLNGMDEELDSPEELGTKRICRIITKDFPQYFAVVSRIKQESNQ
+pdb_id=4d8o, cha... SWKEHFCDY----------GMDEVLDSPEDLEKKRICRIITRDFPQYFAVVSRIKQDSNL
+
+target IGPEGGILSSTTVPLVQASFPEGALTKRIRVGLQAQPVPEETVKKILGNKATFSPIVTVE
+pdb_id=4d8o, cha... IGPEGGVLSSTVVPQVQAVFPEGALTKRIRVGLQAQPMHSELVKKILGNKATFSPIVTLE
+
+target PRRRKFHKPITMTIPVPPPSGEGVSNGYKGDTTPSLRLLCSITGGTSPAQWEDITGTTPL
+pdb_id=4d8o, cha... PRRRKFHKPITMTIPVPKA---------SGD-APTLRLLCSITGGTTPAQWEDITGTTPL
+
+target TFIKDCVSFTTNVSARFWLADCHQVLETVGLASQLYRELICVPYMAKFVVFAKTNDPVES
+pdb_id=4d8o, cha... TFVNECVSFTTNVSARFWLIDCRQIQESVTFASQVYREIICVPYMAKFVVFAKSHDPIEA
+
+target SLRCFCMTDDRVDKTLEQQENFEEVARSKDIEVLEGKPIYVDCYGNLAPLTKGGQQLVFN
+pdb_id=4d8o, cha... RLRCFCMTDDKVDKTLEQQENFAEVARSRDVEVLEGKPIYVDCFGNLVPLT---QHHIFS
+
+target FYSFKENRLPFSIKVRDTSQEPCGRLSFLKEPKTTKGLPQTAVCNLNITLPAHKKAEKAD
+pdb_id=4d8o, cha... FFAFKENRLPLFVKVRDTTQEPCGRLSFMKEP-------HQAICNLNITLPIYT------
+
+target RRQSFTSLALR
+pdb_id=4d8o, cha... -----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.SER129-(KNEDLSELLN)-A.GLY140 by filling A.SER129-(KNEDLSELLN)-A.GLY140 (319 candidates, BB_DB)
+Resolved A.PRO259-(SGEGVSNGY)-A.LYS269 by filling A.PRO257-(PPSGEGVSNGY)-A.LYS269 (85 candidates, BB_DB)
+Resolved A.ASP271-(T)-A.THR273 by filling A.GLY270-(DTT)-A.PRO274 (41 candidates, BB_DB)
+Resolved A.THR411-(KGG)-A.GLN415 by filling A.THR411-(KGGQ)-A.GLN416 (46 candidates, BB_DB)
+Resolved A.PRO452-(KTTKGLP)-A.GLN460 by filling A.PRO452-(KTTKGLP)-A.GLN460 (50 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.87055e+15)
+Perform energy minimization (iteration 2, energy: 13158.6)
+No more stereo-chemical problems -> final energy: 10307.5
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMSHWYDHAIIYQIYPKSFQDSNDDGIGDLNGIRKRIPYLQ
+pdb_id=4gin, cha... -----------------------WWKSAVFYQVYPRSFKDTNGDGIGDFKGLTEKLDYLK
+
+target NLGVNAVWLNPVFVSPQVDNGYDVSNYFAIDSHMGTMEDMENLIKDLHKAGIHIIMDFVL
+pdb_id=4gin, cha... GLGIDAIWINPHYASPNTDNGYDISDYREVMKEYGTMEDFDRLMAELKKRGMRLMVDVVI
+
+target NHTSDQHPWFQDAIKNPDSLYRDYYIF-AGHDNKQPNNWGSFFGGSVWEPDPAGTGQSYF
+pdb_id=4gin, cha... NHSSDQHEWFKSSRASKDNPYRDYYFWRDGKDGHEPNNYPSFFGGSAWEKDPV-TGQYYL
+
+target HLFDKRMPDLNWKNPEVRHAMLEIAEFWLKKGIDGLRLDAFIHIGKADLRQNYPAMDDKP
+pdb_id=4gin, cha... HYFGRQQPDLNWDTPKLREELYAMLRFWLDKGVSGMRFDTVATYSKTPGFPDLTP--EQM
+
+target VIAEPFFANLPQVQEWMRPFCEQIKEDYPDALLLGEAASASVNLAVDYTNKRNHLMDCVI
+pdb_id=4gin, cha... KNFAEAYTQGPNLHRYLQEMHEKVFDH-YDAVTAGEIFGAPLNQVPLFIDSRRKELDMAF
+
+target TFRYFTEDDSKIDKSYSAQYQPKELDLTAFKQNQVVWQQTLADISQPTLYWNNHDMARLA
+pdb_id=4gin, cha... TFDLICYDRA------LDRWHTIPRTLADFRQTIDKVDAIAGEYGWNTFFLGNHDNPRAV
+
+target TRIAKT-----STQAKSLAMLMYLQRGIPIIYYGEELGLKNLHFTSVDQFEDQTVAPWIK
+pdb_id=4gin, cha... SHFGDDRPQWREASAKALATVTLTQRGTPFIFQGDELGMTNYPFKTLQDFDDIEVKGFFQ
+
+target EAQKAG-ISRDAAFAMVSDTHKLPARGPMPWNDTENNGFTSAKPWLNGISQD--DVTVAN
+pdb_id=4gin, cha... DYVETGKATAEELLTNVALTSRDNARTPFQWDDSANAGFTTGKPWLK-VNPNYTEINAAR
+
+target EVNSDNSMFTFYKNMLNLKKE-KLFQDGTYYMIS-TGKDSYVYQRDLGNESAIVAVSLSN
+pdb_id=4gin, cha... EIGDPKSVYSFYRNLISIRHETPALSTGSYRDIDPSNADVYAYTRSQDGETYLVVVNFKA
+
+target KKISIDLPEE-Y-IKELLKA-GEYQL-T--N-GKLTLMPYAGVVLKKEN
+pdb_id=4gin, cha... EPRSFTLPDGMHIAET--LIESSSPAAPAAGAASLELQPWQSGIYKVK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 18).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY420-()-A.ILE421 by relaxing A.GLY420-(I)-A.SER422
+Closed: A.ASP465-()-A.ASP466 by relaxing A.ASP465-(DV)-A.THR468
+Closed: A.SER504-()-A.THR505 by relaxing A.SER504-(T)-A.GLY506
+Closed: A.ASN554-()-A.GLY555 by relaxing A.ASN554-(GK)-A.LEU557
+Trying to merge 14 gap(s) with distance 0.
+Merged gap A.GLU539-()-A.TYR540 and A.TYR540-()-A.ILE541 into A.GLU539-(Y)-A.ILE541
+Merged gap A.LEU552-()-A.THR553 and A.THR553-()-A.ASN554 into A.LEU552-(T)-A.ASN554
+Trying to fill 12 gap(s) by database.
+Resolved A.PHE147-()-A.ALA148 by filling A.PHE147-(AGHD)-A.ASN152 (49 candidates, BB_DB)
+Resolved A.ALA172-(G)-A.THR174 by filling A.ALA172-(GTG)-A.GLN176 (54 candidates, BB_DB)
+Resolved A.ALA234-(MD)-A.ASP237 by filling A.ASN231-(YPAMD)-A.ASP237 (44 candidates, BB_DB)
+Resolved A.ASP266-(Y)-A.PRO268 by filling A.ASP266-(YPDA)-A.LEU271 (136 candidates, BB_DB)
+Resolved A.SER309-(KIDKSY)-A.SER316 by filling A.SER309-(KIDKSYSAQ)-A.TYR319 (50 candidates, BB_DB)
+Resolved A.THR365-()-A.SER366 by filling A.ILE362-(AKTST)-A.GLN368 (62 candidates, BB_DB)
+Resolved A.ASN460-(G)-A.ILE462 by filling A.TRP458-(LNGI)-A.SER463 (80 candidates, BB_DB)
+Resolved A.GLU492-()-A.LYS493 by filling A.GLU492-(KLF)-A.GLN496 (69 candidates, BB_DB)
+Resolved A.GLU539-(Y)-A.ILE541 by filling A.ASP535-(LPEEY)-A.ILE541 (197 candidates, BB_DB)
+Resolved A.GLU543-(LL)-A.LYS546 by filling A.GLU543-(LLKA)-A.GLY548 (73 candidates, BB_DB)
+Resolved A.LEU552-(T)-A.ASN554 by filling A.GLU549-(YQLTNG)-A.LYS556 (85 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.11313e+15)
+Perform energy minimization (iteration 2, energy: 40990.2)
+Perform energy minimization (iteration 3, energy: 32564)
+No more stereo-chemical problems -> final energy: 29871.9
+
+
+Build model with the following alignment:
+target APQQGTNVNDKVHFSNIDIAIDKGHVNQTTGKTEFWATSSDVLKLKANYTIDDSVKEGDT
+pdb_id=1r17, cha... ----GSNVNHLIKVTDQSIT--EGYD---DSDGIIKAHDAENLIYDVTFEVDDKVKSGDT
+
+target FTFKYGQYFRPGSVRLPSQTQNLYNAQGNIIAKGIYDSTTNTTTYTFTNYVDQYTNVRGS
+pdb_id=1r17, cha... MTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAH
+
+target FEQVAFAKRKNATTDKTAYKMEVTLGNDTYSEEIIVDYGNKKAQ---PLISSTNYINNED
+pdb_id=1r17, cha... LKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKN
+
+target LSRNMTAYVNQPKNTYTKQTFVTNLTG-----YKFNPNAKNFKIYEVTDQNQFVDSFTP-
+pdb_id=1r17, cha... HTVEQTIYINPLRYSAKETNVN--ISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIY
+
+target DTSKLKDVTDQFDVIYSNDNKTATVDLMKGQTSSNKQYIIQQVAYPDNSSTDNGKIDYTL
+pdb_id=1r17, cha... DYSEYEDVTNDDYAQLGNN-NDVNINF--GNID--SPYIIKVISKYDPNKDDYTTIQQTV
+
+target D---------TDKTKYSWSNSYSNVNGSSTANGDQKK
+pdb_id=1r17, cha... TMQTTINEYTGEFRTASYDNTIAFSTSSGQGQGDLP-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Trying to merge 10 gap(s) with distance 0.
+Trying to fill 10 gap(s) by database.
+Resolved A.ALA20-(ID)-A.LYS23 by filling A.ALA20-(IDKGH)-A.VAL26 (66 candidates, BB_DB)
+Resolved A.VAL26-(NQT)-A.THR30 by filling A.HIS25-(VNQTT)-A.GLY31 (42 candidates, BB_DB)
+Resolved A.GLN164-()-A.PRO165 by filling A.LYS162-(AQPL)-A.ILE167 (45 candidates, BB_DB)
+Resolved A.VAL199-(TN)-A.LEU202 by filling A.THR197-(FVTN)-A.LEU202 (119 candidates, BB_DB)
+Resolved A.GLY204-()-A.TYR205 by filling A.THR203-(GYKFNP)-A.ASN210 (46 candidates, BB_DB)
+Resolved A.PRO231-()-A.ASP232 by filling A.ASP227-(SFTPD)-A.THR233 (101 candidates, BB_DB)
+Resolved A.ASP250-(N)-A.LYS252 by filling A.TYR247-(SNDN)-A.LYS252 (64 candidates, BB_DB)
+Resolved A.LEU258-(MK)-A.GLY261 by filling A.ASP257-(LMKG)-A.GLN262 (43 candidates, BB_DB)
+Resolved A.SER264-(SN)-A.LYS267 by filling A.THR263-(SSNKQ)-A.TYR269 (54 candidates, BB_DB)
+Resolved A.ASP292-()-A.THR293 by filling A.ASP292-(TDKTK)-A.TYR298 (151 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.25243e+16)
+Perform energy minimization (iteration 2, energy: 25695.1)
+No more stereo-chemical problems -> final energy: 20624.6
+
+
+Build model with the following alignment:
+target MQPTGREGSRALSRRYLRRLLLLLLLLLLRQPVTRAETTPGAPRALSTLGSPSLFTTPGV
+pdb_id=1itu, cha... ------------------------------------------------------------
+
+target PSALTTPGLTTPGTPKTLDLRGRAQALMRSFPLVDGHNDLPQVLRQRYKNVL--QDVNLR
+pdb_id=1itu, cha... -------------------FRDEAERIMRDSPVIDGHNDLPWQLLDMFNNRLQDERANLT
+
+target NFSHGQTSLDRLRDGLVGAQFWSASVSCQSQDQTAVRLALEQIDLIHRMCASYSE-LELV
+pdb_id=1itu, cha... TLAGTHTNIPKLRAGFVGGQFWSVYTPCDTQNKDAVRRTLEQMDVVHRMCRMYPETFLYV
+
+target TSAEGLN---SSQKLACLIGVEGGHSLDSSLSVLRSFYVLGVRYLTLTFTCSTPWAESST
+pdb_id=1itu, cha... TSSAGIRQAFREGKVASLIGVEGGHSIDSSLGVLRALYQLGMRYLTLTHSCNTPWADNWL
+
+target KFRHHMYTNVSGLTSFGEKVVEELNRLGMMIDLSYASDTLIRRVLEVSQAPVIFSHSAAR
+pdb_id=1itu, cha... VDTGDSEPQSQGLSPFGQRVVKELNRLGVLIDLAHVSVATMKATLQLSRAPVIFSHSSAY
+
+target AVCDNLLNVPDDILQLLKKNGGIVMVTLSMGVLQCNLLANVSTVADHFDHIRAVIGSEFI
+pdb_id=1itu, cha... SVCASRRNVPDDVLRLVKQTDSLVMVNFYNNYISCTNKANLSQVADHLDHIKEVAGARAV
+
+target GIGGNYDGTGRFPQGLEDVSTYPVLIEELLSRSWSEEELQGVLRGNLLRVFRQVEKVREE
+pdb_id=1itu, cha... GFGGDFDGVPRVPEGLEDVSKYPDLIAELLRRNWTEAEVKGALADNLLRVFEAVEQASNL
+
+target SRAQSPVEAEFPYGQLSTSCHSHLVPQNGHQATHLEVTKQPTNRVPWRSSNASPYLVPGL
+pdb_id=1itu, cha... --TQAPEEEPIPLDQLGGSCRTHY------------------------------------
+
+target VAAATIPTFTQWLC
+pdb_id=1itu, cha... --------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.GLU173-()-A.LEU174 by relaxing A.TYR171-(SEL)-A.GLU175
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.LEU112-()-A.GLN113 by filling A.ARG107-(YKNVL)-A.GLN113 (193 candidates, BB_DB)
+Resolved A.ASN184-()-A.SER185 by filling A.ASN184-(SSQK)-A.LEU189 (62 candidates, BB_DB)
+Resolved A.GLU414-(SR)-A.ALA417 by filling A.VAL411-(REESR)-A.ALA417 (82 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.39659e+21)
+Perform energy minimization (iteration 2, energy: 3696.26)
+No more stereo-chemical problems -> final energy: 1311.04
+
+
+Build model with the following alignment:
+target GSHMGTE---------------DLKYSLERLREILERLEENPSEKQIVEAIRAIVENNAQ
+pdb_id=5j0h, cha... ------KYELRRALEELEKALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKI
+
+target IVEAIRAIVENNAQIVENNRAIIEALEAIGGGTKILEEMKKQLKDLKRSLERG
+pdb_id=5j0h, cha... IVEVLRIIAE-------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5209.47)
+No more stereo-chemical problems -> final energy: -1703.44
+
+
+Build model with the following alignment:
+target MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT
+pdb_id=2cme, cha... -------VPPALHLVDPQIQLTITR-----------ADPKVYPIILRLGSNLSLSMARRN
+
+target LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK
+pdb_id=2cme, cha... LDSLEARAFQSTPIVVQMTKLATTEELPDEFVVVTAK
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG25-(MENAVGRDQNN)-A.VAL37), only 14 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG25-(MENAVGRDQNN)-A.VAL37), only 14 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG25-(MENAVGRDQNN)-A.VAL37), only 14 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG25-(MENAVGRDQNN)-A.VAL37), only 14 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ARG25-(MENAVGRDQNN)-A.VAL37), only 14 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.ARG25-(MENAVGRDQNN)-A.VAL37 by filling A.THR24-(RMENAVGRDQNN)-A.VAL37 (18 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 28526.1)
+No more stereo-chemical problems -> final energy: 4428.18
+
+
+Build model with the following alignment:
+target MNHKVHHHHHHMKANQVQPLNKYPVVFVHGFLGLVGDNAPALYPNYWGGNKFKVIEELRK
+pdb_id=4fdm, cha... ----------------------APIVLLHGFTGWGREEM--FGFKYWGGVRGDIEQWLND
+
+target QGYNVHQASVSAFGSNYDRAVQLYYYIKGGRVDYGAAHAAKYGHERYGKTYKGIMPNWEP
+pdb_id=4fdm, cha... NGYRTYTLAVGPLSSNWDRACEAYAQLVGGTVDYGAAHAAKHGHARFGRTYPGLLPELKR
+
+target GKKVHLVGHSMGGQTIRLMEEFLRNGNKEEIAYHQAHGGEISPLFTGGHNNMVASITTLA
+pdb_id=4fdm, cha... GGRIHIIAHSQGGQTARMLVSLLENGSQEEREYAKAHNVSLSPLFEGGH-HFVLSVTTIA
+
+target TPHNGSQAADKFGNTEA---VRKIMFALNRFMGNKY---SNIDLGLTQWGFKQLPNESYI
+pdb_id=4fdm, cha... TPHDGTTLVNMVDFTDRFFDLQKAVLEAAAVASNVPYTSQVYDFKLDQWGLRRQPGESFD
+
+target DYIKRVSKSKIWTSDDNAAYDLTLDGSAKLNNMTSMNPNITYTTYTGVSSHTG-PLGYEN
+pdb_id=4fdm, cha... HYFERLKRSPVWTSTDTARYDLSVSGAEKLNQWVQASPNTYYLSFSTERTYRGALTGNHY
+
+target PDLGTFFL-MDTTSRIIGHDA------REEWRKNDGVVPVISS---LHPSNQPFVNVTNN
+pdb_id=4fdm, cha... PELGMNAFSAVVCAPFLGSYRNPTLGIDDRWLENDGIVNTVSMNGPKRGSSDRIVPYDG-
+
+target EPATRRGIWQVKPILQGWDHVDFIGVDFLDFKRKGSELANFYIGIINDLLSVEATEGKGT
+pdb_id=4fdm, cha... --TLKKGVWNDMGT-YNVDHLEIIGVDPNP----SFDIRAFYLRLAEQLAS---------
+
+target QLKAS
+pdb_id=4fdm, cha... -----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA197-()-A.VAL198 by relaxing A.GLU196-(AV)-A.ARG199
+Closed: A.GLY287-()-A.PRO288 by relaxing A.GLY287-(P)-A.LEU289
+Closed: A.LEU301-()-A.MET302 by relaxing A.PHE300-(LM)-A.ASP303
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.ALA39-(PA)-A.LEU42 by filling A.ALA39-(PALYPN)-A.TYR46 (49 candidates, BB_DB)
+Resolved A.HIS169-(N)-A.ASN171 by filling A.HIS169-(NNM)-A.VAL173 (43 candidates, BB_DB)
+Resolved A.TYR213-()-A.SER214 by filling A.MET209-(GNKYS)-A.ASN215 (82 candidates, BB_DB)
+Resolved A.ALA313-()-A.ARG314 by filling A.ILE309-(GHDAR)-A.GLU315 (48 candidates, BB_DB)
+Resolved A.SER329-()-A.LEU330 by filling A.SER329-(LHPSN)-A.GLN335 (41 candidates, BB_DB)
+Resolved A.ASN342-(NEP)-A.ALA346 by filling A.THR341-(NNEPA)-A.THR347 (42 candidates, BB_DB)
+Resolved A.ILE357-(L)-A.GLN359 by filling A.ILE357-(LQGW)-A.ASP362 (46 candidates, BB_DB)
+Resolved A.ASP373-(FKRK)-A.GLY378 by filling A.ASP370-(FLDFKRK)-A.GLY378 (292 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.28523e+19)
+Perform energy minimization (iteration 2, energy: 23649.8)
+No more stereo-chemical problems -> final energy: 18185.7
+
+
+Build model with the following alignment:
+target MAHHHHHHMSKTPLSIAHPWHGPVLTRDDYESLCCYIEITPADSVKFELDKETGILKVDR
+pdb_id=3q5v, cha... -----------------NPFHELEPGPEVPEVVYALIEIPKGSRNKYELDKKTGLLKLDR
+
+target PQKFSNFCPCLYGLLPKTYCGDLSGEYSGQQSNRENIKGDGDPLDICVLTEKNITQGNIL
+pdb_id=3q5v, cha... VLYSPFFYPVDYGIIPQTWY------------------DDGDPFDIMVIMREPVYPLTI-
+
+target LQARPIGGIRILDSEEADDKIIAVLEDDLVYGNIEDISECPGTVLDMIQHYFLTYKATPE
+pdb_id=3q5v, cha... IEARPIGIMKMEDSGDKDWKVLAVPVEDPYFNDWKDISDVPKAFLDEIAHFFQRYKELQ-
+
+target SLIQAKPAKIEIVGLYGKKEAQKVIRLAHEDYCNLFM
+pdb_id=3q5v, cha... ----GK--TTKIEGWGNAEEAKREILRAIEMYKEKF-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Resolved A.ILE119-(L)-A.LEU121 by filling A.THR115-(QGNIL)-A.LEU121 (116 candidates, BB_DB)
+Resolved A.PRO179-(ESLIQ)-A.ALA185 by filling A.THR178-(PESLIQA)-A.LYS186 (63 candidates, BB_DB)
+Resolved A.LYS186-(PA)-A.LYS189 by filling A.ILE183-(QAKPA)-A.LYS189 (49 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.CYS80-(GDLSGEYSGQQSNRENIK)-A.GLY99 by filling A.CYS80-(GDLSGEYSGQQSNRENIKG)-A.ASP100 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.16782e+09)
+No more stereo-chemical problems -> final energy: 14415.1
+
+
+Build model with the following alignment:
+target ARLNITFSPQAFEDYKYFQQNNKKMVKKINELLKSIDRNGALEGIGKPEKLKSNLTGYYS
+pdb_id=6n90, cha... --MKLVWTLSSWDDYEFWQRTDARMVEKINDLIRNAKRTP-FAGLGKPEPLKGDMAGYWS
+
+target RRINHEHRLVYTVDD----NHIKIASCKYHY
+pdb_id=6n90, cha... RRITAEHRFVYRVSGSGSEQRLEVIQCRFHY
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP75-()-A.ASN76 by relaxing A.VAL73-(DD)-A.ASN76
+Trying to fill 1 gap(s) by database.
+Resolved A.GLY40-(A)-A.LEU42 by filling A.ARG38-(NGAL)-A.GLU43 (43 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 21022.7)
+No more stereo-chemical problems -> final energy: 3404.28
+
+
+Build model with the following alignment:
+target MDTQHSALNARKQQATPRGV-GVMCQWYAEKAENATIWDKEGNQFIDFAGGIAVLNTGHR
+pdb_id=4ysn, cha... --DKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHT
+
+target HPKVIAAVTEQLTKFTHTAYQVTPYESYVALAERINERAPIAGP-AKAAFFTTGAEAVEN
+pdb_id=4ysn, cha... HEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGN-SPKMVSFGNSGSDANDA
+
+target AVKIARCYTGRHGIITFGNGFHGRSFMTMAMTGK-TAPYKRDFGVMPAGVFHARYPVPAK
+pdb_id=4ysn, cha... IIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSL-NMTRKIGPMLPSVVHVPYPDSYR
+
+target GI-------SVDAAIESVEDIFSEDIAPHDVAAIVLEPVQGEGGFNVVPAEFLKRLRAIC
+pdb_id=4ysn, cha... TYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFC
+
+target DKHGILLVADEVQSGFARTGKLFAMNHY-ETKADLITMAKSLGGGFPISGVVGRAEVMDA
+pdb_id=4ysn, cha... HEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQS
+
+target PNPGGLGGTYAGSPIAVAAAHAVIDAIEEENLCDRANELGAELVATLKDIQQATGDVVTD
+pdb_id=4ysn, cha... LDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRH-PMIGD
+
+target IRALGSMVAVELET--------AEQAKVVQNYAMENGLLLLTCGKYGNVIRFLYPLTIPA
+pdb_id=4ysn, cha... VRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLA--GNILRFQPPLVIPR
+
+target EQFRQGLDILKQGFATLKAGSAKAMEQSA
+pdb_id=4ysn, cha... EQLDQALQVLDDAFTAVEN----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Closed: A.TYR258-()-A.GLU259 by relaxing A.TYR258-(ET)-A.LYS261
+Trying to merge 9 gap(s) with distance 0.
+Merged gap A.ALA101-(G)-A.PRO103 and A.PRO103-()-A.ALA104 into A.ALA101-(GP)-A.ALA104
+Merged gap A.LYS152-()-A.THR153 and A.THR153-(A)-A.PRO155 into A.LYS152-(TA)-A.PRO155
+Trying to fill 7 gap(s) by database.
+Resolved A.VAL20-()-A.GLY21 by filling A.VAL20-(GVMCQ)-A.TRP26 (40 candidates, BB_DB)
+Resolved A.ALA101-(GP)-A.ALA104 by filling A.PRO99-(IAGP)-A.ALA104 (69 candidates, BB_DB)
+Resolved A.LYS152-(TA)-A.PRO155 by filling A.THR150-(GKTA)-A.PRO155 (47 candidates, BB_DB)
+Resolved A.ILE179-()-A.SER180 by filling A.ALA176-(KGIS)-A.VAL181 (111 candidates, BB_DB)
+Resolved A.THR343-(G)-A.ASP345 by filling A.THR343-(GDV)-A.VAL347 (74 candidates, BB_DB)
+Resolved A.THR363-()-A.ALA364 by filling A.LEU361-(ET)-A.ALA364 (54 candidates, BB_DB)
+Resolved A.GLY385-(KY)-A.GLY388 by filling A.CYS384-(GKYG)-A.ASN389 (51 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.08093e+19)
+Perform energy minimization (iteration 2, energy: 26320.2)
+No more stereo-chemical problems -> final energy: 22052.8
+
+
+Build model with the following alignment:
+target SNAEPSSKRRKHQGVIKRNWEYICSHDKEKTKILGDKNVDPKCEDSENKFDFSVMSYNIL
+pdb_id=4z0v, cha... ----------------------------------------------TEDALIRTVSYNIL
+
+target SQDLLED---NSHLYRHCRRPVLHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGAEIRP
+pdb_id=4z0v, cha... ADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVP
+
+target SLESLGYHCEYKMRTGRKPDGCAICFKHSKFSLLSVNPVEFFRPD---------------
+pdb_id=4z0v, cha... ALEAFGLEGVFRI---KQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVL
+
+target IS-----LLDRDNVGLVLLLQPKIPYAACPAICVANTHLLYNPRRGDIKLTQLAMLLAEI
+pdb_id=4z0v, cha... YPSAQEKVLQRSSVLQVSVLQST--KDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHI
+
+target SSVAHQKDGSFCPIVMCGDFNSVPGSPLYSFIKEGKLNYEGLPIGKVSGQEQSSRGQRIL
+pdb_id=4z0v, cha... RHVSCDL-YPGIPVIFCGDFNSTPSTGMYHFVINGSIPED--------------------
+
+target SIPIWPPNLGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTAEKLSSNLQHHFSLS
+pdb_id=4z0v, cha... -HEDWASN-G-------------------EE---------------ERCNMSLTHFFKLK
+
+target SVYSHYFPDTGIPEVTTCHSRSAITVDYIFYSAEKEDVAGHPGAEVALVGGLKLLARLSL
+pdb_id=4z0v, cha... SAC-------GEPAYTNYVGGFHGCLDYIFIDLNA----------------LEVEQVIPL
+
+target LTEQDLWTVNGLPNENNSSDHLPLLAKFRLEL
+pdb_id=4z0v, cha... PSHEEVTTHQALPSVSHPSDHIALVCDLKWK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Trying to merge 12 gap(s) with distance 0.
+Merged gap A.ASN285-(L)-A.GLY287 and A.GLY287-(ISQNCVYEVQQVPKVEKTD)-A.SER307 into A.ASN285-(LGISQNCVYEVQQVPKVEKTD)-A.SER307
+Trying to fill 11 gap(s) by database.
+Resolved A.ASP67-()-A.ASN68 by filling A.LEU65-(EDN)-A.SER69 (49 candidates, BB_DB)
+Resolved A.MET130-(RTG)-A.ARG134 by filling A.MET130-(RTGRKP)-A.ASP137 (48 candidates, BB_DB)
+Resolved A.ASP162-()-A.ILE163 by filling A.ASP162-(ISLL)-A.ASP167 (51 candidates, BB_DB)
+Resolved A.LYS180-(IP)-A.TYR183 by filling A.LYS180-(IPYAAC)-A.PRO187 (50 candidates, BB_DB)
+Resolved A.LYS224-(D)-A.GLY226 by filling A.LYS224-(DGSFC)-A.PRO230 (121 candidates, BB_DB)
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTD)-A.SER307), only 0 candidates
+Failed at loop insertion (A.ASP308-(LTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Resolved A.TYR340-(SHYFPDT)-A.GLY348 by filling A.TYR340-(SHYFPDTGIP)-A.GLU351 (95 candidates, BB_DB)
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to merge 4 gap(s) with distance 1.
+Merged gap A.ASN285-(LGISQNCVYEVQQVPKVEKTD)-A.SER307 and A.ASP308-(LTQTQLKQTEVLVTA)-A.GLU324 into A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to merge 3 gap(s) with distance 2.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to merge 3 gap(s) with distance 3.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279), only 0 candidates
+Failed at loop insertion (A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324), only 0 candidates
+Failed at loop insertion (A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389), only 0 candidates
+Trying to fill 3 gap(s) by Monte Carlo.
+Resolved A.GLU257-(GLPIGKVSGQEQSSRGQRILS)-A.ILE279 by filling A.GLU257-(GLPIGKVSGQEQSSRGQRILSI)-A.PRO280 (6 candidates, BB)
+Resolved A.ASN285-(LGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324 by filling A.PRO284-(NLGISQNCVYEVQQVPKVEKTDSDLTQTQLKQTEVLVTA)-A.GLU324 (6 candidates, BB)
+Resolved A.LYS372-(EDVAGHPGAEVALVGG)-A.LEU389 by filling A.ALA370-(EKEDVAGHPGAEVALVGG)-A.LEU389 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.06542e+25)
+Perform energy minimization (iteration 2, energy: 46433.8)
+Perform energy minimization (iteration 3, energy: 25730)
+No more stereo-chemical problems -> final energy: 22586.5
+
+
+Build model with the following alignment:
+target DTSNAQNRDILTLENLGDILKYLNSADLTTLDEVSMRAALSLTCAGIRKTSRSMINTLTE
+pdb_id=5vao, cha... --------PKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCE
+
+target QHVSAENLSPDQTQIIKQTYTGIHLDKGGNFEAALWKNWDRRSISLFLQAAISVLNTTPC
+pdb_id=5vao, cha... THLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPC
+
+target ESSKSVISAYNHFLQKPGDIKRTTLGSINSSV
+pdb_id=5vao, cha... ESSAVVVSGLRTLV------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 68997.1)
+No more stereo-chemical problems -> final energy: 5482.95
+
+
+Build model with the following alignment:
+target LPEELVLLERTLADGSTEQIIFSSAGDVNVYDLQALCDKVGWPRRPLTKIAASLRNSYLV
+pdb_id=2k5t, cha... ------------------------------------------------------------
+
+target ATLHSVTMPSKAEGEERKQLIGMARATSDHAFNATIWDVLVDPSYQGQGLGKALMEKVIR
+pdb_id=2k5t, cha... ---------------FNERLLAAVRVTLSGT-EGALDSLRVREVTRRRGVGQYLLEEVLR
+
+target TLLQRDISNITLFA--DN-KVVDFYKNLGFEADPQGIKGMFWYPRFLEHHHHHH
+pdb_id=2k5t, cha... NNPGVSCWWMADAGVEDRGVMTAFMQALGFTTQQG-------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.ALA91-(F)-A.ASN93 by filling A.SER88-(DHAF)-A.ASN93 (83 candidates, BB_DB)
+Resolved A.ALA134-()-A.ASP135 by filling A.ILE130-(TLFAD)-A.ASN136 (53 candidates, BB_DB)
+Resolved A.ASN136-()-A.LYS137 by filling A.LEU132-(FADN)-A.LYS137 (46 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 124711)
+No more stereo-chemical problems -> final energy: 3683.46
+
+
+Build model with the following alignment:
+target GSHMASHKKKGCVVIVGRINLSGDTAYAQQTRGEEGTQETSQTGRDKNVVTGEVQVLSTA
+pdb_id=3sv8, cha... ----------GSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
+
+target TQTFLGTTVGGVIWTVYHGAGSRTLAGAKHPALQMYTNVDQDLVGWPAPPGAKSLEPCAC
+pdb_id=3sv8, cha... TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
+
+target GSSDLYLVTRDADVIPARRRGDSTASLLSPRPLAYLKGSSGGPVMCPSGHVAGIFRAAVS
+pdb_id=3sv8, cha... GSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVS
+
+target TRGVAKSLQFIPVETLSTQARSP
+pdb_id=3sv8, cha... TRGVAKAVAFIPVESLETTMRS-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.56685e+07)
+No more stereo-chemical problems -> final energy: 6884.73
+
+
+Build model with the following alignment:
+target AMGIVIEKAADGYKLSIDGRETYIKGVG--GT--------------YRLDIAAQSGANAF
+pdb_id=4ypj, cha... -FGVRYFKFDENEGFSLNGEYMKLHGVSMHHDLGALGAATNARGVERQMQIMKDMGVNAI
+
+target RTWGGNVEEIKKNLALASEHNMYVMQGI---GMTKDSI-RYYDDEYKNKMREEVRLLAET
+pdb_id=4ypj, cha... RVTHN--PASPELLEAANKLGLFIIEEAFDSWAQSKKPYDYG-RFFNAWAEHDIKEMVDR
+
+target FKNDTSLLAWGIGNEIELGNANIAAAWNFVEELAQLIKSIDKRHLVSTVIS-YNPSA---
+pdb_id=4ypj, cha... GKNEPAIIMWSIGNEIYDTTN--AAGVETARNLVGWVKEIDTTRPTTIGEDKTRGDKVNV
+
+target ---LDSVAKYAPSLDYVGINVYGPMGEVQAVVDRSDYKGAFMITEWGPT----GWWETAS
+pdb_id=4ypj, cha... TPINSYIKEIFNIVDVVGLNYSEN---NYDGYHKQNPSWKLYGSETSSATRSRGVYTHPY
+
+target T---EWKAPI-----EQTSEEKRQVYEERYTQYISANTRCLGSFVFLWG---QKEERTP-
+pdb_id=4ypj, cha... QYNQSTKYADLQQSSYDNDYVGWGRTAEDAWKYDRDLKHIAGQ--FIWTGFDYIGEPTPY
+
+target --------TWFSMFVEDKVDSLPLKGEKTPMVEAMQRVWTGKELDETAPIVRGMTIDGKS
+pdb_id=4ypj, cha... YNSYPAKSSYFGAV--------DTAGFPKDIFYYYQSQWKKE------------------
+
+target AIDNVRIKAGTLFKAEVSVTDKENDSLAYVWEVLKEATVLGFGGSYEPRPERMGDVAVSD
+pdb_id=4ypj, cha... ------------------------------------------------------------
+
+target KNVYETMIKVPGEYRLYVYVLDNTGFVSTANIPFQVID
+pdb_id=4ypj, cha... --------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 17).
+Initialized default backbone scoring for modelling.
+Closed: A.SER151-()-A.TYR152 by relaxing A.SER151-(YN)-A.PRO154
+Trying to merge 16 gap(s) with distance 0.
+Trying to fill 16 gap(s) by database.
+Resolved A.GLY28-()-A.GLY29 by filling A.GLY28-(GTYR)-A.LEU33 (232 candidates, BB_DB)
+Resolved A.GLY49-(NV)-A.GLU52 by filling A.GLY48-(GNVEE)-A.ILE54 (100 candidates, BB_DB)
+Resolved A.ILE72-()-A.GLY73 by filling A.ILE72-(GMTKD)-A.SER78 (128 candidates, BB_DB)
+Resolved A.ILE79-()-A.ARG80 by filling A.SER78-(IR)-A.TYR81 (41 candidates, BB_DB)
+Resolved A.TYR82-(D)-A.ASP84 by filling A.TYR81-(YDD)-A.GLU85 (56 candidates, BB_DB)
+Resolved A.ALA121-(NI)-A.ALA124 by filling A.LEU118-(GNANI)-A.ALA124 (65 candidates, BB_DB)
+Resolved A.ALA156-()-A.LEU157 by filling A.ASN153-(PSA)-A.LEU157 (42 candidates, BB_DB)
+Resolved A.PRO177-(MGE)-A.VAL181 by filling A.ASN173-(VYGPMGE)-A.VAL181 (41 candidates, BB_DB)
+Failed at loop insertion (A.THR202-()-A.GLY203), only 22 candidates
+Resolved A.THR210-()-A.GLU211 by filling A.GLU206-(TASTEW)-A.LYS213 (108 candidates, BB_DB)
+Resolved A.ILE216-()-A.GLU217 by filling A.THR210-(EWKAPI)-A.GLU217 (41 candidates, BB_DB)
+Resolved A.SER244-(FV)-A.PHE247 by filling A.SER244-(FVFLWGQ)-A.LYS252 (85 candidates, BB_DB)
+Resolved A.PRO257-()-A.THR258 by filling A.GLU254-(RTPT)-A.TRP259 (51 candidates, BB_DB)
+Resolved A.PHE263-(VEDKVDSL)-A.PRO272 by filling A.PHE263-(VEDKVDSLPLKG)-A.GLU276 (1751 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR202-()-A.GLY203), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR202-()-A.GLY203), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR202-()-A.GLY203), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.THR202-()-A.GLY203 by filling A.PRO201-(TGWWETASTEW)-A.LYS213 (41 candidates, BB_DB)
+Rebuilding sidechains.
+Trying to fix 2 ring punch(es).
+Trying to merge 2 gap(s) with distance 4.
+Trying to fill 2 gap(s) by database.
+Resolved A.THR46-(W)-A.GLY48 by filling A.ARG45-(TW)-A.GLY48 (55 candidates, BB_DB)
+Resolved A.VAL246-(F)-A.LEU248 by filling A.SER244-(FVF)-A.LEU248 (76 candidates, BB_DB)
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.72692e+19)
+Perform energy minimization (iteration 2, energy: 29278.9)
+Perform energy minimization (iteration 3, energy: 20875.3)
+No more stereo-chemical problems -> final energy: 18401.3
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMAIRAQLDALDAAERPGHLASAIADEIRAVLRS-GDPIDH
+pdb_id=5ttb, cha... ------------------------------------AADYQQLRERLIQELNLTPQQLHE
+
+target HRPLETLGLDALMGLELRNRLEASLGITLPVALVWAYPTISDLATALCERMDYATPAAAQ
+pdb_id=5ttb, cha... ESNLIQAGLDSIRLMRWLHWFRKN-GYRLTLRELYAAPTLAAWNQLMLSR----------
+
+target EISDTEPELSDEEMDLLADLVDASELEAATRGESTSGS
+pdb_id=5ttb, cha... --------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.SER53-()-A.GLY54 by relaxing A.SER53-(GD)-A.PRO56
+Trying to fill 1 gap(s) by database.
+Resolved A.SER83-(L)-A.GLY85 by filling A.GLU81-(ASLG)-A.ILE86 (48 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.29878e+07)
+No more stereo-chemical problems -> final energy: 1228.67
+
+
+Build model with the following alignment:
+target GAMGGSMIKGKLMPNSLKDVQKLICDEGITDNVITTLSRLKPFDLAMLKATSDNKVKTLL
+pdb_id=5t2x, cha... ----------------------------------------------------SKTITDFC
+
+target DSDELKPFWVNKFNKLRLEKDHIFQFRNPDPQSRADFYCGYVLYLAALKEKQKEISSYYD
+pdb_id=5t2x, cha... EEAEQADIWRTHLQNF---NEEHFSFEEYPPLTVSQLVKGIYFYGQAAECREEEGKPFGD
+
+target YLNLSFT----TFNCFYAAQEILTFLIGACKNDTKRENIDLLYNFV--TSQSTQIQEHKT
+pdb_id=5t2x, cha... -NELEFLKKSAYQHCFYAYNSLSTWAYEKYKMGLND------YSLLTLHYAQKACQYHWT
+
+target PGCLLLANAYFYLAGFYLSLDLKAESIECYKECWGQLHLAQLLET--DSEREIHNAYFNK
+pdb_id=5t2x, cha... PGYLLFYKTCLNLAI----LSNA--PSLSYQEALEALLIARKLSEHQYSISAINNAYFGK
+
+target GLATSNAFGLNSISEIKARCLDLASEALPYPARNVMEANAVKTFENRFKDSMSTAGKDDE
+pdb_id=5t2x, cha... GLIHGN----ESWD----------------------------------------------
+
+target RSITRPIIL
+pdb_id=5t2x, cha... ---------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.THR219-()-A.ASP220 by relaxing A.THR219-(DS)-A.GLU222
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.LEU76-(RLE)-A.LYS80 by filling A.LEU76-(RLEKD)-A.HIS82 (59 candidates, BB_DB)
+Resolved A.ASP120-(Y)-A.LEU122 by filling A.TYR119-(DYL)-A.ASN123 (53 candidates, BB_DB)
+Resolved A.THR127-()-A.THR128 by filling A.PHE126-(TTF)-A.ASN130 (74 candidates, BB_DB)
+Resolved A.ARG152-(ENIDLL)-A.TYR159 by filling A.ASN148-(DTKRENIDLL)-A.TYR159 (63 candidates, BB_DB)
+Resolved A.VAL162-()-A.THR163 by filling A.TYR159-(NFV)-A.THR163 (40 candidates, BB_DB)
+Resolved A.GLY189-(FYLS)-A.LEU194 by filling A.GLY189-(FYLSLDL)-A.LYS197 (76 candidates, BB_DB)
+Resolved A.LYS197-(AE)-A.SER200 by filling A.LEU196-(KAES)-A.ILE201 (72 candidates, BB_DB)
+Resolved A.ASN238-(AFGL)-A.ASN243 by filling A.ASN238-(AFGLN)-A.SER244 (63 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.6868e+20)
+Perform energy minimization (iteration 2, energy: 17677.3)
+Perform energy minimization (iteration 3, energy: 13804.7)
+No more stereo-chemical problems -> final energy: 12605.8
+
+
+Build model with the following alignment:
+target MTITAL-PTGLYAEVLSFYGHQMQKLDGRDFAGYAATFTEDGEFRHSPSLPA--------
+pdb_id=3eby, cha... -----EVAQVAQSAIDDFNAAYGLCLDDDRLEQWPTLFVDDCLYQ-VIARENVDNGLPAA
+
+target ---AHTRAGITAVLEDFHRKFDARKIQRRHWFDHTALSQASDGSITATSYCLVLTVHADV
+pdb_id=3eby, cha... VMYCDSKGMLADRVVALRKAN----HFNRHLIGRAVITGVEGDQVSAEASYVVFQTRNDG
+
+target KAPEFGPSCLVHDVLVRGADGELLLRSRHVTHDHVFPA
+pdb_id=3eby, cha... E-TRIYNAGKYVDRFDL-SGGTVRLKSRTCIYDTL---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.ARG44-(H)-A.SER46 by filling A.PHE43-(RHS)-A.PRO47 (102 candidates, BB_DB)
+Resolved A.ALA51-()-A.ALA52 by filling A.HIS45-(SPSLPA)-A.ALA52 (150 candidates, BB_DB)
+Resolved A.PHE69-(DARK)-A.ILE74 by filling A.PHE69-(DARK)-A.ILE74 (170 candidates, BB_DB)
+Resolved A.LYS109-(A)-A.PRO111 by filling A.ALA106-(DVKA)-A.PRO111 (45 candidates, BB_DB)
+Resolved A.ARG125-(G)-A.ALA127 by filling A.ARG125-(GADGE)-A.LEU131 (198 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.86703e+08)
+No more stereo-chemical problems -> final energy: 3370.03
+
+
+Build model with the following alignment:
+target MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSGKKSRMCGYC
+pdb_id=6jdr, cha... -----------------------------------------------------SRMCGYC
+
+target GAPAPYATACGLDVCVYHTHFHQHCPVIIWCGHPAGSGSCSECEPPLGKGTSPLDEVLEQ
+pdb_id=6jdr, cha... GAPAPYATACGLDVCVYHTHFHQHCPVIIWCGHPAGSGSCSECEPPLGKGTSPLDEVLEQ
+
+target VPYKPPRTVIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPDGDYASTALLPTCK
+pdb_id=6jdr, cha... VPYKPPRTVIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPDGDYASTALLPTCK
+
+target EINMVAVASNVLRSRFIIGPPGAGKTHWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFN
+pdb_id=6jdr, cha... EINMVAVASNVLRSRFIIGPPGAGKTHWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFN
+
+target VPAGTTLQFPAPSRTGPWVRILAGGWCPGKNSFLDEAAYCNHLDVLRLLSKTTLTCLGDF
+pdb_id=6jdr, cha... VPAGTTLQFPAPSRTGPWVRILAGGWCPGKNSFLDEAAYCNHLDVLRLLSKTTLTCLGDF
+
+target KQLHPVGFDSHCYVFDIMPQTQLKTIWRFGQNICDAIQPDYRDKLMSMVNTTRVTHVEKP
+pdb_id=6jdr, cha... KQLHPVGFDSHCYVFDIMPQTQLKTIWRFGQNICDAIQPDYRDKLMSMVNTTRVTYVEKP
+
+target VRYGQVLTPYHRDREDGAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFV
+pdb_id=6jdr, cha... VRYGQVLTPYHRDREDSAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFV
+
+target YDPHRQLQSMFDLPAKGTPVNLAVHRDEQLIVLDRNNREITVAQALGNGDKFRATDKRVV
+pdb_id=6jdr, cha... YDPHRQLQSVFDLPAKGTPVNLAVHRDEQLIVLDRNNREITVAQALGNGDKFRATDKRVV
+
+target DSLRAICADLELEHHHHHH
+pdb_id=6jdr, cha... DSL----------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 59302)
+Perform energy minimization (iteration 2, energy: 4628.64)
+No more stereo-chemical problems -> final energy: 2831.91
+
+
+Build model with the following alignment:
+target MELALGCSPAAQNGDTVPLPAVVPAPAAIEQATGAPFRLDASTRI--E--GEA-DAASAL
+pdb_id=4c7g, cha... ---------------PTPLDRVIPAPASVE-PGGAPYRITRGTHIRVDDSREARRVGDYL
+
+target SALLEARTGLAPATGGD-GAVIALRIEGG-GPAESYALTADEASVTVTGADAAGLFYGVQ
+pdb_id=4c7g, cha... ADLLRPATGYRLPVTSHGHGGIRLRLAEGPYGDEGYRLDSGREGVTITARKAAGLFHGVQ
+
+target TLGQLLARDG-------DAWVVPAVSIEDAPRFAYRGVMLDVARHFHPVETVKAYIGHAA
+pdb_id=4c7g, cha... TLRQLLPAAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFSVDEVKRYIDRVA
+
+target SLKLNALHLHLSDDQGWRIELHSRPELTALASSTAVGGDPGGFYTKDDYREIVEYAASRH
+pdb_id=4c7g, cha... LYKYNKLHLHISDDQGWRLAIDSWPRLATYGGSTEVGGGPGGHYTKADYEEIVRYAASRH
+
+target MIVVPEIDMPSHTHAIGLAYPELAEEPVITDPMRETAAATGGALPESGTPYLGIEVGFSS
+pdb_id=4c7g, cha... LEVVPEIDMPGHTNAALASYAELNCDGV--------------AP----PLYTGTKVGFST
+
+target LKIHDEATYDFAADVFGELAGMTPGPYLHLGGDEAHGTAEEDFALFVSRVSTIIADLGKT
+pdb_id=4c7g, cha... LCVDKDVTYDFVDDVLGELAALTPGRYLHIGGDQAHSTPQADFVAFMKRVQPIVAKYGKT
+
+target PVAWHEAGDAGGLAGATVGQYWGYVTPTDGMDDRARGFVSNGGQLILSPADAIYLDMKYP
+pdb_id=4c7g, cha... VVGWHQL-AGAEPVEGALVQYWGLDRTSDAEKAQVAAAARNGTGLILSPADRTYLDMKYT
+
+target TGPDLGLSWANGPTSVQRAYDWEPSTVIPGIDDADILGVEAPLWSETLRSLDDIETMAFP
+pdb_id=4c7g, cha... KDTPLGLSWA-GYVEVRRSYDWDPAAYLPGAPAEAVRGVEAPLWTETLSDPDQLDFMAFP
+
+target RIAAAAEAAWSPATGASDLRTWESFRARVGALGPLWTSLGIGFHPSGEIDWATEKGQFLE
+pdb_id=4c7g, cha... RLPGVAELGWSPA----STHDWDTYKVRLAGQAPHWEAMGIDYYRSPQVPWT--------
+
+target HHHHHH
+pdb_id=4c7g, cha... ------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA49-()-A.ASP50 by relaxing A.GLU48-(ADA)-A.ALA52
+Closed: A.GLY83-()-A.GLY84 by relaxing A.GLY83-(G)-A.PRO85
+Trying to merge 10 gap(s) with distance 0.
+Merged gap A.ILE45-()-A.GLU46 and A.GLU46-()-A.GLY47 into A.ILE45-(E)-A.GLY47
+Trying to fill 9 gap(s) by database.
+Resolved A.GLU30-(Q)-A.ALA32 by filling A.GLU30-(QATG)-A.ALA35 (58 candidates, BB_DB)
+Resolved A.ILE45-(E)-A.GLY47 by filling A.ILE45-(EGEA)-A.ASP50 (43 candidates, BB_DB)
+Resolved A.ASP72-()-A.GLY73 by filling A.ALA68-(TGGD)-A.GLY73 (44 candidates, BB_DB)
+Resolved A.GLY123-()-A.ASP124 by filling A.LEU119-(ARDGD)-A.ALA125 (221 candidates, BB_DB)
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Resolved A.LEU270-(PESG)-A.THR275 by filling A.ALA269-(LPESGT)-A.PRO276 (40 candidates, BB_DB)
+Resolved A.ALA353-(G)-A.ASP355 by filling A.ALA353-(GDAGG)-A.LEU359 (54 candidates, BB_DB)
+Resolved A.ALA416-(N)-A.GLY418 by filling A.TRP415-(ANGP)-A.THR420 (53 candidates, BB_DB)
+Resolved A.ALA479-(TGAS)-A.ASP484 by filling A.PRO478-(ATGASD)-A.LEU485 (44 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL254-(ITDPMRETAAATGG)-A.ALA269), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.VAL254-(ITDPMRETAAATGG)-A.ALA269 by filling A.PRO253-(VITDPMRETAAATGG)-A.ALA269 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.20456e+17)
+No more stereo-chemical problems -> final energy: 34211.3
+
+
+Build model with the following alignment:
+target MAVTSESVPEQQITAYLLKIQRGGFIQPFGSMIAVDEPSFRILAYSDNARDMLGITPQSV
+pdb_id=4our, cha... ------------ITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIM----
+
+target PSLDDKNDAAFALGTDIRTLFTHSSAVLLEKAFSAREISLMNPIWIHSRTSGKPFYGILH
+pdb_id=4our, cha... ---------ILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTGKPFYAILH
+
+target RIDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDVKLLCDTVVESVRE
+pdb_id=4our, cha... RIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRD
+
+target LTGYDRVMVYRFHEDEHGEVVAETKRPDLEPYIGLHYPATDIPQASRFLFKQNRVRMIVD
+pdb_id=4our, cha... LTGYDRVMVYKFHEDEHGEVVAESKRDDLEPYIGLHYPATDIPQASRFLFKQNRVRMIVD
+
+target CHASAVRVVQDEALVQPLCLVGSTLRAPHGCHAQYMANMGSTASLVMAVIINGNDEEGV-
+pdb_id=4our, cha... CNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIING-------
+
+target --GGRTSMRLWGLVVCHHTSARCIPFPLRYACEFLMQAFGLQLNMELQLAAQSLEKRVLR
+pdb_id=4our, cha... ------SMRLWGLVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLR
+
+target TQTLLCDMLLRDSPTGIVTQSPSIMDLVKCDGAALYYQGNYYPLGVTPTEAQIRDIIEWL
+pdb_id=4our, cha... TQT-------------------SIMDLVKCDGAA---------LGVAPSEVQIKDVVEWL
+
+target LAFHRDSTGLSTDSLADAGYPGAASLGDAVCGMAVAYITEKDFLFWFRSHTAKEIKWGGA
+pdb_id=4our, cha... L-------GLSTDSL----YPGAAALGDAVCGMAVA------FLFWFRSHTAKEIKWGGA
+
+target KHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWENAEMDAIHSLQLILRDSFKDAEHHHH
+pdb_id=4our, cha... KHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQPWETAEMDAIHSLQLILRDS---------
+
+target HH
+pdb_id=4our, cha... --
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 7).
+Initialized default backbone scoring for modelling.
+Trying to merge 7 gap(s) with distance 0.
+Trying to fill 7 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Resolved A.GLY293-(NDEEGVGGRT)-A.SER304 by filling A.GLY293-(NDEEGVGGRT)-A.SER304 (62 candidates, BB_DB)
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Resolved A.ALA391-(LYYQGNYYP)-A.LEU401 by filling A.ALA391-(LYYQGNYYP)-A.LEU401 (49 candidates, BB_DB)
+Resolved A.LEU418-(AFHRDST)-A.GLY426 by filling A.LEU418-(AFHRDST)-A.GLY426 (140 candidates, BB_DB)
+Resolved A.LEU432-(ADAG)-A.TYR437 by filling A.SER431-(LADAG)-A.TYR437 (136 candidates, BB_DB)
+Resolved A.ALA453-(YITEKD)-A.PHE460 by filling A.ALA453-(YITEKD)-A.PHE460 (288 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR56-(PQSVPSLDDKNDA)-A.ALA70), only 0 candidates
+Failed at loop insertion (A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.THR56-(PQSVPSLDDKNDA)-A.ALA70 by filling A.THR56-(PQSVPSLDDKNDAA)-A.PHE71 (6 candidates, BB)
+Resolved A.THR360-(LLCDMLLRDSPTGIVTQSP)-A.SER380 by filling A.THR360-(LLCDMLLRDSPTGIVTQSPS)-A.ILE381 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.0151e+16)
+Perform energy minimization (iteration 2, energy: 18019.3)
+No more stereo-chemical problems -> final energy: 14771.3
+
+
+Build model with the following alignment:
+target GHMVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDI
+pdb_id=5yya, cha... ---MWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDV
+
+target MYHVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQVVMANYNVDYPRKRGFWYDVE
+pdb_id=5yya, cha... IYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAE
+
+target ICRKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALR
+pdb_id=5yya, cha... ISRKRETRTARELYANVVLG-DDSLNDCRIIFVDEVFKIERPG-----------------
+
+target NTGKSGP
+pdb_id=5yya, cha... -------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.LEU140-(N)-A.ASP142 by filling A.LEU140-(NDS)-A.GLN144 (43 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.96155e+20)
+No more stereo-chemical problems -> final energy: -1456.99
+
+
+Build model with the following alignment:
+target MGHHHHHHHHHHSSGMTELPPNAPNPENATNELAQELLRKLRQKQGNWVEWGQAIASLQK
+pdb_id=4wt3, cha... -----------------------PIPTQFRSLDSAGKIEILAGRMALWFEYAPLISSLYT
+
+target SGYNPQDIFEATGFEPVQQNQVIVGSQVYNSLEKSGASAATLAHYATRGSDVLYELRLLT
+pdb_id=4wt3, cha... DGFTPPTIEELTGISSIEQNRLIVGAQVRDSILQSIHEPELISAFDTGGAELLYEIRLLS
+
+target HEERAAAGDLTFTHKVDADEAREIAKAIKDFSRFRILP--EGFS-NHPGDAVAYQAWKLA
+pdb_id=4wt3, cha... TTQRVAAATFIIDRNIDSKGAQDLARAIKDYPNRRGDVGWLDFDYNLPGDCLSFLYYRQS
+
+target RQYSD-LQERSRLIARGLRFAHSETARKQIEQLLVDFTVVSQRPAPIPPFFRFDTEDELP
+pdb_id=4wt3, cha... RENKNPSDQRTSMLLQALGVAESEKAKNRLNTELYGDKE---------------------
+
+target RIVPVVGQLPLKAEELKAVPLVEEIEPFRLVKFSGEQAWVALPGWQVLLAAEDPVTILAT
+pdb_id=4wt3, cha... ------------------------------------------------------------
+
+target SDRFPKQNQTEPGPVLVVVDRSQREWNDFSYFVVDHDGELDFQWFETKPEFPILGKVIIL
+pdb_id=4wt3, cha... ------------------------------------------------------------
+
+target VRPRRILDENVTKDSWQIDE
+pdb_id=4wt3, cha... --------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.SER162-()-A.ASN163 by relaxing A.SER162-(N)-A.HIS164
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.PRO158-()-A.GLU159 by filling A.ARG155-(ILPE)-A.GLY160 (97 candidates, BB_DB)
+Resolved A.ASP182-()-A.LEU183 by filling A.GLN179-(YSDL)-A.GLN184 (199 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.4658e+06)
+Perform energy minimization (iteration 2, energy: 1230.65)
+No more stereo-chemical problems -> final energy: 260.865
+
+
+Build model with the following alignment:
+target MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLIL
+pdb_id=5d92, cha... MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLIL
+
+target ERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSN
+pdb_id=5d92, cha... ERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSN
+
+target DNLKTAEKLLLSSLIGSGSSKVPFLSRAAFARITLPLARALLRIGLTPDAVTIIGTTASV
+pdb_id=5d92, cha... DNLKTAEKLLLSSLIGS--GSLNKYARGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVM
+
+target AGALVLFPMGKLFPGACVVWFFVLFDMLDGAMARLRSGGTRFGAVLDAACDRISDGAVFS
+pdb_id=5d92, cha... AGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFT
+
+target GLLWWIAFGMRDRLLVVATLTCLVTSQVISYIKARAEASGLRGDGGIIERPERLIIVLVG
+pdb_id=5d92, cha... GIVIWFFLGGANPTIAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVA
+
+target AGVSDFPFIAWP-PALPVAMWVLAVASVITLGQRLHTVWTSPGATDRIPATGGRTETQGH
+pdb_id=5d92, cha... TGLVGLG---IPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWT--------------
+
+target PEPGNPGKTQQ
+pdb_id=5d92, cha... -----------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.PRO312-()-A.PRO313 by relaxing A.PRO312-(P)-A.ALA314
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.SER137-(GS)-A.SER140 by filling A.ILE135-(GSGS)-A.SER140 (103 candidates, BB_DB)
+Resolved A.PRO307-(FIA)-A.TRP311 by filling A.PHE306-(PFIAWP)-A.PRO313 (67 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.49814e+12)
+No more stereo-chemical problems -> final energy: 12842.1
+
+
+Build model with the following alignment:
+target GAMGHAPAPSESQRLVRRVVIAGGGTAGWMAAAALSKLLGRQLQITLVESDEIGTVGVGE
+pdb_id=6p00, cha... -------------GKIDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDIPTLGVGE
+
+target ATIPSLVT-FHRLLEIDEAQFMAATQATFKVGIAFEHWRDVD-------------RHYIH
+pdb_id=6p00, cha... ATMPNLQTAFFDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTSEARELDGGPDHFYH
+
+target SFGHTGTDHWSAGFQHFWLKAH--ARGVARDFGDYCLELRAAQEGRFAHL-P-NGGMNYA
+pdb_id=6p00, cha... PFGLLK-YHEQIPLSHYWFDRLYRGKTVEPFDYACYKEPVILDANRSPRRLDGSKVTSYA
+
+target YHLDAGLYARFLRRFSEGF-GVQRIEGRIGSVQTDAHSGDIAALVLDDGTRIEGDLFLDC
+pdb_id=6p00, cha... WHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRD-ANGNIESVRTATGRVFDADLFVDC
+
+target TGFRALLIGQTLGVGSEDWSRWLFADSALAVQTESVG---APVTFTRARADRAGWMWRIP
+pdb_id=6p00, cha... SGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIP
+
+target LQHRVGNGIVYSSRYTDQDSAAQVLEHNLQGRA-LTTPRALRFTPNQRHRVWEKNCVALG
+pdb_id=6p00, cha... MLGRFGTGYVYSSRFATEDEAVREFCEMWHLDPETQPLNRIRFRVGRNRRAWVGNCVSIG
+
+target LASGFLEPIESTNIHLIQRGIVRLLQTFPQ-VIDPVDIAEYNRQAAEEIAHIRDFVILHY
+pdb_id=6p00, cha... TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSFNPVLTARFNREIETMFDDTRDFIQAHF
+
+target HATDRRDTAFWRDCASMEIPDSLRHRMELFRQSG----RV------FHQGN-----ELFA
+pdb_id=6p00, cha... YFSPRTDTPFWRANKELRLADGMQEKIDMYRAGMAINAPA---------NFEEEFRNLWN
+
+target ENSWIQVMLGQGIVPRHHHPVADLMGD--AELSQFLEGIRQRVEATLARLPPHAEFLRRY
+pdb_id=6p00, cha... NSSYYCVLAGLGLVPDAPSPRLAHMPRATESVDEVFGAVKDQQRNLLETLPSLHEFLRQQ
+
+target CPAPAPPAPMPQPAPGTPLAAPAA
+pdb_id=6p00, cha... H-----------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Closed: A.THR68-()-A.PHE69 by relaxing A.VAL67-(T)-A.PHE69
+Closed: A.PHE181-()-A.GLY182 by relaxing A.GLU179-(GF)-A.GLY182
+Closed: A.ALA311-()-A.LEU312 by relaxing A.ARG310-(AL)-A.THR313
+Closed: A.GLN367-()-A.VAL368 by relaxing A.GLN367-(V)-A.ILE369
+Trying to merge 11 gap(s) with distance 0.
+Merged gap A.LEU154-()-A.PRO155 and A.PRO155-()-A.ASN156 into A.LEU154-(P)-A.ASN156
+Trying to fill 10 gap(s) by database.
+Resolved A.ASP101-()-A.ARG102 by filling A.ARG98-(DVDR)-A.HIS103 (60 candidates, BB_DB)
+Resolved A.GLY112-(T)-A.ASP114 by filling A.HIS110-(TGT)-A.ASP114 (42 candidates, BB_DB)
+Resolved A.HIS128-()-A.ALA129 by filling A.ALA127-(HAR)-A.GLY131 (40 candidates, BB_DB)
+Resolved A.LEU154-(P)-A.ASN156 by filling A.HIS153-(LPNGG)-A.MET159 (59 candidates, BB_DB)
+Resolved A.ASP196-(A)-A.HIS198 by filling A.ASP196-(AHS)-A.GLY200 (48 candidates, BB_DB)
+Resolved A.GLY258-()-A.ALA259 by filling A.SER256-(VGA)-A.PRO260 (49 candidates, BB_DB)
+Resolved A.GLY430-()-A.ARG431 by filling A.LEU425-(FRQSG)-A.ARG431 (158 candidates, BB_DB)
+Resolved A.VAL432-(FHQ)-A.GLY436 by filling A.GLY430-(RVFHQ)-A.GLY436 (164 candidates, BB_DB)
+Resolved A.ASN437-()-A.GLU438 by filling A.GLY436-(NELFA)-A.GLU442 (96 candidates, BB_DB)
+Resolved A.ASP468-()-A.ALA469 by filling A.ASP468-(AEL)-A.SER472 (66 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.44243e+18)
+Perform energy minimization (iteration 2, energy: -5760.88)
+No more stereo-chemical problems -> final energy: -9617.54
+
+
+Build model with the following alignment:
+target SNAMTNMKLKFDLLLKS-YHLSHRFVYK--ANPGNAGDGVIASATYDFFERNALTYI--P
+pdb_id=5ax7, cha... --------NLLFTYYKHYFAGIKKVALIGFPDHPNKGDSAIYVAEKKLLDALNIEVVYIT
+
+target YR----------DGERYSSETDI-LIFGGGGNLIEGLYSEGHDFIQNNIGKF--HKVIIM
+pdb_id=5ax7, cha... AQEADYSASELKSIISDIPRDEFALAFHGGGNFGDLY-PDHQHLRELVVRDFPSFTTISF
+
+target PSTIRG-YSDLFINNI------DKFVVFCRENITFDYIKSLNY-EPNKNVFITDDMAFYL
+pdb_id=5ax7, cha... PQSVWYNEQQLLEQASILYAENPNITLVTRDRQSYGFAVDAFGKHNE--VLLTPDIVFFM
+
+target D-LNKYLSLKPVYKKQANCFRTDSESLTGDYKEN-------------N-HDISLTWNG--
+pdb_id=5ax7, cha... GPIPEIREATPITHDVLILARL---------------DTLNAANLTYSVEDWLLWDPPVA
+
+target DYWDN---EFLARNSTRCMINFLEEYKVVNTDRLHVAILASLLGKEVNFYPNS-YYKNEA
+pdb_id=5ax7, cha... QNPDSSFDDRGQ-ARYEAGAEFLASARVVITDRLHAHILSTLMGIPHIVVENSQMGKITN
+
+target VYNYSLFNRY--PKTCFITAS
+pdb_id=5ax7, cha... YHNTWLHG-CTLDGVSVVV--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 20).
+Initialized default backbone scoring for modelling.
+Closed: A.TYR138-()-A.GLU139 by relaxing A.ASN137-(YE)-A.PRO140
+Closed: A.GLY197-()-A.ASP198 by relaxing A.GLY197-(D)-A.TYR199
+Trying to merge 18 gap(s) with distance 0.
+Merged gap A.THR175-(DSESLTGDYKEN)-A.ASN188 and A.ASN188-()-A.HIS189 into A.THR175-(DSESLTGDYKENN)-A.HIS189
+Merged gap A.ASN261-(R)-A.TYR263 and A.TYR263-()-A.PRO264 into A.ASN261-(RY)-A.PRO264
+Trying to fill 16 gap(s) by database.
+Resolved A.SER17-()-A.TYR18 by filling A.SER17-(YHLS)-A.HIS22 (170 candidates, BB_DB)
+Resolved A.LYS27-()-A.ALA28 by filling A.TYR26-(KANPGN)-A.ALA33 (46 candidates, BB_DB)
+Resolved A.ILE54-()-A.PRO55 by filling A.ILE54-(PYRDG)-A.GLU60 (41 candidates, BB_DB)
+Resolved A.ILE68-()-A.LEU69 by filling A.SER64-(ETDI)-A.LEU69 (135 candidates, BB_DB)
+Resolved A.LEU81-(Y)-A.SER83 by filling A.GLY80-(LYS)-A.GLU84 (90 candidates, BB_DB)
+Resolved A.PHE96-()-A.HIS97 by filling A.ILE93-(GKFH)-A.LYS98 (54 candidates, BB_DB)
+Resolved A.GLY108-()-A.TYR109 by filling A.ILE106-(RGYS)-A.ASP111 (99 candidates, BB_DB)
+Resolved A.ILE117-()-A.ASP118 by filling A.ASN116-(IDKF)-A.VAL121 (286 candidates, BB_DB)
+Resolved A.ASN141-(KN)-A.VAL144 by filling A.TYR138-(EPNKN)-A.VAL144 (86 candidates, BB_DB)
+Resolved A.ASP155-()-A.LEU156 by filling A.TYR153-(LDLN)-A.LYS158 (70 candidates, BB_DB)
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Resolved A.ASN202-()-A.GLU203 by filling A.GLY197-(DYWDN)-A.GLU203 (48 candidates, BB_DB)
+Resolved A.ALA206-(R)-A.ASN208 by filling A.PHE204-(LARN)-A.SER209 (66 candidates, BB_DB)
+Resolved A.SER247-()-A.TYR248 by filling A.SER247-(YYK)-A.ASN251 (46 candidates, BB_DB)
+Resolved A.ASN261-(RY)-A.PRO264 by filling A.PHE260-(NRY)-A.PRO264 (69 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.THR175-(DSESLTGDYKENN)-A.HIS189), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.THR175-(DSESLTGDYKENN)-A.HIS189 by filling A.THR175-(DSESLTGDYKENNH)-A.ASP190 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.98528e+11)
+Perform energy minimization (iteration 2, energy: 16112.4)
+No more stereo-chemical problems -> final energy: 13292.3
+
+
+Build model with the following alignment:
+target GMANDQDLSNPEYLYTEDDINQLLKHYLGLDDRISI-----IQHVALNESLLLKQTLHQ-
+pdb_id=5ham, cha... -----------DYWYTENEITHLLTAQLD-EKKFSVQPAITFRNTALTE-EMLKDYTAKG
+
+target ------------------------------------------------V-----------
+pdb_id=5ham, cha... EEKNKILAEVQETIKIANLIPDKEERALMLGDAKKREEILKLSDAEREKLKNDLLRGGEA
+
+target ----LSDI-------FSG-MQEKAVIPLHTGNNHWVAMAIKKGMNDD-IVISYNDPMGVS
+pdb_id=5ham, cha... QQQINEDILNRATKDIKDNGKEAAVIPIEMGYGHWTVLVAKYDKKDNQIILTFNDSLGNS
+
+target I----DDKVTLINCIKELCPGA-KINDLQTVQQTNVYDCGPFVVDNLIKMSQGQPILSTE
+pdb_id=5ham, cha... INYDGQKLPKLIDKTLGNLPNKPIIIDEQTKQQTDQSACGVFTVDNGIKIAKGQAILSTE
+
+target EAKQ-QAQNIRQSQVNFLSENRMITSAAAALADTLLKNNNRITEGVLVDRIFDNKILSVQ
+pdb_id=5ham, cha... ESKGEKGLRLREHHAQILTD-AMFKQDAQWIRQQ--------------------------
+
+target EKQQLLNNLLDNHIKENKSLTKESLTRMLASTHFVQQQANVLLN
+pdb_id=5ham, cha... --------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY62-()-A.MET63 by relaxing A.SER61-(G)-A.MET63
+Closed: A.ASP90-()-A.ILE91 by relaxing A.GLY86-(MNDD)-A.ILE91
+Closed: A.ILE103-()-A.ASP104 by relaxing A.ILE103-(DD)-A.LYS106
+Closed: A.ALA120-()-A.LYS121 by relaxing A.CYS117-(PGA)-A.LYS121
+Trying to merge 8 gap(s) with distance 0.
+Merged gap A.GLN54-()-A.VAL55 and A.VAL55-()-A.LEU56 into A.GLN54-(V)-A.LEU56
+Trying to fill 7 gap(s) by database.
+Resolved A.GLY29-(L)-A.ASP31 by filling A.GLY29-(LDD)-A.ARG33 (65 candidates, BB_DB)
+Failed at loop insertion (A.ILE36-()-A.ILE37), only 0 candidates
+Resolved A.GLU44-(S)-A.LEU46 by filling A.ALA41-(LNES)-A.LEU46 (115 candidates, BB_DB)
+Failed at loop insertion (A.GLN54-(V)-A.LEU56), only 0 candidates
+Resolved A.ILE59-()-A.PHE60 by filling A.ASP58-(IFSGMQ)-A.GLU65 (209 candidates, BB_DB)
+Resolved A.GLN161-()-A.GLN162 by filling A.LYS160-(QQA)-A.GLN164 (54 candidates, BB_DB)
+Resolved A.GLU176-(N)-A.ARG178 by filling A.SER175-(ENRM)-A.ILE180 (54 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ILE36-()-A.ILE37), only 0 candidates
+Failed at loop insertion (A.GLN54-(V)-A.LEU56), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ILE36-()-A.ILE37), only 0 candidates
+Failed at loop insertion (A.GLN54-(V)-A.LEU56), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ILE36-()-A.ILE37), only 0 candidates
+Failed at loop insertion (A.GLN54-(V)-A.LEU56), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Resolved A.ILE36-()-A.ILE37 by filling A.TYR27-(LGLDDRISI)-A.ILE37 (103 candidates, BB_DB)
+Resolved A.GLN54-(V)-A.LEU56 by filling A.LEU46-(LLKQTLHQV)-A.LEU56 (71 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.40749e+13)
+No more stereo-chemical problems -> final energy: 13603.5
+
+
+Build model with the following alignment:
+target QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYY
+pdb_id=6mxt, cha... QVQLQESGGGLVQPGGSLRLSCAASGFAFSSYELRWYRQAPGKQHELVAGITTG-GNTYY
+
+target ADSVKGRFTISRDKAKNTVYLQMNSLKYEDTAVYYCARTENVRSLLSDYATWPYDYWGQG
+pdb_id=6mxt, cha... ADSVKGRFTISRDNAKNTVYLQMSNLRPEDTAVYACNANWD---L-------LSDYWGQG
+
+target TQVTVSSKHHHHHH
+pdb_id=6mxt, cha... TQVTVSSH------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Merged gap A.ASN101-(VRS)-A.LEU105 and A.LEU105-(LSDYATW)-A.PRO113 into A.ASN101-(VRSLLSDYATW)-A.PRO113
+Trying to fill 2 gap(s) by database.
+Resolved A.SER54-(G)-A.GLY56 by filling A.ARG52-(WSG)-A.GLY56 (43 candidates, BB_DB)
+Resolved A.ASN101-(VRSLLSDYATW)-A.PRO113 by filling A.ASN101-(VRSLLSDYATWP)-A.TYR114 (1282 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.20156e+16)
+No more stereo-chemical problems -> final energy: 3353.83
+
+
+Build model with the following alignment:
+target GMPPPADIVKVAIEWPGAYPKLMEIDQKKPLSAIIKEVCDGWSLANHEYFALQHADSSNF
+pdb_id=6idx, cha... -----SDIVKVAIEWPGANAQLLEIDQKRPLASIIKEVCDGWSLPNPEYYTLRYADGPQL
+
+target YITEKNRNEIKNGTILRLTTSPAQNAQQLHERIQSSSMDAKLEALKDLASLSRD
+pdb_id=6idx, cha... YITEQTRSDIKNGTILQLAISPSRAARQLMERTQSSNMETRLDAMKELAKLSAD
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 19948.4)
+No more stereo-chemical problems -> final energy: 5761.6
+
+
+Build model with the following alignment:
+target SNAGFQQSHYFVALYRFKALEKDDLDFRPGEKITVIDDSNEESWRGKIGEKVGFFPPNFI
+pdb_id=6b25, cha... --------NTYVALYKFVPQENEDLEMRPGDIITLLEDSNEDWWKGKIQDRIGFFPANFV
+
+target IRVRAGERVHRVTRSFVGNREIGQITLKKDQIVVQKGDEAGGYVKVYTGRKVGLFPTDFL
+pdb_id=6b25, cha... QRLQQNEKIFRCVRTFIGCKEQGQITLKENQICVSSEEEQDGFIRVLSGKKKGLIPLDVL
+
+target EEI
+pdb_id=6b25, cha... ENI
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.14056e+17)
+No more stereo-chemical problems -> final energy: 1298.98
+
+
+Build model with the following alignment:
+target MADAPVIKNADVAYPSFKGSDDPMKTAANNTTYNPAVSYLQETFDNDVKNLAGIDTDHDF
+pdb_id=5mqr, cha... ------------------------------------------------------------
+
+target WIDKILTRTGAQPTGKGTNDKGAYSYEGSDGNNYLFTRGRAAYMYTHTPNQLGFVGDTAY
+pdb_id=5mqr, cha... ------------------------------------------------------------
+
+target WDQTSRSGFTVTVNADGSNQTLNEDASQRKQTPSYFTSLFQTGGKSLKIKEVKYITYNNV
+pdb_id=5mqr, cha... ------------------------------------------------------------
+
+target MVANLTVESTQDRDVTLTTASPFAAEGADGATELTGRVNVKNNLTTIYPRFSANNQDGSN
+pdb_id=5mqr, cha... ------------------------------------------------------------
+
+target WIVSGGKLTSTLSLKANEPQTVKIQLGLIANELPDSTKEYEARYTGDLKDAAASYKDSVT
+pdb_id=5mqr, cha... --------------------------------KYADFSHYAESFNG--ME-DENIVQAIP
+
+target TY--NKWWVDNAPYVDTPEDNIDKTVVYRWWLSRFNMLDANMPG--NTFQYPTSIEGVLG
+pdb_id=5mqr, cha... NAKASEWMEENIPLFECPQRNFEEMYYYRWWSLRKHIKETPVGYGMTEFLVQRSYS---D
+
+target YNNQIVLTSGMFMMDTKWFRNPEYSY---GTWLSAGDTAKKSKAGYYYYHDNPGDPANWN
+pdb_id=5mqr, cha... KYNLIACAIGHHIYESRWLRDPKYLDQIIHTWYR----------------GNDGGPMKKM
+
+target HSYTQYITRAGWDSYKVHGGPSTVAEELADQGAEDVQGLLASKSEPDNNDNQNNNDNSLI
+pdb_id=5mqr, cha... DKFSSWNADAVLARYMVDGDKDFMLDMTKD-----LETEYQRWE------RTNRLKNGLY
+
+target DWSWWSMTGNDADAVSFSEPGRSGQRMDRADGSANMWANANAAAQAYKAAGDTANAEKMQ
+pdb_id=5mqr, cha... ---W---QGDVQDGMEESISGGRNKKYARPTINSYMYGNAKALSIMGILSGDEGMAMRYG
+
+target AIADKIQKEVTTELWDKSDNLLKHKWLNDGAFAKYKEINNYYPYSEGLMPTGNEDYNKAL
+pdb_id=5mqr, cha... MRADTLKSLVENDLWNTRHQFFETM--RTDSSANVREAIGYIPWYFNLPD-TTKKYEVAW
+
+target RLFEDSNEFP-IFPFFTANQADKAALNF-PG-------SNNFSIINAQPLLQVYSAGIRN
+pdb_id=5mqr, cha... KEIMDEKGFSAPYGLTTAERRHPEFRTRGVGKCEWDGAIWPFA---SAQTLTAMANFMNN
+
+target YDAAKNGYITNEQFKKLLYWVAFAHYQGGDNNYP-DQNEFWNEDNNNVGDVNGDGVINNL
+pdb_id=5mqr, cha... Y---PQTVLSDSVYFRQMELYVESQYHRGRPYIGEYLDEVTGYWL---------------
+
+target DKNLDAAQNGGKITYRSWIHHTQLGTTNWTMVEDVAGMVPREDNKIELNPIEIP-GWNYF
+pdb_id=5mqr, cha... -----K---GDQER-SRYYNHSTF---NDLMITGLIGLRPRLDDTIEINPLIPADKWDWF
+
+target TVNNLRYHDQDVSIVWDKDGSHYGGPAGYSLYVGGKLAFTSDKLAHLIYDPAAGTVEVKD
+pdb_id=5mqr, cha... CLDNVLYHGHNLTILWDKNGDRYHCGKGLRIFVNGKEAGHADTLTRLVCEN---------
+
+target DSSAQVTVGAEAVKNVKAANQVTFNADQRVTDLFAKSGTNVLEHHHHHH
+pdb_id=5mqr, cha... -------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 24).
+Initialized default backbone scoring for modelling.
+Closed: A.PRO603-()-A.ILE604 by relaxing A.PHE602-(PIF)-A.PRO606
+Closed: A.PHE620-()-A.PRO621 by relaxing A.LEU618-(NF)-A.PRO621
+Closed: A.PRO678-()-A.ASP679 by relaxing A.PRO678-(DQN)-A.GLU682
+Closed: A.PRO757-()-A.GLY758 by relaxing A.ILE756-(P)-A.GLY758
+Trying to merge 20 gap(s) with distance 0.
+Merged gap A.ILE473-(DWS)-A.TRP477 and A.TRP477-(WSM)-A.THR481 into A.ILE473-(DWSWWSM)-A.THR481
+Merged gap A.ASN688-(NNVGDVNGDGVINNLDKNLD)-A.ALA709 and A.ALA709-(AQN)-A.GLY713 into A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713
+Trying to fill 18 gap(s) by database.
+Resolved A.GLY286-(DL)-A.LYS289 by filling A.ARG283-(YTGDL)-A.LYS289 (54 candidates, BB_DB)
+Resolved A.ASP290-(A)-A.ALA292 by filling A.LYS289-(DAAA)-A.SER294 (87 candidates, BB_DB)
+Resolved A.TYR302-()-A.ASN303 by filling A.VAL299-(TTY)-A.ASN303 (126 candidates, BB_DB)
+Resolved A.GLY342-()-A.ASN343 by filling A.ASP337-(ANMPG)-A.ASN343 (86 candidates, BB_DB)
+Resolved A.GLU352-(GVL)-A.GLY356 by filling A.SER350-(IEGVL)-A.GLY356 (111 candidates, BB_DB)
+Resolved A.TYR382-()-A.GLY383 by filling A.SER381-(YGTW)-A.LEU386 (59 candidates, BB_DB)
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Resolved A.ASP443-(QGAED)-A.VAL449 by filling A.ASP443-(QGAEDVQG)-A.LEU452 (66 candidates, BB_DB)
+Resolved A.SER457-(EPDNND)-A.ASN464 by filling A.LYS456-(SEPDNNDNQ)-A.ASN466 (53 candidates, BB_DB)
+Resolved A.ILE473-(DWSWWSM)-A.THR481 by filling A.ASP469-(NSLIDWSWWSM)-A.THR481 (126 candidates, BB_DB)
+Resolved A.LYS558-(WL)-A.ASN561 by filling A.LYS558-(WLNDG)-A.ALA564 (46 candidates, BB_DB)
+Resolved A.PRO583-(T)-A.GLY585 by filling A.PRO583-(TGN)-A.GLU587 (42 candidates, BB_DB)
+Resolved A.GLY622-()-A.SER623 by filling A.ALA617-(LNFPG)-A.SER623 (115 candidates, BB_DB)
+Resolved A.SER627-(IIN)-A.ALA631 by filling A.ASN624-(NFSIIN)-A.ALA631 (54 candidates, BB_DB)
+Resolved A.TYR645-(DAA)-A.LYS649 by filling A.ASN644-(YDAAK)-A.ASN650 (77 candidates, BB_DB)
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Resolved A.THR717-(Y)-A.ARG719 by filling A.ILE716-(TYR)-A.SER720 (47 candidates, BB_DB)
+Resolved A.LEU727-(GTT)-A.ASN731 by filling A.GLN726-(LGTTN)-A.TRP732 (46 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404), only 0 candidates
+Failed at loop insertion (A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.SER387-(AGDTAKKSKAGYYYYH)-A.ASP404 by filling A.SER387-(AGDTAKKSKAGYYYYHD)-A.ASN405 (6 candidates, BB)
+Resolved A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQN)-A.GLY713 by filling A.ASN688-(NNVGDVNGDGVINNLDKNLDAAQNG)-A.GLY714 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.41096e+25)
+Perform energy minimization (iteration 2, energy: 48628.9)
+No more stereo-chemical problems -> final energy: 36045
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMAGQGESGNPPATDKERFIASLMARMSNAEKIGQLRLVSV
+pdb_id=5tf0, cha... ----------------------------------MDRFIDALMKKMTVEEKIGQLNLPVS
+
+target G----ADHPKEALMADIRAGKVGAIFNTVTRPDIRAMQDQV-RHSRLKIPLFHAYDVAHG
+pdb_id=5tf0, cha... G---------SDVAKKIEQGLVGGLLNLKGVEKIRDVQKLAIEKSRLGIPLIFGMDVVHG
+
+target HRTIFPISLGLAASWDPEVVARSARISALEASADGLDMSFSPMVDITRDARWGRVSEGFG
+pdb_id=5tf0, cha... YETIFPIPLGLSCSWDMEAIRKSARVAAIEASADGISWTFSPMVDISRDPRWGRVSEGNG
+
+target EDTYLTSLLSGVMVRAYQG---SNL-AAPDSIMAAVKHFALYGAAEGGRDYNTVDMSLPR
+pdb_id=5tf0, cha... EDPFLGGAIAKAMVSGYQGIDLNNQLKRNDEIMACVKHFALYGAGEAGRDYNTVDMSRNR
+
+target MFQDYLPPYKAAVDAGAGAVMVSLNTINGVPATANRWLLTDLLRQQWGFKGLTISNHGAV
+pdb_id=5tf0, cha... MFNEYMYPYQAAVDAGVGSVMASFNEIDGIPATANKWLMTDVLRKQWGFDGFVVTDFTGI
+
+target KELIKHGLAGNERDATRLAIQAGVDMNMNDDLYSTWLPKLLAAGEIDQADIDRACRDVLA
+pdb_id=5tf0, cha... SEMIAHGIG-DLQTVSARALNAGVDMDMVSEGFTGTIKKSIDEGKISMETLDKACRRILE
+
+target AKYDLGLFADPYRRLGKPDDPPFDTNAESRLHRQAAREVAREGLVLLKNRD------GLL
+pdb_id=5tf0, cha... AKYKLGLFDNPYKYC---DLKRPKRDIFTKEHRDAARKIAGESFVLLKNDKS--SANPTL
+
+target PLKKQGRIAVIGPLAKSQRDVIGSWSAAGVPRQAVTVYQGLANAVGERATLLYAKGANVS
+pdb_id=5tf0, cha... PLKKEGTVAVIGPLANTRSNMPGTWSVAARLNDYPSVYEGLKEMMKGKVNITYAKGSNLI
+
+target GDQAILDYLNSYNPEVEVDPRSAEAMLEEALRTARDADLVVAVVGESQGMAHEASSRTDL
+pdb_id=5tf0, cha... SDAAYEERATMFGRSLNRDNRTDKEMLDEALKVAANADVIIAALGESSEMSGESSSRTNL
+
+target RIPASQRRLLKALKATGKPLVLVLMNGRPLSLGWEQENADAILETWFSGTEGGNAIADVL
+pdb_id=5tf0, cha... ALPDVQRTLLEALLKTGKPVVLTLFTGRPLTLTWEQEHVPAILNVWFGGSEAAYAIGDVL
+
+target FGEHNPSGKLTMSFPRSVGQVPVYYNHLNTGRPMDHD-NPGKYTSRYFDEANGPLYPFGY
+pdb_id=5tf0, cha... FGDVNPSGKLTMTFPKNVGQIPLFYNHKNTGRPLLEGKWFEKFRSNYLDVDNDPLYPFGY
+
+target GLSYTEFSLSPLRLSSERLARGATLEARVTLSNSGKRAGATVVQLYLQDPVASLSRPVKE
+pdb_id=5tf0, cha... GLSYTNFQYSDITLSAPTMGQDGSVTAMVTVTNTGKYDGAEVVQLYIRDLVGSITRPVKE
+
+target LRGFRKVMLEPGESREIVFRLGEADLKFYDSQLRHTAEPGEFKVFVGLDSAQTESRSFTL
+pdb_id=5tf0, cha... LKGFDKIFLKAGESKTVSFKITPELLRFYDYELNYVAEPGDFDIMIGGNSQSVKTTHLSL
+
+target L
+pdb_id=5tf0, cha... -
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 8).
+Initialized default backbone scoring for modelling.
+Closed: A.VAL97-()-A.ARG98 by relaxing A.GLN96-(VR)-A.HIS99
+Closed: A.LEU197-()-A.ALA198 by relaxing A.ASN196-(LA)-A.ALA199
+Closed: A.ASP622-()-A.ASN623 by relaxing A.HIS621-(DNP)-A.GLY625
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.GLY61-(ADHPK)-A.GLU67 by filling A.SER59-(VGADHPK)-A.GLU67 (130 candidates, BB_DB)
+Resolved A.GLY194-()-A.SER195 by filling A.GLN193-(GSNLA)-A.ALA199 (40 candidates, BB_DB)
+Resolved A.ALA300-(G)-A.ASN302 by filling A.GLY298-(LAG)-A.ASN302 (90 candidates, BB_DB)
+Resolved A.LEU366-(GKP)-A.ASP370 by filling A.ARG365-(LGKPDD)-A.PRO372 (44 candidates, BB_DB)
+Resolved A.ASP402-()-A.GLY403 by filling A.ASN400-(RDG)-A.LEU404 (74 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.7099e+26)
+No more stereo-chemical problems -> final energy: 3422.74
+
+
+Build model with the following alignment:
+target TMTSVGVRALRQQASELLRRVEAGETIEITDRGRPVALLSPLPQ
+pdb_id=4zlx, cha... -MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKAT
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.1544e+14)
+No more stereo-chemical problems -> final energy: -2271.52
+
+
+Build model with the following alignment:
+target GSHMQALSTRTAKNTLPRAFAMPQPQVPARQPIALISVHGDPAADVGHESAGGQNIYVRQ
+pdb_id=6n1x, cha... ------------------------------MKIGITC---YPS-------MGGSGIIATE
+
+target LGEALAAAGWHVDMFTRKTDPNDPDVIEHSPHCRTIRLQAGPLTYIPREKLFETLPKFVE
+pdb_id=6n1x, cha... LGIKLAERGHEVHFITSNIPFRI---RKPLPNMIFHQVEVNQYAVFQY---PPYDITLST
+
+target AFKAYHAKYGYPLIHTNYWL-SGWVGWQLRQQ--FNFQWLHTYHSLGVVKYQVASEQAQR
+pdb_id=6n1x, cha... KIAEVIKEYDLDLLHMHYAVPHAICGILAREMSGKDIKIMTTLHGTDITVLG---Y---D
+
+target DETRLMVEKAILENADCVIVTSPQEEAYLRR-WVSKAGQTRLIPCGTNLKLFYPVA--DA
+pdb_id=6n1x, cha... H-SLQGAIKFGIEKSDIVTSVSKSLAQETHEIIET-NKEIIPIYNFVRENEFPTKHNTAL
+
+target RAQLNLPADEPIVLYVGRFDRRKGIETLVAAMAQIP---QGQLLLVGGSDPQRSDGAERR
+pdb_id=6n1x, cha... KSQFGIAPDEKVLIHVSNFRQVKRIDTIIETFAKVREKIPSKLILLGD-------GPELV
+
+target RIEGLVQEYNLGDRVTFVGQIDHEYLAVYYSAANVCVVPSYYEPFGLVAIEAMACGTPVI
+pdb_id=6n1x, cha... PMRQLTKELNVEEDVLFLGK--QDCVSEFYQLSDLVLLLSEKESFGLTLLEAMKTGVVPI
+
+target ASAVGGLQFTVIPEETGLLVPPQDANALANAIQRILADPAWARTLGKNGRERVQALFNWE
+pdb_id=6n1x, cha... GSNAGGIKEVIKHGETGFVVDVGDCDSASDYAIRLLEDKVLYNKLQKNMLADIAERFGSE
+
+target AIALQMGQLYRQLFAASLMGNSPRLEMVKNTASLAAVTKAALAS
+pdb_id=6n1x, cha... LITDQYEYYYQKMLN-----------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Closed: A.LEU140-()-A.SER141 by relaxing A.LEU140-(S)-A.GLY142
+Trying to merge 14 gap(s) with distance 0.
+Merged gap A.GLN169-(VAS)-A.GLU173 and A.GLU173-(QAQ)-A.ARG177 into A.GLN169-(VASEQAQ)-A.ARG177
+Trying to fill 13 gap(s) by database.
+Resolved A.SER37-(VHG)-A.ASP41 by filling A.LEU35-(ISVHGD)-A.PRO42 (43 candidates, BB_DB)
+Resolved A.ALA43-(ADVGHES)-A.ALA51 by filling A.GLY40-(DPAADVGHESA)-A.GLY52 (57 candidates, BB_DB)
+Resolved A.ASP83-(PDV)-A.ILE87 by filling A.PRO81-(NDPDV)-A.ILE87 (54 candidates, BB_DB)
+Resolved A.ARG108-(EKL)-A.PHE112 by filling A.TYR105-(IPREKL)-A.PHE112 (47 candidates, BB_DB)
+Resolved A.GLN151-()-A.PHE152 by filling A.LEU148-(RQQ)-A.PHE152 (66 candidates, BB_DB)
+Resolved A.GLN169-(VASEQAQ)-A.ARG177 by filling A.GLN169-(VASEQAQR)-A.ASP178 (58 candidates, BB_DB)
+Resolved A.ASP178-(E)-A.THR180 by filling A.ALA175-(QRDE)-A.THR180 (59 candidates, BB_DB)
+Resolved A.ARG208-()-A.TRP209 by filling A.ARG207-(RWV)-A.SER211 (82 candidates, BB_DB)
+Resolved A.SER211-(K)-A.ALA213 by filling A.SER211-(KAG)-A.GLN215 (41 candidates, BB_DB)
+Resolved A.ALA232-()-A.ASP233 by filling A.VAL231-(ADAR)-A.ALA236 (65 candidates, BB_DB)
+Resolved A.PRO270-()-A.GLN271 by filling A.ILE269-(PQGQ)-A.LEU274 (40 candidates, BB_DB)
+Resolved A.GLY279-(SDPQRSD)-A.GLY287 by filling A.GLY278-(GSDPQRSDG)-A.ALA288 (44 candidates, BB_DB)
+Resolved A.GLN311-(ID)-A.HIS314 by filling A.GLY310-(QIDHE)-A.TYR316 (156 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.69782e+16)
+Perform energy minimization (iteration 2, energy: 17205.7)
+Perform energy minimization (iteration 3, energy: 11942.8)
+No more stereo-chemical problems -> final energy: 10334.3
+
+
+Build model with the following alignment:
+target MTTADLILINNWHVVANVEDCKPG-----SITTARLLGVKLVLWRSQEQNSPIQVWQDYC
+pdb_id=6icp, cha... ---EREYLRHFWHPVCTVTELEKAHPSSLGPLAVKLLNEQLVVAKL---GDEYVAMRDRC
+
+target PHRGVPLSMGEVANNTLVCPYHGWRYNQAGKCVQIPAHPDMVPPASAQAKTYHCQERYGL
+pdb_id=6icp, cha... AHRSAKLSLGTVSGNRLQCPYHGWQYDTHGACQLVPACPNSPIPNKAKVDRFDCEERYGL
+
+target VWVCLGNPV--NDIPSFPEWDDPNYHKTYTKSYLIQASPFRVMDNSIDVSHFPFIHDGWL
+pdb_id=6icp, cha... IWIRLDSSFDCTEIPYFSAANDPRLRIVIQEPYWWDATAERRWENFTDFSHFAFIHPGTL
+
+target GDRNYTKVEDF---EVKV-DKDGLTMGKYQFQTSRIVSHIEDDSWVNWFRLSHPLCQYC-
+pdb_id=6icp, cha... FDPNNAEPPIVPMDRFNGQFRFVYDTP---------------PIGSFSYTCSMPFAINLE
+
+target VSE-SPEMRIVDLMTIAPIDEDNSVLRMLIMWNGSEMLESKMLTEYDETIEQDIRILHSQ
+pdb_id=6icp, cha... VSKYSSSSLHVLFNVSCPVDSHTTKNFLIFAREQSDDSDYLHIAFQDLVLAEDKPVIESQ
+
+target QPARLPLLAPKQINTQGLPQEIHVPSDRGTVAYRRWLKELGVTYGVC
+pdb_id=6icp, cha... WPKDAPA---------D---EVSVVADKVSIQYRKWLRELKE-----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Trying to merge 10 gap(s) with distance 0.
+Merged gap A.LEU294-(LAPKQINTQ)-A.GLY304 and A.GLY304-(LPQ)-A.GLU308 into A.LEU294-(LAPKQINTQGLPQ)-A.GLU308
+Trying to fill 9 gap(s) by database.
+Resolved A.GLY24-()-A.SER25 by filling A.PRO23-(GSIT)-A.THR28 (134 candidates, BB_DB)
+Resolved A.SER41-(QEQ)-A.ASN45 by filling A.SER41-(QEQNS)-A.PRO47 (89 candidates, BB_DB)
+Resolved A.VAL124-()-A.ASN125 by filling A.GLY121-(NPVN)-A.ASP126 (81 candidates, BB_DB)
+Resolved A.PHE184-()-A.GLU185 by filling A.PHE184-(EVKVD)-A.LYS190 (82 candidates, BB_DB)
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Resolved A.CYS228-()-A.VAL229 by filling A.CYS228-(VSESPE)-A.MET235 (308 candidates, BB_DB)
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212), only 0 candidates
+Failed at loop insertion (A.LEU294-(LAPKQINTQGLPQ)-A.GLU308), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.GLY196-(KYQFQTSRIVSHIED)-A.ASP212 by filling A.GLY196-(KYQFQTSRIVSHIEDD)-A.SER213 (6 candidates, BB)
+Resolved A.LEU294-(LAPKQINTQGLPQ)-A.GLU308 by filling A.LEU294-(LAPKQINTQGLPQE)-A.ILE309 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.67984e+13)
+Perform energy minimization (iteration 2, energy: 18996.3)
+Perform energy minimization (iteration 3, energy: 15782.1)
+Perform energy minimization (iteration 4, energy: 14495.5)
+Perform energy minimization (iteration 5, energy: 13767.4)
+No more stereo-chemical problems -> final energy: 13240.1
+
+
+Build model with the following alignment:
+target MGSHHHHHHASEQYPTAIVADREVPFDPEQLRRIREHPCFSEKACHAFGRMHLPVAPKCN
+pdb_id=6fz6, cha... -------------------------------------------------TVCVSCQVGCA
+
+target IQCKYCIRDFDCVNESRPGVTSRVLTPQEALERVDEVLSKYH----YIKVVAVAGPGEPL
+pdb_id=6fz6, cha... VGCSFCATGMM-------GL-TRNLTAGEMVAQVVAAARRAREAGRTLTNIVMMGMGEPF
+
+target AN-EETFETLRLVGEKYPHL-----ILCISTNGLLLPDRIEDLDRIGVT-NITVTLNAVD
+pdb_id=6fz6, cha... QNYEATMRMVRILHEEE-GMNFGARRITVSTSGLV--PFIDRLAREPFQVKLAVSLHAPN
+
+target PTIGEQIYDYVIYKGERYEGLEAAKILLDNQLKGIEEA-VRRKKIVKVNTVLIPGIND--
+pdb_id=6fz6, cha... DDLRSSLVPL----NRRY--------PIGELIAACRRYVGETGRRVTFEYVLIDGVNDSD
+
+target KHVFDIARKIKSMGVFIHNVMPLIPQYKFAHIKPPTPEEKRAIQDELSKIIKQMRHCRQC
+pdb_id=6fz6, cha... ANAEELARLLRGLLC-HVNLIPLNPTPAA-PFGRPSVERINRFEQILRAR----------
+
+target RSDAIGRLGCDIQQELEKGKKKS
+pdb_id=6fz6, cha... -----------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 14).
+Initialized default backbone scoring for modelling.
+Closed: A.HIS102-()-A.TYR103 by relaxing A.HIS102-(YI)-A.LYS105
+Closed: A.ASN118-()-A.GLU119 by relaxing A.ALA117-(NE)-A.GLU120
+Closed: A.ALA207-()-A.VAL208 by relaxing A.GLU206-(AV)-A.ARG209
+Closed: A.ASP226-()-A.LYS227 by relaxing A.ASP226-(KH)-A.VAL229
+Trying to merge 10 gap(s) with distance 0.
+Trying to fill 10 gap(s) by database.
+Resolved A.ASP71-(CVNESRP)-A.GLY79 by filling A.ASP69-(FDCVNESRPG)-A.VAL80 (83 candidates, BB_DB)
+Resolved A.VAL80-(T)-A.SER82 by filling A.SER76-(RPGVT)-A.SER82 (44 candidates, BB_DB)
+Resolved A.TYR132-(P)-A.HIS134 by filling A.GLY129-(EKYPHL)-A.ILE136 (40 candidates, BB_DB)
+Resolved A.LEU145-(LP)-A.ASP148 by filling A.ASN142-(GLLLP)-A.ASP148 (45 candidates, BB_DB)
+Resolved A.THR159-()-A.ASN160 by filling A.ARG155-(IGVT)-A.ASN160 (93 candidates, BB_DB)
+Resolved A.TYR179-(VIYK)-A.GLY184 by filling A.ASP178-(YVIYKGER)-A.TYR187 (46 candidates, BB_DB)
+Resolved A.TYR187-(EGLEAAKI)-A.LEU196 by filling A.LYS183-(GERYEGLEAAKI)-A.LEU196 (145 candidates, BB_DB)
+Resolved A.VAL241-(F)-A.ILE243 by filling A.SER238-(MGVF)-A.ILE243 (50 candidates, BB_DB)
+Resolved A.PHE255-(A)-A.HIS257 by filling A.TYR253-(KFAH)-A.ILE258 (71 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.07141e+14)
+Perform energy minimization (iteration 2, energy: 14672.6)
+No more stereo-chemical problems -> final energy: 9638.79
+
+
+Build model with the following alignment:
+target MALDRPDRSGAVRVSAPARLSFTLISLDGSSLR-----RNGIAAMAVDRPGLTAEVREAA
+pdb_id=5v2l, cha... ----------MLSGKARAHTNIALIKYWGKANEEYILPMNSSLSLTLDAFYTETTVTFDA
+
+target ----DGIVAVTGTA-----EETARELAAALEALRKLWDG-PAARVDVLEALPQHSGFGSK
+pdb_id=5v2l, cha... HYSEDV-FILNGILQNEKQTKKVKEFLNLVRQQ---ADCTWFAKVESQNFVPTAAGLASS
+
+target TSTLLAVGHAYGRLCGVEPDLRELARTLGRGRTSGASTGLSAYGGFLVD-GGHVNPPDFA
+pdb_id=5v2l, cha... ASGLAALAGACNVALGLNLSAKDLSRLARRG--SGS-ACRSIFGGFAQWNKGHSDET---
+
+target EAPQKYLRPSRFAQQVAPPKPVVRLDFP-DWPVLVL-LTHGR-HLGGQEELEWFHSVAPI
+pdb_id=5v2l, cha... SFA------------ENIPA----NNWENELAMLFILIN------SSRDGMKRTVETSSF
+
+target PAEESWRTSHLVFMGLAPAVLEQDFDAFCAAVNEIT--FTG-HFKQAQI-AFQGD---AV
+pdb_id=5v2l, cha... YQGWLDN-VEKDLSQVHEAIKTKDFPRLGEIIEANGLRMHGTTLGAVPPFTYWSPGSLQA
+
+target ADVLEAGRAAPSVDAIALSVTGPACFAFTKRPEDAERWAWELKNRGLIRDFWFTRANNQG
+pdb_id=5v2l, cha... MALVRQARAKG-IPCYFTMDAGPNVKVLVEKK-NLEALKTFLSEHFSKEQLVPAFA-GPG
+
+target LATTVVS
+pdb_id=5v2l, cha... IELF---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 23).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY85-()-A.PRO86 by relaxing A.GLY85-(PAA)-A.ARG89
+Closed: A.ASP154-()-A.GLY155 by relaxing A.ASP154-(GGH)-A.VAL158
+Closed: A.PRO192-()-A.ASP193 by relaxing A.ASP190-(FPD)-A.TRP194
+Closed: A.GLY260-()-A.HIS261 by relaxing A.THR259-(GH)-A.PHE262
+Trying to merge 19 gap(s) with distance 0.
+Trying to fill 19 gap(s) by database.
+Resolved A.ARG33-()-A.ARG34 by filling A.SER30-(SLRRN)-A.GLY36 (111 candidates, BB_DB)
+Failed at loop insertion (A.ALA55-()-A.ASP56), only 1 candidates
+Resolved A.GLY57-(I)-A.VAL59 by filling A.GLU53-(AADGI)-A.VAL59 (54 candidates, BB_DB)
+Resolved A.ALA65-()-A.GLU66 by filling A.VAL61-(TGTAE)-A.GLU67 (117 candidates, BB_DB)
+Resolved A.LEU79-(RKL)-A.TRP83 by filling A.LEU79-(RKLWDG)-A.PRO86 (69 candidates, BB_DB)
+Resolved A.GLY136-(RT)-A.SER139 by filling A.GLY134-(RGRTSG)-A.ALA141 (46 candidates, BB_DB)
+Resolved A.ALA141-(S)-A.THR143 by filling A.THR138-(SGAS)-A.THR143 (77 candidates, BB_DB)
+Resolved A.PRO161-(DFA)-A.GLU165 by filling A.HIS157-(VNPPDFAE)-A.ALA166 (141 candidates, BB_DB)
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Resolved A.LYS184-(PVVR)-A.LEU189 by filling A.ALA181-(PPKPVVR)-A.LEU189 (82 candidates, BB_DB)
+Failed at loop insertion (A.LEU199-()-A.LEU200), only 0 candidates
+Resolved A.THR201-(HGRHL)-A.GLY207 by filling A.THR201-(HGRHL)-A.GLY207 (165 candidates, BB_DB)
+Resolved A.ARG228-(T)-A.SER230 by filling A.SER226-(WRTS)-A.HIS231 (83 candidates, BB_DB)
+Resolved A.THR257-()-A.PHE258 by filling A.ILE256-(TF)-A.THR259 (42 candidates, BB_DB)
+Resolved A.ILE267-()-A.ALA268 by filling A.LYS263-(QAQI)-A.ALA268 (89 candidates, BB_DB)
+Resolved A.ASP272-()-A.ALA273 by filling A.ILE267-(AFQGD)-A.ALA273 (389 candidates, BB_DB)
+Resolved A.PRO285-(S)-A.VAL287 by filling A.ALA283-(APSV)-A.ASP288 (75 candidates, BB_DB)
+Resolved A.PRO306-(E)-A.ASP308 by filling A.THR303-(KRPE)-A.ASP308 (51 candidates, BB_DB)
+Resolved A.ALA330-(N)-A.ASN332 by filling A.THR328-(RAN)-A.ASN332 (51 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Resolved A.LEU199-()-A.LEU200 by filling A.LEU199-(LTHGRH)-A.LEU206 (68 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO167-(QKYLRPSRFAQQ)-A.VAL180), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.PRO167-(QKYLRPSRFAQQ)-A.VAL180 by filling A.PRO167-(QKYLRPSRFAQQV)-A.ALA181 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.36795e+20)
+No more stereo-chemical problems -> final energy: 15816.2
+
+
+Build model with the following alignment:
+target MARGFQGVMLRGLGARDHQATVVDKEYIAPHFVRVRLVSPTLFDEVIVEPTSWLRFWFPD
+pdb_id=5u1d, cha... ------------------------------------------------------------
+
+target PDGSDTEFQRAYTITESDPETGRFAVDMVLHEPAGPASTWARTVEPGATIAVMSMGSRGF
+pdb_id=5u1d, cha... ------------------------------------------------------------
+
+target SVPEDPEDRPVGYLLIGDSASTPAINGIIEVVPHDIPIELYLEQHHDDDVLIPLAEHPRL
+pdb_id=5u1d, cha... ------------------------------------------------------------
+
+target RVHRVSRDDASSLAAALELRDWSNWYCWAGPEAGALKQVRTRLRDEFGFPKREVYAQAYW
+pdb_id=5u1d, cha... ------------------------------------------------------------
+
+target TEGRAMGSSRGETSTPAKPAAKTAPAKAAAKPAAASGAGTPEHAAAPAAATTGAPQAAPA
+pdb_id=5u1d, cha... ------------------------------------------------------------
+
+target PGAAQPRTPVRGRWRAEAGSRLLAPLKKPLIVSGVLQALITLIELAPFVLLVELARLLLG
+pdb_id=5u1d, cha... ---------------VRRLLGCLGSETRRLSLFLVLVVLSSLGEMAIPFFTGRLTDWILQ
+
+target GAEAERLWTLGLTAVSLIGLGAVLAAAMTLWLHRVDARFAHELRGRLLTKLSRLPLGWFT
+pdb_id=5u1d, cha... DGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQGEVFGAVLRQETEFFQ
+
+target RRGSASTKQLVQDDTLALHYLITHAIPDAVAAVVAPVAVLVYLFVADWRVALVLFIPVLV
+pdb_id=5u1d, cha... QNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIMLW--VSLTMVTLITLPL
+
+target YLVLMSVMTIQSGSKIAQAPRWAERMGGEAGAFLEGQPVIRIFGG--AAASRFRRRLDDY
+pdb_id=5u1d, cha... LFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFANEEGEAQKFREKLQEI
+
+target IDFLVSWQRPFVGKKTLMDLVTRPATFLWIILVAGVPLVVTGRMDPVNLLPFLLLGTTFG
+pdb_id=5u1d, cha... KTLNQKEAVAYAVNSWTTSISGM--LLKVGILYIGGQLVTSGAVSSGNLVTFVLYQMQFT
+
+target ARLLGIGYGLSGIQTGMLAARRIQTVLDEPELVVRDRTGQAGTDHASGDQARPGTVELDR
+pdb_id=5u1d, cha... QAVEVLLSIYPRVQKAVGSSEKIFEYLDR-------GL-------L-TPLHLEGLVQFQD
+
+target VSFEYRP--GVPVIRDVTLTLRPGTVTALVGPSGSGKSTLAALVARFHDVTQGAIRVDGR
+pdb_id=5u1d, cha... VSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGK
+
+target DIRTLTADELYRRVGFVLQDAQLVHGSVAENIALAEP-DAGLERIRTAARDAQIHDRITR
+pdb_id=5u1d, cha... PLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISG
+
+target MPDGYDSVLGAGSA-LSGGERQRVTIARAILADTPVLVLDEATAFADPESEYLVQQAINR
+pdb_id=5u1d, cha... LPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYE
+
+target LT--RDRTVLVIAHRLHTITHADQIVVLDDGRIVEVGTHDELLAAGGRYRGLWDSGRYSS
+pdb_id=5u1d, cha... SPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMVQA-----
+
+target PDAGRPVSADAVEVGR
+pdb_id=5u1d, cha... ----------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY525-()-A.ALA526 by relaxing A.GLY525-(A)-A.ALA527
+Closed: A.PRO665-()-A.GLY666 by relaxing A.PRO665-(GV)-A.PRO668
+Closed: A.PRO753-()-A.ASP754 by relaxing A.GLU752-(PD)-A.ALA755
+Closed: A.ALA789-()-A.LEU790 by relaxing A.SER788-(AL)-A.SER791
+Trying to merge 6 gap(s) with distance 0.
+Merged gap A.THR636-(GQAGTDH)-A.ALA644 and A.ALA644-(S)-A.GLY646 into A.THR636-(GQAGTDHAS)-A.GLY646
+Trying to fill 5 gap(s) by database.
+Resolved A.VAL465-(AD)-A.TRP468 by filling A.PHE464-(VADW)-A.ARG469 (122 candidates, BB_DB)
+Resolved A.ARG561-(PA)-A.THR564 by filling A.VAL559-(TRPAT)-A.PHE565 (43 candidates, BB_DB)
+Resolved A.GLU627-(PELVVRD)-A.ARG635 by filling A.GLU627-(PELVVRD)-A.ARG635 (865 candidates, BB_DB)
+Resolved A.THR636-(GQAGTDHAS)-A.GLY646 by filling A.ASP634-(RTGQAGTDHAS)-A.GLY646 (173 candidates, BB_DB)
+Resolved A.THR836-()-A.ARG837 by filling A.THR836-(RDR)-A.THR840 (164 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.04877e+18)
+Perform energy minimization (iteration 2, energy: 3584.38)
+No more stereo-chemical problems -> final energy: -1362.95
+
+
+Build model with the following alignment:
+target SFSNFPISEETIKLLKGRGVTFLFPIQAKTFHHVYSGKDLIAQARTGTGKTFSFAIPLIE
+pdb_id=6em3, cha... ------------------------------------------------------------
+
+target KLHGELQDRKRGRAPQVLVLAPTRELANQVSKDFSDITK--KLSVACFYGGTPYGGQFER
+pdb_id=6em3, cha... ------------------------------------------------------------
+
+target MRNGIDILVGTPGRIKDHIQNGK-LDLTKLKHVVLDEVDQMLDMGFADQVEEILSVAYKK
+pdb_id=6em3, cha... ------------------------------------------------------------
+
+target DSEDNPQTLLFSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAIKCHWTQR
+pdb_id=6em3, cha... --------------------------------------------------GYVVCDSDKR
+
+target AAVIGDVIRVYSGHQGRTIIFCETKKEAQELSQN-SAIKQDAQSLHGDIPQKQREITLKG
+pdb_id=6em3, cha... FLLLFSFLKRN--QKKKIIVFLSSCNSVKYYAELLNYIDLPVLELHGKQKQQKRTNTFFE
+
+target FRNGSFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESYIHRSGRTGR-AGRTGVCICFY
+pdb_id=6em3, cha... FCNAERGILICTDVAARGLDIPAVDWIIQFDPPDDPRDYIHRVGR--------GKSLMFL
+
+target QHKEEYQLVQVEQKAGIKFKRI
+pdb_id=6em3, cha... TPN--------------P----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.ASN271-()-A.SER272 by relaxing A.GLN270-(NS)-A.ALA273
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.TYR248-(SG)-A.HIS251 by filling A.VAL247-(YSGH)-A.GLN252 (42 candidates, BB_DB)
+Resolved A.ARG341-(TGRAGRT)-A.GLY349 by filling A.ARG341-(TGRAGRTG)-A.VAL350 (44 candidates, BB_DB)
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373 by filling A.LYS358-(EEYQLVQVEQKAGI)-A.LYS373 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 37144.5)
+No more stereo-chemical problems -> final energy: 4718.34
+
+
+Build model with the following alignment:
+target GDEEEKHLRDMMEIVIKLFMTGDWDAFHEMADPDVKFQVDVGDKHIHRHGREEVVEELIR
+pdb_id=1ohs, cha... ----PEHMTAVVQRFVAALNAGDLDGIVALFADDATVENPVGS--EPRSGTAAIREFYAN
+
+target LLEHWRVRNIRIHDIKLIGDKLVVEGRWETSYGDKSHDEDVELIVIVV-DGKIKKVRIII
+pdb_id=1ohs, cha... SLKLPLAVELTQEVR-AVANEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRAL-
+
+target R
+pdb_id=1ohs, cha... -
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.VAL108-()-A.ASP109 by relaxing A.VAL108-(D)-A.GLY110
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.ASP43-(KH)-A.ILE46 by filling A.ASP40-(VGDKH)-A.ILE46 (48 candidates, BB_DB)
+Resolved A.ILE75-(K)-A.LEU77 by filling A.ILE72-(HDIK)-A.LEU77 (48 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.21481e+07)
+No more stereo-chemical problems -> final energy: 1856.75
+
+
+Build model with the following alignment:
+target DNVEEGNHLYN----AGKYQEALTFFMKPDAVNNPATMNRIGYMYDEGQGVKKDPKEAFK
+pdb_id=6onw, cha... ----LGTLYANGTHVKADPHEAEKWLSRAAGQGSPMVQLYLGLMYGHGKGVPRDLNKSLF
+
+target WYKKAADANLPVAQFNLGLMYQHGTGVSKDINESIKWFRKAAEQNDPDAEMKMGYLTATG
+pdb_id=6onw, cha... WVEKAADRGLPHAQLARGLFASFSHYYPRDDEKAVLYLTKAAKQGMPMAQFYLALMYQRG
+
+target TGVKKDYQEAIQWYQRAAEHGDSAAYAQIGLFYTLGNGVKKDVNRAVQYYIMGAQKGDAR
+pdb_id=6onw, cha... RGVEQSNEQALHWNMLAAEQGYPDAEYAMSRMAELGIGVTADKAWSMMWLDRAAHHGMPL
+
+target AQAFLGKAYALGRGIQPDSEKALYWYKTAARNGNVNAMKELGSIYAKGRLGVKPDQQEAQ
+pdb_id=6onw, cha... AQYLMGMAYLEGKSVPQDLPVAAAWFYKAAMQGNADAQLRLGYMYARG-IGVPVDKPKAV
+
+target RWNDMARKAEQKN
+pdb_id=6onw, cha... AWLEKAASAG---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.ASN11-()-A.ALA12 by filling A.ASN11-(AGK)-A.TYR15 (42 candidates, BB_DB)
+Resolved A.GLY224-(R)-A.LEU226 by filling A.LYS223-(GRLG)-A.VAL228 (73 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.23971e+11)
+No more stereo-chemical problems -> final energy: 12570.1
+
+
+Build model with the following alignment:
+target MLNSPTRQQRIELSLPESPLVQFSSAEHTVEVVKVGHPDYEYEIKPGDNLSTIFNQLGFA
+pdb_id=3slu, cha... ---------------------------------VQTAYWVQEAVQPGDSLADVLARSGMA
+
+target YTELMKVMETDLNYLALDTLRPGNVLRFWKGSDNTLAKMELEFSLV---DRAVYTRLNDG
+pdb_id=3slu, cha... RDEIARITEKY------RHLRADQSVHVLVGGDGGAREVQFFTDEDGERNLVALEKKGG-
+
+target SYEFEERKIPGTWKVEPLIGEVDGSFSLSANRAGLGAADVDQIVTLLKDKINFGRDLRRG
+pdb_id=3slu, cha... IWRRSASEADMKVLPTLRSVVVKTSARGSLARAEVPVEIRESLSGIFAGRFSL-DGLKEG
+
+target DRFEVVLSRQLVGEKLTGNSEIQAIKIFNRGKEITAYLH---QD----GQYYDKNGDSLQ
+pdb_id=3slu, cha... DAVRLIYDSLYFHGQQVAAGDILAAEVVKGGTRHQAFYYRSDK----GGNYYDEDGRVLQ
+
+target R--AFQRYPVDSKWRISSNFDPRRLHPVTKRVAPHNGTDFAMPIGTPVYTSGDGVVVMTR
+pdb_id=3slu, cha... ---GFNIEPLVYT-RISSPFG-YRMHPILHTWRLHTGIDYAAPQGTPVRASADGVITFKG
+
+target NHPYAGNYVVIQHGNTYMTRYLHLSKILVKKGQKVSRGQRIGLSGNTGRVTGPHLHYELI
+pdb_id=3slu, cha... RKGGYGNAVMIRHANGVETLYAHLSAF-SQAQGNVRGGEVIGFVGSTGRSTGPHLHYEAR
+
+target VRGRPVNAMKANIPMASSVPKKEMAQFIAKRKELDQMLARQESMLAAQHHHHHH
+pdb_id=3slu, cha... INGQPVNPVSVALPTPE-LTQADKAAFAAQKQKADALLAR--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Trying to merge 11 gap(s) with distance 0.
+Merged gap A.HIS216-()-A.GLN217 and A.GLN217-(D)-A.GLY219 into A.HIS216-(QD)-A.GLY219
+Trying to fill 10 gap(s) by database.
+Resolved A.ASP71-(LNYLAL)-A.ASP78 by filling A.ASP71-(LNYLALD)-A.THR79 (112 candidates, BB_DB)
+Resolved A.VAL106-()-A.ASP107 by filling A.PHE103-(SLV)-A.ASP107 (84 candidates, BB_DB)
+Resolved A.ASP116-(G)-A.SER118 by filling A.ARG113-(LNDG)-A.SER118 (87 candidates, BB_DB)
+Resolved A.PHE170-(G)-A.ARG172 by filling A.LYS167-(INFG)-A.ARG172 (53 candidates, BB_DB)
+Resolved A.HIS216-(QD)-A.GLY219 by filling A.LEU215-(HQDG)-A.GLN220 (70 candidates, BB_DB)
+Resolved A.GLN230-(R)-A.ALA232 by filling A.LEU229-(QRAF)-A.GLN234 (127 candidates, BB_DB)
+Resolved A.LYS241-(W)-A.ARG243 by filling A.SER240-(KWR)-A.ILE244 (52 candidates, BB_DB)
+Resolved A.ASP249-(P)-A.ARG251 by filling A.SER246-(NFDP)-A.ARG251 (42 candidates, BB_DB)
+Resolved A.ILE315-(L)-A.VAL317 by filling A.ILE315-(LVKKG)-A.GLN321 (109 candidates, BB_DB)
+Resolved A.SER365-(S)-A.VAL367 by filling A.ALA364-(SSV)-A.PRO368 (97 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.91608e+10)
+Perform energy minimization (iteration 2, energy: 7457.72)
+No more stereo-chemical problems -> final energy: 3437.91
+
+
+Build model with the following alignment:
+target MEKGDTHILVFPFPAQGHINPLLQLSKHLIA-KGIKVSLVTTL-H-V---SNRMQLQGAY
+pdb_id=6jtd, cha... ---SKPHVFLLASPGMGHLIPFLELSKRLVTLNTLQVTLFIVSNEATKARSHLMESSNNF
+
+target SNSVKIEVISD-GSEDRL-ETDTLRQ-YLDRFRQKMTKNLEDFLQKAMVSSNPPKFIIYD
+pdb_id=6jtd, cha... HPDLELVDLTPANLSELLSTDATVFKRIFLIT-QAAIKDLESRISSMS---TPPAALIVD
+
+target STMPWVLEVAKEFGLDRAPFYTQSCALNSINYHVLHG--QLKLPPE--TPTISLPSMPLL
+pdb_id=6jtd, cha... VFSMDAFPVADRFGIKKYVFVTLNAWFLALTTYVRTLDREIEGEYVDLPEPIAIPGCKPL
+
+target RPSDLPAYDFDPASTDTIIDLLTSQYSNIQDANLLFCNTFDKLEGEIIQWMETLG-----
+pdb_id=6jtd, cha... RPEDVFDPM-LSR-SSDGYRPYLGMSERLTKADGLLLNTWEALEPVSLKALRE-NEKLNQ
+
+target ---RPVKTVGPTVPSAYLDKRVENDKHYGLSLFKPNEDVCLKWLDSKPSGSVLYVSYGSL
+pdb_id=6jtd, cha... IMTPPLYPVGPVART----TV---QE----VV---GNE-CLDWLSKQPTESVLYVALGSG
+
+target VEMGEEQLKELALGIKETGKFFLWVVRDTE-----------------A-EKLPPNFVESV
+pdb_id=6jtd, cha... GIISYKQMTELAWGLEMSRQRFIWVVRLPTMEKDGACRFFSDVNVKGPLEYLPEGFLDRN
+
+target AEK-GLVVSWCSQLEVLAHPSVGCFFTHCGWNSTLEALCLGVPVVAFPQWADQVTNAKFL
+pdb_id=6jtd, cha... KELGMVLPNWGPQDAILAHPSTGGFLSHCGWNSSLESIVNGVPVIAWPLYAEQKMNATLL
+
+target -EDVWKVGKRVKRN-EQRLASKEEVRSCIWEVMEGERASEFKSNSMEWKKWAKEAVDEGG
+pdb_id=6jtd, cha... TEE-LGVAVRPEVLPTKAVVSRDEIEKMVRRVIESKEGKMKRNRARSVQSDALKAIEKGG
+
+target SSDKNIEEFVAMLKQT
+pdb_id=6jtd, cha... SSYNTLIEVAKEFEK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 26).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA31-()-A.LYS32 by relaxing A.ILE30-(AKG)-A.ILE34
+Closed: A.ASP65-()-A.GLY66 by relaxing A.ILE63-(SD)-A.GLY66
+Closed: A.LEU71-()-A.GLU72 by relaxing A.ARG70-(LET)-A.ASP74
+Closed: A.GLN78-()-A.TYR79 by relaxing A.ARG77-(QYL)-A.ASP81
+Closed: A.GLU155-()-A.THR156 by relaxing A.PRO154-(ETPT)-A.ILE159
+Closed: A.ALA310-()-A.GLU311 by relaxing A.ALA310-(E)-A.LYS312
+Closed: A.ASN393-()-A.GLU394 by relaxing A.ASN393-(E)-A.GLN395
+Trying to merge 19 gap(s) with distance 0.
+Merged gap A.LEU42-()-A.HIS43 and A.HIS43-()-A.VAL44 into A.LEU42-(H)-A.VAL44
+Merged gap A.LEU42-(H)-A.VAL44 and A.VAL44-()-A.SER45 into A.LEU42-(HV)-A.SER45
+Merged gap A.THR220-(L)-A.GLY222 and A.GLY222-()-A.ARG223 into A.THR220-(LG)-A.ARG223
+Trying to fill 16 gap(s) by database.
+Resolved A.LEU42-(HV)-A.SER45 by filling A.THR40-(TLHV)-A.SER45 (56 candidates, BB_DB)
+Resolved A.PHE83-(R)-A.GLN85 by filling A.PHE83-(RQKM)-A.THR88 (60 candidates, BB_DB)
+Resolved A.MET99-(VSS)-A.ASN103 by filling A.GLN96-(KAMVSS)-A.ASN103 (74 candidates, BB_DB)
+Resolved A.GLY148-()-A.GLN149 by filling A.GLY148-(QLKL)-A.PRO153 (87 candidates, BB_DB)
+Resolved A.ASP176-(F)-A.ASP178 by filling A.TYR175-(DFD)-A.PRO179 (52 candidates, BB_DB)
+Resolved A.ALA180-(S)-A.THR182 by filling A.PRO179-(AST)-A.ASP183 (45 candidates, BB_DB)
+Resolved A.THR220-(LG)-A.ARG223 by filling A.GLU219-(TLGRP)-A.VAL225 (87 candidates, BB_DB)
+Resolved A.SER234-(AYLD)-A.LYS239 by filling A.PRO233-(SAYLDK)-A.ARG240 (62 candidates, BB_DB)
+Resolved A.ARG240-(VEN)-A.ASP244 by filling A.LYS239-(RVEND)-A.LYS245 (43 candidates, BB_DB)
+Resolved A.LYS245-(HYGL)-A.SER250 by filling A.ASP244-(KHYGLS)-A.LEU251 (161 candidates, BB_DB)
+Resolved A.LEU251-(FKP)-A.ASN255 by filling A.GLY248-(LSLFKPN)-A.GLU256 (51 candidates, BB_DB)
+Resolved A.ASP257-(V)-A.CYS259 by filling A.LYS253-(PNEDV)-A.CYS259 (63 candidates, BB_DB)
+Resolved A.GLU309-()-A.ALA310 by filling A.VAL305-(RDTEA)-A.GLU311 (90 candidates, BB_DB)
+Resolved A.LYS324-()-A.GLY325 by filling A.VAL321-(AEK)-A.GLY325 (87 candidates, BB_DB)
+Resolved A.LEU380-()-A.GLU381 by filling A.ALA377-(KFLE)-A.ASP382 (58 candidates, BB_DB)
+Resolved A.ASP382-(V)-A.TRP384 by filling A.PHE379-(LEDV)-A.TRP384 (44 candidates, BB_DB)
+Rebuilding sidechains.
+Trying to fix 1 ring punch(es).
+Trying to fill 1 gap(s) by database.
+Resolved A.ARG82-(F)-A.ARG84 by filling A.ARG82-(FR)-A.GLN85 (47 candidates, BB_DB)
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.02593e+18)
+Perform energy minimization (iteration 2, energy: 38158.8)
+No more stereo-chemical problems -> final energy: 32065.3
+
+
+Build model with the following alignment:
+target DLQLLHQKVEEQAAKYKHRVPKKCCYDGARENKYETCEQRVARVTIGPHCIRAFNECCTI
+pdb_id=4p3a, cha... NLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTI
+
+target ADKIRKESHHKGMLLGR
+pdb_id=4p3a, cha... ANKIRKES---------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8054.73)
+No more stereo-chemical problems -> final energy: -1157.99
+
+
+Build model with the following alignment:
+target SDEVDKHVLRKYDILQKLGKGAYGIVWKSTDRRTNETVALKKIFDAFQNATDAQRTFREI
+pdb_id=5z33, cha... ----DFIVDERYTVTKELGQGAYGIVCAAVNNQTSEGVAIKKVTNVFSKKILAKRALREI
+
+target MFLQELAGHENIVRLKNVLKADND--KDIYLVFDYMETDLHAVIRA-DILEEIHKQYIVY
+pdb_id=5z33, cha... KLLQHFRGHRNITCLYDMDIPRPDNFNETYLYEELMECDLAAIIRSGQPLTDAHFQSFIY
+
+target QLLRAIKYMHSGELLHRDMKPSNVLLNSECQVKVADFGLARSVAHSESNNSEAGGNPVLT
+pdb_id=5z33, cha... QILCGLKYIHSANVLHRDLKPGNLLVNADCELKICDFGLARGFSVDPEEN-----AGYMT
+
+target DYVATRWYRAPEILLGSTSYTKGVDMWSLGCILGELLSGRPIFPGTSTMNQLERIMTLTG
+pdb_id=5z33, cha... EYVATRWYRAPEIMLSFQSYTKAIDVWSVGCILAELLGGRPFFKGRDYVDQLNQILHILG
+
+target RPSPEDVDAVKSPFAATMMESLPLGKVKNFKDAFPNASPEALDLLKQLLQFNPNKRISAE
+pdb_id=5z33, cha... TPNEETLSRIGSPRAQEYVRNLPFMAKKPFPTLFPNANPDALDLLDRMLAFDPSSRISVE
+
+target KGLEHPYVRQFHSPEDEPVCGKIIAIPIDDNTKYSVEDYRDKVYSEVIKKKHDQRRHRTA
+pdb_id=5z33, cha... QALEHPYLHIWHDASDEPDCPTTFNFDFEVVE--DVGEMRKMILDEVYRFRQLV------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ASP84-()-A.LYS85 by filling A.ASP82-(NDK)-A.ASP86 (46 candidates, BB_DB)
+Resolved A.ALA104-()-A.ASP105 by filling A.ARG103-(ADILE)-A.GLU109 (53 candidates, BB_DB)
+Resolved A.ASN167-(SEAGG)-A.ASN173 by filling A.ASN167-(SEAGGNPVL)-A.THR177 (63 candidates, BB_DB)
+Resolved A.THR329-(KY)-A.SER332 by filling A.ASP327-(NTKY)-A.SER332 (43 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.47076e+20)
+Perform energy minimization (iteration 2, energy: 14193.1)
+Perform energy minimization (iteration 3, energy: 10348)
+No more stereo-chemical problems -> final energy: 8988.51
+
+
+Build model with the following alignment:
+target MRKRVVVTGVGAIHPDGNDVTAIKSKVIQKLLGQES-KNN----------------TTAS
+pdb_id=4na1, cha... --EPVAIVGISGRFPGAMDIDEFWKNLEEGKDSITEVPKDRWDWREHYGNPDTDVNKTDI
+
+target SIIRTLSD---FDGAKY-INNRLRRKIDEFSVYGIVAVEMALKASRLDVDKLDPNRVGIY
+pdb_id=4na1, cha... KWGGFIDGVAEFDPLFFGISPREADYVDPQQRLLMTYVWKALEDAGCSPQSLSGTGTGIF
+
+target VGNCFGGWQHIEDEVKALHIEGIKGMGPYVATA-WFPAALQGQLSLLYGFSAQSKTFSTS
+pdb_id=4na1, cha... IGTGNTGYKDLFH------RAN-LPIEGHAATGHMIPSVGPNRMSYFLNIHGPSEPVETA
+
+target DVAGMQAIGYAAEAISNGVAEVMLCGASEHLSSPLVK---NLLEKTSSQKHSEVFGEKQP
+pdb_id=4na1, cha... CSSSLVAIHRAVTAMQNGDCEMAIAGGVNTILTEEAHISYSKAGMLSTDGRCKTFSADAN
+
+target GD-FSEGAAFLVLEERQHALERGASILCELTGFVDYFAPDKNTR------NN--TLEYTA
+pdb_id=4na1, cha... GYVRGEGVGMVMLKKLEDAERDGNHIYGVIRGTAENHGGRANTLTSPNPKAQADLLVRAY
+
+target ELFNHNENAV--FIMD---GIYDDEKEITSKAFSNKEIKTSFI-----------------
+pdb_id=4na1, cha... RQADIDPSTVTYIEAHGTGTELGDPIEIN--GL-----KAAFKELSNM------DVPDHR
+
+target ---NL-RPYLDNQFSVSGVIDSVLASSFLSESHGDEEQQSKKINEFSNTNQIIIQRFSNQ
+pdb_id=4na1, cha... CGIGSVKSNIGHLELAAGISGLIKVLLQMKHK----------------------------
+
+target GHVCALSFSAI
+pdb_id=4na1, cha... -----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 17).
+Initialized default backbone scoring for modelling.
+Closed: A.SER36-()-A.LYS37 by relaxing A.GLU35-(SK)-A.ASN38
+Closed: A.LEU306-()-A.ARG307 by relaxing A.LEU306-(RP)-A.TYR309
+Trying to merge 15 gap(s) with distance 0.
+Trying to fill 15 gap(s) by database.
+Resolved A.ASN39-()-A.THR40 by filling A.ASN39-(TTASS)-A.ILE45 (78 candidates, BB_DB)
+Resolved A.ASP51-()-A.PHE52 by filling A.SER50-(DFDGAK)-A.TYR57 (157 candidates, BB_DB)
+Resolved A.TYR57-()-A.ILE58 by filling A.ALA55-(KYI)-A.ASN59 (101 candidates, BB_DB)
+Resolved A.ASP112-(EVKALH)-A.ILE119 by filling A.HIS109-(IEDEVKALHI)-A.GLU120 (49 candidates, BB_DB)
+Resolved A.GLY121-(I)-A.LYS123 by filling A.ILE119-(EGI)-A.LYS123 (56 candidates, BB_DB)
+Resolved A.ALA132-()-A.TRP133 by filling A.ALA132-(WFPA)-A.ALA137 (83 candidates, BB_DB)
+Resolved A.LYS195-()-A.ASN196 by filling A.LYS195-(NLLE)-A.LYS200 (60 candidates, BB_DB)
+Resolved A.ASP217-()-A.PHE218 by filling A.GLU212-(KQPGD)-A.PHE218 (41 candidates, BB_DB)
+Resolved A.ARG258-()-A.ASN259 by filling A.ASP254-(KNTR)-A.ASN259 (116 candidates, BB_DB)
+Resolved A.ASN260-()-A.THR261 by filling A.ASN259-(NT)-A.LEU262 (72 candidates, BB_DB)
+Resolved A.VAL276-()-A.PHE277 by filling A.ASN272-(ENAV)-A.PHE277 (65 candidates, BB_DB)
+Resolved A.ASP280-()-A.GLY281 by filling A.MET279-(DGIYD)-A.ASP285 (111 candidates, BB_DB)
+Resolved A.THR290-(SK)-A.ALA293 by filling A.GLU286-(KEITSK)-A.ALA293 (56 candidates, BB_DB)
+Resolved A.PHE294-(SNKEI)-A.LYS300 by filling A.PHE294-(SNKEIKTSF)-A.ILE304 (48 candidates, BB_DB)
+Failed at loop insertion (A.ILE304-()-A.ASN305), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ILE304-()-A.ASN305), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ILE304-()-A.ASN305), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.ILE304-()-A.ASN305), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.ILE304-()-A.ASN305 by filling A.ASN296-(KEIKTSFI)-A.ASN305 (298 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8.8352e+16)
+Perform energy minimization (iteration 2, energy: 26655.4)
+No more stereo-chemical problems -> final energy: 23306
+
+
+Build model with the following alignment:
+target MAHHHHHHSSGLEVLFQGPTGTGATSTGPQGLPQTGTPTFQGGDPLVPIDETVEPTFEDG
+pdb_id=5k8g, cha... ------------------------------------------------------------
+
+target SKEKTIPGQ-GTYTIVPDGTVTFTPDKQF----VGKPDPVTVKRVDKNGTPVTATYSPEF
+pdb_id=5k8g, cha... ----SIEGQYGNLVLNSDGSYVYDVTASVSDIPAGATESFAYLIQDQDGSTSSANLSINV
+
+target TKV
+pdb_id=5k8g, cha... G--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.GLN69-()-A.GLY70 by relaxing A.PRO67-(GQG)-A.THR71
+Trying to fill 1 gap(s) by database.
+Resolved A.PHE88-()-A.VAL89 by filling A.GLN87-(FVGK)-A.PRO92 (72 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.58432e+09)
+No more stereo-chemical problems -> final energy: 5539.26
+
+
+Build model with the following alignment:
+target MPGIAVCNMDSAGGVILPGPNVKCFYKGQPFAVIGCAVAGHGRTPH----DSARMIQGSV
+pdb_id=5iv5, cha... --------------VVNAT-QSKVFTGGIAVLVAGDPITEHTEIKKPYETHGGVTQPRTS
+
+target KMAIAGIPVCLQGSMASCGHTAT-GRPNLTCGS
+pdb_id=5iv5, cha... KVYVTGKKAVQMADPISCGDTVAQASSKVF---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLY19-(P)-A.ASN21 by filling A.PRO18-(GPNV)-A.LYS23 (124 candidates, BB_DB)
+Resolved A.HIS46-()-A.ASP47 by filling A.GLY42-(RTPHDS)-A.ALA49 (69 candidates, BB_DB)
+Resolved A.THR79-()-A.GLY80 by filling A.THR77-(ATGRP)-A.ASN83 (43 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.79376e+14)
+No more stereo-chemical problems -> final energy: 7037.53
+
+
+Build model with the following alignment:
+target MKFKLNLITLALLANTGFAIAADGYGLANANTEKVKMSAWSCKGCVVETGTSGTVGVGVG
+pdb_id=5odw, cha... ------------------------------------------------------------
+
+target YNSEEDIRSANAFGTSNEVAGKLDADVTFRGEKGYRASVEAYQLGMDGGRLEVNAGKQGQ
+pdb_id=5odw, cha... ------------------------------------------------------------
+
+target YNVNVNYRQIATYNSNSALTPYSGVGSDNLTLPDNWVTAGSSSQMPLLMDSLNSLELSLK
+pdb_id=5odw, cha... ------------------------------------------------------------
+
+target RERTGLGFDYQGESLWSTHVSYMREEKTGLKKASGGFFNQSMMLAEPVDYTTDSIEAGIK
+pdb_id=5odw, cha... ------------------------------------------------ERKTSVYYGILE
+
+target LK-GDNWFTALNYNGSIFKNEYNQLNFD--SAFNPTFGA-------QTSGSIALDPDNQS
+pdb_id=5odw, cha... FDLNPDTMLTVGADYQDNDPKGSG--WSGSFPLFDSQGNRNDVSRSFNNGAKWSSWEQYT
+
+target HTVSLMGQYNDS-TNVLSARLLTGQMSQDQALV-TSG---Y-GYQVP--TEALDAKVDLI
+pdb_id=5odw, cha... RTVFANLEHNFANGWVGKVQLDHKINGYHAPLGAIMGDWPAPDNSAKIVAQKYTGETKSN
+
+target GLNLKVVSKV---TNSLRLSGSYDYNDRDNNTQI----EEWTQ--VSINNVNGKV-----
+pdb_id=5odw, cha... SLDIYLTGPFQFLGREHELVVGTSASFSHWEGKSYWNLRNYDNTTDDFINWDGDIGKPDW
+
+target ---AYNTPYDNTSQRFKVAADYRITRGMKLDGGYDFRRDERNYQD--RETTDENTVWARF
+pdb_id=5odw, cha... GTPSQYIDDKTRQLGSYMTARFNVTDDLNLFLGGRVVDYRVTGLNPTIRESGRFIPYVGA
+
+target RVNSFETWDMWVKGSYGQRDGSEYQASEWTSSETNSLLRKYNLANRDRTQVEARVTHSPI
+pdb_id=5odw, cha... VYDLNDTYSVYASYTDIFMPQDSWY-----RDSSNKLLEPD-----EGQNYEIGIKGEYL
+
+target -ESLTIDFGARYALDD-YTD----------------TVIGLTESKDTSYDANISYMITDD
+pdb_id=5odw, cha... DGRLNTSLAYFEIHEENRAEEDALYNSKPTNPAITYAYKGIK-AKTKGYEAEISGELAPG
+
+target LLANAFYNYQIIESEQAGSS-NYSTPTWTGFIEDKVDVVGAGISYNNL-LENKLRMGLDY
+pdb_id=5odw, cha... WQVQAGYTHKIIRDDS-GKKVSTWEPQ---------DQLSLYTSYKFKGALDKLTVGGGA
+
+target TYSDSNSNTQVRQ-G---ITGDYGDYFAKVHNINLYAQYQATEKMALRFDYKIENYKDND
+pdb_id=5odw, cha... RWQGKSWQMVYNNPRSRWEKFSQE----DYWLVDLMARYQITDKLSAS--VNVNNVFDKT
+
+target AANDIAVNGIWNVVGFGDNSHDYTAQMIMLSMSYKI
+pdb_id=5odw, cha... YYTNIG-FY-TS-------ASYGDPRNLMFSTRWDF
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 31).
+Initialized default backbone scoring for modelling.
+Closed: A.SER302-()-A.THR303 by relaxing A.ASP301-(ST)-A.ASN304
+Closed: A.GLN616-()-A.GLY617 by relaxing A.ARG615-(Q)-A.GLY617
+Trying to merge 29 gap(s) with distance 0.
+Merged gap A.GLY325-()-A.TYR326 and A.TYR326-()-A.GLY327 into A.GLY325-(Y)-A.GLY327
+Trying to fill 28 gap(s) by database.
+Resolved A.LYS242-()-A.GLY243 by filling A.LEU241-(KGD)-A.ASN245 (192 candidates, BB_DB)
+Resolved A.GLN263-(LN)-A.PHE266 by filling A.GLU260-(YNQLN)-A.PHE266 (42 candidates, BB_DB)
+Resolved A.ASP267-()-A.SER268 by filling A.ASN262-(QLNFD)-A.SER268 (125 candidates, BB_DB)
+Resolved A.ALA276-()-A.GLN277 by filling A.ASN271-(PTFGAQ)-A.THR278 (44 candidates, BB_DB)
+Resolved A.VAL322-()-A.THR323 by filling A.GLN319-(ALVTS)-A.GLY325 (235 candidates, BB_DB)
+Failed at loop insertion (A.GLY325-(Y)-A.GLY327), only 38 candidates
+Failed at loop insertion (A.PRO331-()-A.THR332), only 0 candidates
+Resolved A.VAL352-()-A.THR353 by filling A.VAL352-(TNSL)-A.ARG357 (106 candidates, BB_DB)
+Failed at loop insertion (A.ILE373-()-A.GLU374), only 0 candidates
+Resolved A.GLN378-()-A.VAL379 by filling A.THR377-(QVSINN)-A.VAL384 (70 candidates, BB_DB)
+Failed at loop insertion (A.VAL388-()-A.ALA389), only 0 candidates
+Resolved A.ASP430-()-A.ARG431 by filling A.ASN427-(YQD)-A.ARG431 (86 candidates, BB_DB)
+Resolved A.GLN468-(ASEWT)-A.SER474 by filling A.GLY464-(SEYQASEWT)-A.SER474 (59 candidates, BB_DB)
+Resolved A.TYR484-(NLANR)-A.ASP490 by filling A.LEU481-(RKYNLANRD)-A.ARG491 (111 candidates, BB_DB)
+Resolved A.ILE503-()-A.GLU504 by filling A.SER501-(PIE)-A.SER505 (108 candidates, BB_DB)
+Resolved A.ASP518-()-A.TYR519 by filling A.LEU516-(DDY)-A.THR520 (51 candidates, BB_DB)
+Resolved A.ASP521-()-A.THR522 by filling A.THR520-(DTV)-A.ILE524 (111 candidates, BB_DB)
+Resolved A.THR527-(E)-A.SER529 by filling A.ILE524-(GLTE)-A.SER529 (67 candidates, BB_DB)
+Resolved A.GLN561-(A)-A.GLY563 by filling A.SER559-(EQA)-A.GLY563 (40 candidates, BB_DB)
+Resolved A.SER565-()-A.ASN566 by filling A.SER565-(NYST)-A.PRO570 (97 candidates, BB_DB)
+Failed at loop insertion (A.THR571-(WTGFIEDKV)-A.ASP581), only 18 candidates
+Resolved A.LEU592-()-A.LEU593 by filling A.LEU592-(LENK)-A.LEU597 (114 candidates, BB_DB)
+Resolved A.GLY617-()-A.ILE618 by filling A.GLN613-(VRQG)-A.ILE618 (51 candidates, BB_DB)
+Resolved A.GLY623-(DYFA)-A.LYS628 by filling A.TYR622-(GDYFAKV)-A.HIS630 (246 candidates, BB_DB)
+Resolved A.ARG647-(FD)-A.TYR650 by filling A.LEU646-(RFDY)-A.LYS651 (51 candidates, BB_DB)
+Resolved A.ALA665-(V)-A.ASN667 by filling A.ASN662-(DIAVN)-A.GLY668 (82 candidates, BB_DB)
+Resolved A.GLY668-(I)-A.TRP670 by filling A.ALA665-(VNGI)-A.TRP670 (40 candidates, BB_DB)
+Resolved A.ASN671-(VVGFGDN)-A.SER679 by filling A.ASN667-(GIWNVVGFGDN)-A.SER679 (102 candidates, BB_DB)
+Trying to merge 5 gap(s) with distance 1.
+Trying to fill 5 gap(s) by database.
+Failed at loop insertion (A.GLY325-(Y)-A.GLY327), only 39 candidates
+Failed at loop insertion (A.PRO331-()-A.THR332), only 0 candidates
+Failed at loop insertion (A.ILE373-()-A.GLU374), only 0 candidates
+Failed at loop insertion (A.VAL388-()-A.ALA389), only 0 candidates
+Failed at loop insertion (A.THR571-(WTGFIEDKV)-A.ASP581), only 18 candidates
+Trying to merge 5 gap(s) with distance 2.
+Trying to fill 5 gap(s) by database.
+Failed at loop insertion (A.GLY325-(Y)-A.GLY327), only 39 candidates
+Failed at loop insertion (A.PRO331-()-A.THR332), only 0 candidates
+Failed at loop insertion (A.ILE373-()-A.GLU374), only 0 candidates
+Failed at loop insertion (A.VAL388-()-A.ALA389), only 0 candidates
+Failed at loop insertion (A.THR571-(WTGFIEDKV)-A.ASP581), only 18 candidates
+Trying to merge 5 gap(s) with distance 3.
+Trying to fill 5 gap(s) by database.
+Failed at loop insertion (A.GLY325-(Y)-A.GLY327), only 39 candidates
+Failed at loop insertion (A.PRO331-()-A.THR332), only 0 candidates
+Failed at loop insertion (A.ILE373-()-A.GLU374), only 0 candidates
+Failed at loop insertion (A.VAL388-()-A.ALA389), only 0 candidates
+Failed at loop insertion (A.THR571-(WTGFIEDKV)-A.ASP581), only 18 candidates
+Trying to fill 5 gap(s) by database.
+Resolved A.GLY325-(Y)-A.GLY327 by filling A.LEU321-(VTSGYGYQ)-A.VAL330 (46 candidates, BB_DB)
+Resolved A.PRO331-()-A.THR332 by filling A.TYR326-(GYQVPT)-A.GLU333 (56 candidates, BB_DB)
+Failed at loop insertion (A.ILE373-()-A.GLU374), only 25 candidates
+Resolved A.VAL388-()-A.ALA389 by filling A.GLN378-(VSINNVNGKVA)-A.TYR390 (52 candidates, BB_DB)
+Failed at loop insertion (A.THR571-(WTGFIEDKV)-A.ASP581), only 18 candidates
+Trying to fill 2 gap(s) by database.
+Resolved A.ILE373-()-A.GLU374 by filling A.ILE373-(EEWTQVSI)-A.ASN382 (530 candidates, BB_DB)
+Resolved A.THR571-(WTGFIEDKV)-A.ASP581 by filling A.THR571-(WTGFIEDKVD)-A.VAL582 (129 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.75734e+25)
+Perform energy minimization (iteration 2, energy: 43124.1)
+Perform energy minimization (iteration 3, energy: 23760.5)
+Perform energy minimization (iteration 4, energy: 19547.7)
+Perform energy minimization (iteration 5, energy: 16910.7)
+Perform energy minimization (iteration 6, energy: 15381.9)
+Perform energy minimization (iteration 7, energy: 14418.2)
+Perform energy minimization (iteration 8, energy: 13621.7)
+Perform energy minimization (iteration 9, energy: 12518.2)
+Perform energy minimization (iteration 10, energy: 11950.5)
+Perform energy minimization (iteration 11, energy: 11444.2)
+Perform energy minimization (iteration 12, energy: 10952.3)
+Stereo-chemical problem in sidechain of residue A.ARG482
+Stereo-chemical problem in sidechain of residue A.ARG513
+Stereo-chemical problem in sidechain of residue A.TYR554
+
+
+Build model with the following alignment:
+target GSHMGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRF
+pdb_id=3hxj, cha... --------------------------------------------------------KWEF
+
+target KTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYV
+pdb_id=3hxj, cha... LIGNSIDSSPILAKNGTIYLGSSNKNLYAINTDGSVKWFFKSGEIIECRPSIGKDGTIYF
+
+target GSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRF
+pdb_id=3hxj, cha... GSDK--VYAINPDGTEKWRFDT-----SDFTI-FEDILYVTSMDGHLYAINTDGTEKWRF
+
+target KTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYV
+pdb_id=3hxj, cha... KTKKAIYATPIVSEDGTIYVGSNDNYLYAINPDGTEKWRFKTNDAITSAASIGKDGTIYF
+
+target GSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRF
+pdb_id=3hxj, cha... GS--DKVYAINPDGTEKWNFYAGYWTVTRPAISEDGTIYVTSLDGHLYAINPDGTEKWRF
+
+target KTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYV
+pdb_id=3hxj, cha... KTGKRIESSPVIGNTDTIYFGSYDGHLYAINPDGTEKWNFETGSWIIATPVIDENGTIYF
+
+target GSNDGHLYAINP
+pdb_id=3hxj, cha... GTRNGKFYAL--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ASP124-(GH)-A.LEU127 by filling A.SER122-(NDGH)-A.LEU127 (72 candidates, BB_DB)
+Resolved A.THR142-(GKAIE)-A.ALA148 by filling A.THR142-(GKAIE)-A.ALA148 (83 candidates, BB_DB)
+Resolved A.ILE152-(G)-A.GLU154 by filling A.ILE152-(GEDG)-A.THR157 (107 candidates, BB_DB)
+Resolved A.SER242-(ND)-A.GLY245 by filling A.GLY241-(SNDGH)-A.LEU247 (52 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.40724e+10)
+Perform energy minimization (iteration 2, energy: 25912)
+No more stereo-chemical problems -> final energy: 23308.6
+
+
+Build model with the following alignment:
+target GDKFQLTFPLRTNYMYAKVKKSLP-EMYAFTVCMWLKSSATP-GVGTPFSYAVPGQANEL
+pdb_id=4pbo, cha... ---KVLQFKTATDNSYVKLYPEKPLSLSAFTLCMRVATELPLDREVILFAYYT-PDVDEL
+
+target VLIEWGNNPMEILI-NDKVAKL-PFVINDGKWHHICVTWTTRDGVWEAYQDGTQGGSGEN
+pdb_id=4pbo, cha... NVWRERDGRVSLYIQSSKDAAFFRLPPLSTLQTHLCVAWESATGLTAFWMDGRRSLH-QV
+
+target LAPYHPIKPQGVLVLGQEQDTLGGGFDATQAFVGELAHFNIWDRKLTPGEVYNLATCSTK
+pdb_id=4pbo, cha... YRKGYSIRSGGTVVLGQDPDSYVGSFDVDQSFVGEIANLQMWDYVLSSAQIKAVYYNQDN
+
+target ALSGNVIAWAESHIEIYGGATKWTFEACR
+pdb_id=4pbo, cha... RVKGNVFDWDTIEYDVTGNVLVVPD----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.PRO24-()-A.GLU25 by relaxing A.LEU23-(PE)-A.MET26
+Closed: A.PRO41-()-A.GLY42 by relaxing A.THR40-(P)-A.GLY42
+Closed: A.ILE72-()-A.ASN73 by relaxing A.ILE72-(ND)-A.LYS75
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.VAL51-(P)-A.GLY53 by filling A.ALA50-(VPGQ)-A.ALA55 (80 candidates, BB_DB)
+Resolved A.LEU79-()-A.PRO80 by filling A.LEU79-(PFVI)-A.ASN84 (53 candidates, BB_DB)
+Resolved A.SER113-(G)-A.GLU115 by filling A.GLN110-(GGSG)-A.GLU115 (69 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.12374e+09)
+No more stereo-chemical problems -> final energy: 19071.2
+
+
+Build model with the following alignment:
+target GAGAGAGAGAQTVKPFKEGDRAVFLGNSITDGGR----------------YHSFIWLYYM
+pdb_id=4q9a, cha... -------------INLKKDCVILFQGDSITDCGRDRNSNRCNTMEQFGSGYVLFTATQLL
+
+target TRFPNMPIRVFNGGIGGDTAYDMNKRLDGDIFSKNPTVLMVTFGMNDSGYYEYNGDNAKE
+pdb_id=4q9a, cha... EGKAALQPKIYNRGISGNKVYQLRERWEIDCLAFQPDVLSILIGVNDYWHTLTH------
+
+target FGEQKYQESIKNFQQMEKRFKEL-PHTRIVMTGTSPYDETAQIKDNTVFKKKNETIKRII
+pdb_id=4q9a, cha... GYKGTVETYENDLRALLKYTKEKLPNTQIVLCEPFTLRDGAAI-E---DSKWYPMFDEFR
+
+target EYQRESAARNGWEFTDWNAPMVAINQELQQKDPSFTLCGNDRIHPDNDGHMVMAYLFLKA
+pdb_id=4q9a, cha... KSARKLSEEFNTIFVPFQSGFDAAVKLA---PARY--WSNDGVHPDLPGRQLMANMWMEA
+
+target QGFAGKDVANMEINANKKQAVKAEGCTISNIKKIGKDISFDYLAEALPYPLDTIARGWGS
+pdb_id=4q9a, cha... TGL---------------------------------------------------------
+
+target KKSQAEVIKEVPFMEEMNTELLKVTGLKGQYKLLIDDQEIGTWDAADLAKGINLAAESKT
+pdb_id=4q9a, cha... ------------------------------------------------------------
+
+target PQYQQALTIMHLNEYRWELERTFREYAWCQFGFFQQKGLLFANDRKAIEVMDENVEKNMW
+pdb_id=4q9a, cha... ------------------------------------------------------------
+
+target LKGRRDLYSKMMFKEIRDAREQEMDVLISKIYEINKPVVRKIVLRKI
+pdb_id=4q9a, cha... -----------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 7).
+Initialized default backbone scoring for modelling.
+Closed: A.LEU127-()-A.PRO128 by relaxing A.LYS125-(EL)-A.PRO128
+Trying to merge 6 gap(s) with distance 0.
+Merged gap A.ILE146-(K)-A.ASP148 and A.ASP148-(NTV)-A.PHE152 into A.ILE146-(KDNTV)-A.PHE152
+Trying to fill 5 gap(s) by database.
+Resolved A.ARG34-()-A.TYR35 by filling A.ASP31-(GGR)-A.TYR35 (42 candidates, BB_DB)
+Resolved A.ASN98-(GDNAKE)-A.PHE105 by filling A.ASN98-(GDNAKEFG)-A.GLU107 (62 candidates, BB_DB)
+Resolved A.ILE146-(KDNTV)-A.PHE152 by filling A.ALA144-(QIKDNTV)-A.PHE152 (74 candidates, BB_DB)
+Resolved A.LEU191-(QQK)-A.ASP195 by filling A.GLN189-(ELQQKD)-A.PRO196 (122 candidates, BB_DB)
+Resolved A.PHE198-(TL)-A.CYS201 by filling A.PHE198-(TLCGNDRI)-A.HIS207 (40 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.64878e+17)
+Perform energy minimization (iteration 2, energy: 8627.39)
+No more stereo-chemical problems -> final energy: 6369.36
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPAGSHMEFAQHPLTPNGRKAGSAGDTALAFWKDHLSWWHDWTPAP
+pdb_id=5u22, cha... ------------------------------------------------------------
+
+target SSPKGAGLVPVSMLWGGGNNGQKDAQRLQQFEHLNSTPAYVMGFNEPDCSGADVSADIDV
+pdb_id=5u22, cha... ---------------------------------------GNEIWNEPDVTWK-----DSN
+
+target NTG-VSLWNSLIAPMGQK--GAALGSPAMCRQKDESWLKQFNQQQL--TKSWDFTSIHIF
+pdb_id=5u22, cha... GLSFNQMWKQTYDLLRQIDPNEKIIGPSFSW-YEENKMKNFLQFSKQNNCLPDIIAWHEL
+
+target KSDMTGVQADIDYYWN---TYQ---KPLWVTEFACVFDQNNFTPCTDQNQINQWISDIVD
+pdb_id=5u22, cha... SG-IDGVSSHFRSYRNLEKSLGISERPITINEYCDEN-----------------------
+
+target LFEANEHVLAYAYTDGLGLGSVWPPVNSDGSLSQSGQAYLNAISKYHSR
+pdb_id=5u22, cha... -------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 8).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY123-()-A.VAL124 by relaxing A.GLY123-(V)-A.SER125
+Trying to merge 7 gap(s) with distance 0.
+Trying to fill 7 gap(s) by database.
+Resolved A.ALA112-(DVSAD)-A.ILE118 by filling A.CYS109-(SGADVSAD)-A.ILE118 (110 candidates, BB_DB)
+Resolved A.LYS137-()-A.GLY138 by filling A.GLN136-(KGAAL)-A.GLY142 (83 candidates, BB_DB)
+Resolved A.ARG148-(Q)-A.LYS150 by filling A.ARG148-(QKD)-A.GLU152 (58 candidates, BB_DB)
+Resolved A.LEU163-()-A.THR164 by filling A.LEU163-(TKSWD)-A.PHE169 (61 candidates, BB_DB)
+Resolved A.SER177-(D)-A.MET179 by filling A.SER177-(DMT)-A.GLY181 (61 candidates, BB_DB)
+Resolved A.ASN191-()-A.THR192 by filling A.TRP190-(NTYQK)-A.PRO196 (84 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.07374e+15)
+No more stereo-chemical problems -> final energy: 11965.9
+
+
+Build model with the following alignment:
+target TSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNDSAQN
+pdb_id=6okd, cha... -------------------------------------KLSKVWRDQHFVKIQVKDS-AQN
+
+target SVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVR
+pdb_id=6okd, cha... SVIIVD--GRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVR
+
+target AGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSASHHHHHH
+pdb_id=6okd, cha... AGKITFAEKVANAESLNAIGVLIYMDQTKFPI--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.ASP56-(S)-A.ALA58 by filling A.ASN55-(DSA)-A.GLN59 (51 candidates, BB_DB)
+Resolved A.ASP66-(KN)-A.GLY69 by filling A.VAL65-(DKNG)-A.ARG70 (88 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 24201.1)
+No more stereo-chemical problems -> final energy: 9336.76
+
+
+Build model with the following alignment:
+target MSSSHHHHHHMPTKKQKSKSKLKPFFALVRRTNPSYGKLAFALALSVVTTLVSLLIPLLT
+pdb_id=5u1d, cha... ------------------------VRRLLGCLGSETRRLSLFLVLVVLSSLGEMAIPFFT
+
+target KQLVDGFSMS-NLS--GTQIGLIALVFFVQAGLSAYATYALNYNGQKIISGLRELLWKKL
+pdb_id=5u1d, cha... GRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQGEVFGAV
+
+target IKLPVSYFDTNASGETVSRVTNDTMVVKELITTHISGFITGIISVIGSLTILFIMNWKLT
+pdb_id=5u1d, cha... LRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIMLW--VSLT
+
+target LLVLVVVPLAALILVPIGRKMFSISRETQDETARFTGLLNQILPEIRLVKASNAEDVEYG
+pdb_id=5u1d, cha... MVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFANEEGEAQ
+
+target RGKMGISSLFKLGVREAKVQSLVGPLISLVLMAALVAVIGYGGMQVSSGELTAGALVAFI
+pdb_id=5u1d, cha... KFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSSGNLVTFV
+
+target LYLFQIIMPMGQITTFFTQLQKSIGATERMIEILA-EEEEDTVTGKQIENAHLPIQLDRV
+pdb_id=5u1d, cha... LYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDR-------GLLTPLHLEGLVQFQDV
+
+target SFGYKP--DQLILKEVSAVIEAGKVTAIVGPSGGGKTTLFKLLERFYSPTAGTIRLGDEP
+pdb_id=5u1d, cha... SFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGKP
+
+target VDTYSLESWREHIGYVSQESPLMSGTIRENICYGLERDVTDAEIEKAAEMAYALNFIKEL
+pdb_id=5u1d, cha... LPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGL
+
+target PNQFDTEVGERGIMLSGGQRQRIAIARALLRNPSILMLDAATSSLDSQSEKSVQQALEVL
+pdb_id=5u1d, cha... PQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYES
+
+target M--EGRTTIVIAHRLSTVVDADQLLFVEKGEITGRGTHHELMASHGLYRDFAEQQLKMNA
+pdb_id=5u1d, cha... PERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMVQA------
+
+target DLENKAG
+pdb_id=5u1d, cha... -------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.PRO362-()-A.ASP363 by relaxing A.TYR360-(KP)-A.ASP363
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.SER70-()-A.ASN71 by filling A.SER70-(NLS)-A.GLY74 (66 candidates, BB_DB)
+Resolved A.ILE171-(MN)-A.TRP174 by filling A.ILE168-(LFIMN)-A.TRP174 (88 candidates, BB_DB)
+Resolved A.ALA332-(EEEEDTV)-A.THR340 by filling A.ALA332-(EEEEDTV)-A.THR340 (829 candidates, BB_DB)
+Resolved A.MET535-()-A.GLU536 by filling A.MET535-(EGR)-A.THR539 (62 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.2741e+21)
+Perform energy minimization (iteration 2, energy: 36652.8)
+No more stereo-chemical problems -> final energy: 31585.1
+
+
+Build model with the following alignment:
+target GAMSEEKNLKTASVLSFERKLDPSDALFFSGNWSNKSDDKAWQPIHLREKSVRGTISNRL
+pdb_id=6b47, cha... -------ILSTASVLAFERKLDPSDALMSAGAWAQRDASQEWPAVTVREKSVRGTISNRL
+
+target KKGEA-DPAKLNAAIEKPNLQTVDVATLPFDSDTLKVEFTLRVLGGVGEPAACNSMEYRS
+pdb_id=6b47, cha... KTK-DRDPAKLDASIQSPNLQTVDVANLPSDADTLKVRFTLRVLGGAGTPSACNDAAYRD
+
+target KLVATISHYIDTHGLDILGNRYAANLANGRFLWRNRLGADAISIQITRLSGDESTLVGVF
+pdb_id=6b47, cha... KLLQTVATYVNDQGFAELARRYAHNLANARFLWRNRVGAEAVEVRINHIRQGEVARAWRF
+
+target DALAHPLRQFEEKSVSEELEALAKLITAGLAGQEHVLLRVKAFIRMGEGQEVFPSQELLL
+pdb_id=6b47, cha... DALAIGLRDFKADA--E-LDALAELIASGLSGSGHVLLEVVAFARIGDGQEVFPSQELIL
+
+target DK--GKSTKSRFLYSVGQDEKAIAAIHSQKIGNALRTIDTWYPDAEINGPIAVEPYGSVT
+pdb_id=6b47, cha... DKGDKKGQKSKTLYSVR----DAAAIHSQKIGNALRTIDTWYPDEDGLGPIAVEPYGSVT
+
+target TQGVAYRQPKAKKDFYSLLDAWVLKDKEPTIEDQHFVAAVLVRGGVFGDAS
+pdb_id=6b47, cha... SQGKAYRQPKQKLDFYTLLDNWVLRDEAPAVEQQHYVIANLIRGGVFGE--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Trying to merge 6 gap(s) with distance 0.
+Merged gap A.GLY63-(E)-A.ALA65 and A.ALA65-()-A.ASP66 into A.GLY63-(EA)-A.ASP66
+Merged gap A.SER193-(VS)-A.GLU196 and A.GLU196-(E)-A.LEU198 into A.SER193-(VSEE)-A.LEU198
+Trying to fill 4 gap(s) by database.
+Resolved A.GLY63-(EA)-A.ASP66 by filling A.LYS62-(GEA)-A.ASP66 (49 candidates, BB_DB)
+Resolved A.SER193-(VSEE)-A.LEU198 by filling A.GLU190-(EKSVSEE)-A.LEU198 (92 candidates, BB_DB)
+Resolved A.LYS241-()-A.GLY242 by filling A.LYS241-(GKST)-A.LYS246 (64 candidates, BB_DB)
+Resolved A.GLY254-(QDEK)-A.ALA259 by filling A.VAL253-(GQDEKA)-A.ILE260 (943 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.92571e+13)
+No more stereo-chemical problems -> final energy: 14507.8
+
+
+Build model with the following alignment:
+target MEALWLWIGFVGMLLGTLYFAFL-LTNAPEGTRYFFVITATITGIAAIAYLVMATGSGST
+pdb_id=3coc, cha... PEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLT
+
+target VLP---DGREFYWARYIDWVITTPLLLLDLCLLALADPRRNVTFIASLIALDVVMILTGL
+pdb_id=3coc, cha... MVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGT----ILALVGAAGIMIGTGL
+
+target WAGATVNVAGRAILFIISTAAFIGVLYLLVSRLFAEASRRTPAVAQIFRTLAVLTIVLWI
+pdb_id=3coc, cha... VGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWS
+
+target CYPIVWLIGTEGFGAVSLSVEVFLFMVLDLLAKVGFGLLLLSSRQALSD-IGSGAVAGTA
+pdb_id=3coc, cha... AYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG------------
+
+target RRVA
+pdb_id=3coc, cha... ----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.LEU23-()-A.LEU24 by relaxing A.PHE22-(LL)-A.THR25
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.PRO62-()-A.ASP63 by filling A.LEU61-(PDG)-A.ARG65 (49 candidates, BB_DB)
+Resolved A.ARG96-(NVTF)-A.ILE101 by filling A.ASP93-(PRRNVTF)-A.ILE101 (46 candidates, BB_DB)
+Rebuilding sidechains.
+Trying to fix 1 ring punch(es).
+Trying to fill 1 gap(s) by database.
+Resolved A.LEU61-(P)-A.ASP63 by filling A.VAL60-(LPDG)-A.ARG65 (86 candidates, BB_DB)
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.07539e+14)
+No more stereo-chemical problems -> final energy: 12444.4
+
+
+Build model with the following alignment:
+target MATSFDNLLYDLDAATGVLTLTVNRPAKLNALNAATIAELDTAAQQALADPAVRAILLTG
+pdb_id=4jwv, cha... -----ADIDFR--IEGHVAHVRLNRPQGLNAITQEMDDLLLDAWTEVNANSDIWAVVLSA
+
+target SGEKAFVAGADIAELASLTAVQAAGASAYGQRVFAQFERSPKPVVAAVNGFALGGGCELA
+pdb_id=4jwv, cha... EGEKAFCIGADV-----RKT-R-MALGGGLTGIGGPLVTCKKPMVAAVQGFCVGGGFELA
+
+target MACHLRVAADTARFGLPEVSLGLLPGYGGTQRLPQLVGKAKALELMLTADMIKADEALRL
+pdb_id=4jwv, cha... MCADIIVAADTAQFGLPETKVGIIGECGVVHRAMRQLPYHIALQLILTGERIKADEARHY
+
+target GLVNHVVPLAELLGFCQQLLAKMLSKGPVALGLVIECVNAGYD-PRQDGYVAETEAFGRA
+pdb_id=4jwv, cha... GLVNEVVPFAELEEAALRWASKLNAASPLAVQAAKAAALGRLGHPLEVALMTRFEPIEEY
+
+target FQTDDFKEGTQAFVEKRPAVFQGK
+pdb_id=4jwv, cha... AATEDKKEGERAAGERRKPVWTGK
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP223-()-A.PRO224 by relaxing A.GLY221-(YD)-A.PRO224
+Trying to merge 4 gap(s) with distance 0.
+Merged gap A.ALA80-(V)-A.GLN82 and A.GLN82-(A)-A.ALA84 into A.ALA80-(VQA)-A.ALA84
+Trying to fill 3 gap(s) by database.
+Resolved A.ASP11-(LD)-A.ALA14 by filling A.ASP11-(LDAA)-A.THR16 (49 candidates, BB_DB)
+Resolved A.ILE72-(AELAS)-A.LEU78 by filling A.ILE72-(AELAS)-A.LEU78 (286 candidates, BB_DB)
+Resolved A.ALA80-(VQA)-A.ALA84 by filling A.THR79-(AVQAA)-A.GLY85 (79 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.60816e+14)
+Perform energy minimization (iteration 2, energy: 15135.3)
+No more stereo-chemical problems -> final energy: 13311.9
+
+
+Build model with the following alignment:
+target MKNSLKMKNLLPALVITMAMSAVMSLCIAPNAYASKWDAKMTPEQVEATLDKKFAEGNYS
+pdb_id=2e84, cha... ------------------------------------------------------------
+
+target PKGADSCLMCHKKSEKVMDLFKGVHGAIDSSKSPMAGLQCEACHGPLGQHNKGGNEPMIT
+pdb_id=2e84, cha... ------------------------------------------------------------
+
+target FGKQSTLSAEKQNSVCMSCHQDD----KRVSWNGSHHDNADVACASCHQVHVAKDPVLSK
+pdb_id=2e84, cha... ----------DPQKNCGACHHVYDEAAKKLSWVK----NKEDSCRACHGDARVEKKPSLR
+
+target NTEMEVCTSCHTKQKADMNKRSSHPLKWAQMTCSDCHNPHGSMTDSDLNKPSINETCYSC
+pdb_id=2e84, cha... EAAHTQCITCHRSVAAAPAKA-----DSGPVSCAGCHDPAMQ------------------
+
+target HAEKRGPKLWEHAPVTENCVTCHNPHGSVNDAMLKTRAPQLCQQCHASDGHASNAYLGNT
+pdb_id=2e84, cha... ------------------------------------------------------------
+
+target GLGSNVGDNAFTGGRSCLNCHSQVHGSNHPSGKLLQR
+pdb_id=2e84, cha... -------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.ASP143-()-A.LYS144 by filling A.ASP143-(KRV)-A.SER147 (41 candidates, BB_DB)
+Resolved A.GLY150-(SHHD)-A.ASN155 by filling A.ASN149-(GSHHDN)-A.ALA156 (59 candidates, BB_DB)
+Resolved A.ARG197-(SSHPL)-A.LYS203 by filling A.ARG197-(SSHPLKW)-A.ALA205 (47 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.27122e+09)
+No more stereo-chemical problems -> final energy: 8554.55
+
+
+Build model with the following alignment:
+target MAHHHHHHGVRHVALSVDASEWRQPVFKQKVLAILRRLHVPRWSSPLLTPTNIHLQKVSG
+pdb_id=1nw1, cha... ------------------------PELKERAHMLCARFLGGAWKTV--PLEHLRISRIKG
+
+target ALTNAVFFVSFNPAPNPTSPSESPLLTPTIPPSDPSHPPPLTPEQYPHTLLFRVYGPSSD
+pdb_id=1nw1, cha... GMSNMLFLCRLSEVYPPI-------------------------RNEPNKVLLRVY-FNPE
+
+target ALISRSEELRILHVLSTQYGIGPRVFGTFTNGRVEEFFPSRALTAQELRDPIISRGIARR
+pdb_id=1nw1, cha... TESHLVAESVIFTLLS-ERHLGPKLYGIFSGGRLEEYIPSRPLSCHEISLAHMSTKIAKR
+
+target MRELHSVDLRRLGYEQGRATEPA-LWICLKEWSEAAEDVISSLTALGGTLEAWVERFSLH
+pdb_id=1nw1, cha... VAKVHQLEVPIW-------KEPDYLCEALQRWLKQLTGTVDAEHRFDLPEECGVSSVNCL
+
+target RIREEVTIYRNFVESQSGKGNGVVFAHNDTQYGNLLRLDVELP-----P-----------
+pdb_id=1nw1, cha... DLARELEFLRAHISL---SKSPVTFCHNDLQEGNILLPK---------------------
+
+target ---NTPEHCRYIVIDFEYASPNPRGYDIANHFHEWRANYHHPTHSHSLIPHFPYPTPIQR
+pdb_id=1nw1, cha... ---------RLVLIDFEYASYNYRAFDFANHFIEWTIDYDIDEAPFYKIQTENFPENDQM
+
+target EDFYRSYLSVEVDGRNGEEVVGKRKDVPADKVAALEHEVRIWSPGCSINWALWGLVQAEE
+pdb_id=1nw1, cha... LEFFLNYLREQGN-TR--------ENELYKKSEDLVQETLPFVPVSHFFWGVWGLLQVEL
+
+target QVCALATKKEGYVPEFDYLSYAAERLEMFRDEAKKLGVPL
+pdb_id=1nw1, cha... S-----------PVGFGFADYGRDRLSLYFKHK-QL----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA203-()-A.LEU204 by relaxing A.ALA203-(L)-A.TRP205
+Trying to merge 11 gap(s) with distance 0.
+Trying to fill 11 gap(s) by database.
+Resolved A.PRO46-(LL)-A.THR49 by filling A.SER44-(SPLL)-A.THR49 (102 candidates, BB_DB)
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Resolved A.TYR115-(G)-A.PRO117 by filling A.TYR115-(GPSS)-A.ASP120 (68 candidates, BB_DB)
+Resolved A.SER136-(T)-A.GLN138 by filling A.LEU135-(STQY)-A.GLY140 (45 candidates, BB_DB)
+Resolved A.LEU192-(GYEQGRA)-A.THR200 by filling A.LEU189-(RRLGYEQGRA)-A.THR200 (139 candidates, BB_DB)
+Resolved A.SER254-(QSG)-A.LYS258 by filling A.VAL252-(ESQSGK)-A.GLY259 (68 candidates, BB_DB)
+Resolved A.ASP278-(VELPPNTPEHC)-A.ARG290 by filling A.ASP278-(VELPPNTPEHCR)-A.TYR291 (98 candidates, BB_DB)
+Resolved A.ASP353-(G)-A.ARG355 by filling A.VAL350-(EVDGR)-A.ASN356 (60 candidates, BB_DB)
+Resolved A.ASN356-(GEEVVGKR)-A.LYS365 by filling A.VAL352-(DGRNGEEVVGKR)-A.LYS365 (75 candidates, BB_DB)
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 0 candidates
+Resolved A.ALA433-(K)-A.LYS435 by filling A.GLU432-(AKK)-A.LEU436 (137 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104), only 0 candidates
+Failed at loop insertion (A.GLN401-(VCALATKKEGY)-A.VAL413), only 2 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.THR78-(SPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104 by filling A.ASN76-(PTSPSESPLLTPTIPPSDPSHPPPLTP)-A.GLU104 (7 candidates, BB)
+Resolved A.GLN401-(VCALATKKEGY)-A.VAL413 by filling A.GLN401-(VCALATKKEGYV)-A.PRO414 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.54324e+21)
+Perform energy minimization (iteration 2, energy: 14363)
+Perform energy minimization (iteration 3, energy: 7588.28)
+No more stereo-chemical problems -> final energy: 5232.2
+
+
+Build model with the following alignment:
+target MRGSHHHHHHSGQRMGMVIGIKPEHIDEYKRLHAAVWPAVLARLAEAHVRNYSIFLREPE
+pdb_id=1x8d, cha... --------------KAFVMQVNPDAHEEYQRRHNPIWPELEAVLKSHGAHNYAIYLDKAR
+
+target NLLFGYWEYHGTDYAADMEAIAQDPETRRWWTFCGPCQEPLASRQPGEHWAHMEEVFHVD
+pdb_id=1x8d, cha... NLLFAMVEI--ES-EERWNAVASTDVCQRWWKYMTDVMPANPDNSPVS--SELQEVFYLP
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.TYR69-(HG)-A.THR72 by filling A.TYR66-(WEYHGT)-A.ASP73 (75 candidates, BB_DB)
+Resolved A.ASP73-(Y)-A.ALA75 by filling A.TYR69-(HGTDY)-A.ALA75 (59 candidates, BB_DB)
+Resolved A.GLU108-(HW)-A.ALA111 by filling A.GLY107-(EHWA)-A.HIS112 (42 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.57274e+06)
+Perform energy minimization (iteration 2, energy: 4554.89)
+No more stereo-chemical problems -> final energy: 3981.74
+
+
+Build model with the following alignment:
+target GHMTGTNTHSDVWIRQYRPAHPTAPQLICLPHAGGSATFYHPVAAALAPRCDVLAVQYPG
+pdb_id=3fla, cha... ---------AEKWLRRFERAPDARARLVCLPHAGGSASFFFPLAKALAPAVEVLAVQYPG
+
+target RQDRRAEKPLEDIDELANQLFPVLRARVHQPVALFGHSMGATLAFELARRFE-SAGISLE
+pdb_id=3fla, cha... RQDRRHEPPVDSIGGLTNRLLEVLRPFGDRPLALFGHSMGAIIGYELALRMPEAGLPAPV
+
+target ALLVSARPAPSRQRTGGTVHLLSDEELVAELRTLDGTAEQVFHDEELVRMALPAIRGDYR
+pdb_id=3fla, cha... HLFASGRRAPSRYRD-DDVRGASDERLVAELRKLGGSDAAMLADPELLAMVLPAIRSDYR
+
+target AAETYRYRPGPKLRCPIHALTGDDDPMVTPVEARAWSEHTDGPFTLDTFAGGHFYLLEHR
+pdb_id=3fla, cha... AVETYRHEPGRRVDCPVTVFTGDHDPRVSVGEARAWEEHTTGPADLRVLPGGHFFLVDQA
+
+target DAILGIIAEHLRTCSRAPGDRSGLTRE
+pdb_id=3fla, cha... APMIATMTEKLA---------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.GLU112-()-A.SER113 by relaxing A.ARG110-(FES)-A.ALA114
+Trying to fill 1 gap(s) by database.
+Resolved A.THR134-(G)-A.GLY136 by filling A.ARG133-(TGG)-A.THR137 (72 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.12494e+10)
+Perform energy minimization (iteration 2, energy: -3203.08)
+No more stereo-chemical problems -> final energy: -4624
+
+
+Build model with the following alignment:
+target LILDFNKVQMRSQQLAPGVYAHLPADSAELNAKGGVAGTSGGLIVGTRGAMLIETMLNRR
+pdb_id=2cfu, cha... ---------YGLFEVAEGIYQVRGFDL-----------ANITFIRGDSGWIVVDTLTTPA
+
+target LFDQVQALAKK-EALGLPLLYAVNTSYHGDHSYGNMYLKA-------PTRVIQSTKTRDY
+pdb_id=2cfu, cha... TARAAYELVSRELG-ERPIRTVIYSHAHADHFGGVRGLVEPQQVASGAVQIIAPAGFMEA
+
+target VDGHLADDK----AFMVK---NFGA-GRGVE----------QITARTGDILVPPGGRVS-
+pdb_id=2cfu, cha... A----I---VLAGNAMMRRATYQYGTQLPKGPQGQVDMAIGKGLARGPLSLLAPTRLIEG
+
+target ----VDLGGKTVEIIDFGFAQ-TGGDLFVWEPQSKVMWTGNAVVASKPALPWLLDG---K
+pdb_id=2cfu, cha... EGEDLVLDGVPFTF-QNTPGTESPAEMNIWLPRQKALLMAENVVGTLHNLYTLRGAEVRD
+
+target LV---ETLATLQKVYDFLPPDATIVPGHG-VPMA----REGLRWHLDYLAAVQAGVKDAL
+pdb_id=2cfu, cha... ALGWSKYINQALHRFG--RQAEVMFAVHNWPRWGNAEIVEVLEKQRDLYGYLHDQTLHLA
+
+target ARKLSLEQTVTELKMPE--FRGYVLFDFVHPDLNVPAAYENLYFQ
+pdb_id=2cfu, cha... NQGVTIGQVHNRLRLPPSLDQEWYD--------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 18).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA99-()-A.PRO100 by relaxing A.LYS98-(APT)-A.ARG102
+Closed: A.ALA130-()-A.GLY131 by relaxing A.GLY129-(AG)-A.ARG132
+Closed: A.ALA235-()-A.ARG236 by relaxing A.PRO233-(MA)-A.ARG236
+Trying to merge 15 gap(s) with distance 0.
+Merged gap A.VAL113-(DGHL)-A.ALA118 and A.ALA118-(DDK)-A.ALA122 into A.VAL113-(DGHLADDK)-A.ALA122
+Trying to fill 14 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 0 candidates
+Resolved A.LYS71-()-A.GLU72 by filling A.LEU68-(AKKE)-A.ALA73 (70 candidates, BB_DB)
+Resolved A.ALA73-(L)-A.GLY75 by filling A.LYS71-(EAL)-A.GLY75 (47 candidates, BB_DB)
+Resolved A.VAL113-(DGHLADDK)-A.ALA122 by filling A.VAL113-(DGHLADDK)-A.ALA122 (578 candidates, BB_DB)
+Resolved A.LYS126-()-A.ASN127 by filling A.LYS126-(NFGAG)-A.ARG132 (151 candidates, BB_DB)
+Resolved A.GLU135-()-A.GLN136 by filling A.GLY133-(VEQI)-A.THR138 (166 candidates, BB_DB)
+Resolved A.SER153-()-A.VAL154 by filling A.GLY149-(GRVSV)-A.ASP155 (247 candidates, BB_DB)
+Resolved A.ILE163-(I)-A.ASP165 by filling A.ILE163-(IDFG)-A.PHE168 (69 candidates, BB_DB)
+Resolved A.GLN170-()-A.THR171 by filling A.PHE168-(AQTGG)-A.ASP174 (49 candidates, BB_DB)
+Resolved A.GLY204-()-A.LYS205 by filling A.LEU198-(PWLLDG)-A.LYS205 (86 candidates, BB_DB)
+Resolved A.VAL207-()-A.GLU208 by filling A.ASP203-(GKLV)-A.GLU208 (84 candidates, BB_DB)
+Resolved A.ASP218-(FL)-A.PRO221 by filling A.ASP218-(FLPPDA)-A.THR225 (83 candidates, BB_DB)
+Resolved A.GLY231-()-A.VAL232 by filling A.PRO228-(GHGV)-A.PRO233 (74 candidates, BB_DB)
+Resolved A.GLU274-()-A.PHE275 by filling A.LYS271-(MPE)-A.PHE275 (169 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER27-(AELNAKGGVAG)-A.THR39), only 1 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.SER27-(AELNAKGGVAG)-A.THR39 by filling A.ASP26-(SAELNAKGGVAG)-A.THR39 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8.79886e+17)
+Perform energy minimization (iteration 2, energy: 29156.9)
+Perform energy minimization (iteration 3, energy: 20109.5)
+No more stereo-chemical problems -> final energy: 17682
+
+
+Build model with the following alignment:
+target ADEFLPTPAPRVTVYVDP-PAYPMPRYNYTERWHTT-GPIPSPFADGREQPVEVRYA-TS
+pdb_id=5x5v, cha... -------------------PTFPPPAYPYTESWQLTLTTVPSPFVG----PADVYHTRPL
+
+target AAACDMLALIADPQVGRTLWEAVRRHARAYNATVIWYKIESGCARPLYYMEYTECEPRKH
+pdb_id=5x5v, cha... EDPCGVVALISDPQVDRLLNEAVAHRRPTYRAHVAWYRIADGCAHLLYFIEYADCDPRQV
+
+target FGYCRYRTPPFWDSFLAGFAYPTDDELGLIMAAPARLVEGQYRRALYIDGTVAYTDFMVS
+pdb_id=5x5v, cha... FGRCRRRTTPMWWTPSADYMFPTEDELGLLMVAPGRFNEGQYRRLVSVDGVNILTDFMVA
+
+target LPAG-DCWFSKLGAARGYTFGACFPARDYEQKKVLRLTYLTQYYPQEAHKAIVDYWFMRH
+pdb_id=5x5v, cha... LPEGQECPFARVDQHRTYKFGACWSDDSFKRG-VDVMRFLTPFYQQPPHREVVNYWYRKN
+
+target GGVVPPYFEESKGYEPPPAADGG-SPAP---------------------PGDDEAREDEG
+pdb_id=5x5v, cha... GRTLPRAYAAATPYAIDPAR----------------------------------------
+
+target ETEDGAAGREGNGGP-PGPEGDGESQTPEANGHHHHHH
+pdb_id=5x5v, cha... --------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.THR35-()-A.GLY36 by relaxing A.THR34-(TG)-A.PRO37
+Closed: A.ALA55-()-A.THR56 by relaxing A.TYR54-(ATS)-A.ALA58
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.ASP44-(GREQ)-A.PRO49 by filling A.ALA43-(DGREQP)-A.VAL50 (66 candidates, BB_DB)
+Resolved A.GLY181-()-A.ASP182 by filling A.LEU178-(PAG)-A.ASP182 (56 candidates, BB_DB)
+Resolved A.LYS208-(K)-A.VAL210 by filling A.GLN207-(KKV)-A.LEU211 (42 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.6561e+20)
+No more stereo-chemical problems -> final energy: 5936.73
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPAGSHMADYYTIAANPGSGKRGLAYNNINLLTAFEGGPFSWSYNW
+pdb_id=5u22, cha... ------------------------------------------------------------
+
+target EPRPGGYTAGIEYVPML---WGP-----RGYGSWNADAEAGIA----AGSKNL---LAFN
+pdb_id=5u22, cha... -------SPGARVTIELADILPGWPYRWPGIQTWFNEIRSFINDKKKSGLTNFYGNEIWN
+
+target EPDIASQANMSPEAA-AAAYQKYMNPYAAR---ARLGSPAVSNGAPPKGLGWMQGFLDVC
+pdb_id=5u22, cha... EPDVTW--KDSNGLSFNQMWKQTYDLLRQIDPNEKIIGPSFSWY----EENKMKNFLQFS
+
+target A-GNCKIDFLAVHWHGPSGNVDDFKRYVSEAIALGQKYG--IGTVWVTEFEGQ-----GD
+pdb_id=5u22, cha... KQNNCLPDIIAWHELSG---IDGVSSHFRSYRNLEKSLGISERPITINEYCDENHDLEGQ
+
+target EEAQVNFLKEVLPWLDSNAGVERYASFFVDNLVKGGALTSVGKAYKTI
+pdb_id=5u22, cha... PGSSARFIGR--------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA95-()-A.ALA96 by relaxing A.ILE94-(AAG)-A.SER98
+Closed: A.ALA120-()-A.ALA121 by relaxing A.ALA120-(A)-A.ALA122
+Closed: A.ALA162-()-A.GLY163 by relaxing A.CYS161-(AGN)-A.CYS165
+Trying to merge 9 gap(s) with distance 0.
+Trying to fill 9 gap(s) by database.
+Resolved A.LEU77-()-A.TRP78 by filling A.LEU77-(WGPR)-A.GLY82 (68 candidates, BB_DB)
+Resolved A.LEU101-()-A.LEU102 by filling A.ALA95-(AGSKNL)-A.LEU102 (69 candidates, BB_DB)
+Resolved A.SER111-(QA)-A.ASN114 by filling A.ILE109-(ASQA)-A.ASN114 (47 candidates, BB_DB)
+Resolved A.ARG134-()-A.ALA135 by filling A.TYR131-(AARA)-A.ARG136 (75 candidates, BB_DB)
+Resolved A.GLY145-(APPK)-A.GLY150 by filling A.ASN144-(GAPPKG)-A.LEU151 (45 candidates, BB_DB)
+Resolved A.PRO177-(SGN)-A.VAL181 by filling A.HIS175-(GPSGNV)-A.ASP182 (58 candidates, BB_DB)
+Resolved A.GLY199-()-A.ILE200 by filling A.GLY195-(QKYG)-A.ILE200 (78 candidates, BB_DB)
+Resolved A.GLN211-()-A.GLY212 by filling A.PHE208-(EGQG)-A.ASP213 (70 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.46931e+12)
+Perform energy minimization (iteration 2, energy: 16875.6)
+No more stereo-chemical problems -> final energy: 15178.8
+
+
+Build model with the following alignment:
+target MAHHHHHHMRRKIVAGNWKLHGSRQFANELLGQVAAGLPL---EGVDVVILPPLPYLGEL
+pdb_id=4y9a, cha... -----------PLMAGNWKMNLNHLEAIAHVQKLAFALADKDYDAVEVAVLAPFTDLRSV
+
+target VEDFGET--GLAFGAQDVSSNEKGAYTGEVCAAMLVEVGARYGLVGHSERRQYHHESSEL
+pdb_id=4y9a, cha... QTLVDGDKLKIKYGAQDISAHDGGAYTGEISGPMLAKLKCTYVAVGHSERRQYHAETDEI
+
+target VARKFAAAQHAGLVPVLCVGETLEQREAGQTEAVIASQLAPVLELVGAAGFAQAVVAYEP
+pdb_id=4y9a, cha... VNAKVKAAYKHGLTPILCVGEELDVREAGNHVEHTLAQVEGGLKDLAAEQAESVVIAYEP
+
+target VWAIGTGRTATKEQAQQVHAFIRGEVARI-DARIADSLPIVYGGSVKPDNAGELFAQPDV
+pdb_id=4y9a, cha... VWAIGTGKVCGADDAQEVCAAIRGKLAELYSQELADKVRIQYGGSVKSGNVAEIMAKPDI
+
+target DGGLVGGASLVAADFLAIARAAAAN
+pdb_id=4y9a, cha... DGALVGGASLDSDEFVKIVRFR---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.LEU40-()-A.GLU41 by filling A.GLY37-(LPLE)-A.GLY42 (54 candidates, BB_DB)
+Resolved A.THR64-()-A.GLY65 by filling A.ASP60-(FGET)-A.GLY65 (50 candidates, BB_DB)
+Resolved A.ILE204-()-A.ASP205 by filling A.ALA202-(RIDA)-A.ARG207 (55 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.26768e+15)
+No more stereo-chemical problems -> final energy: 14857.1
+
+
+Build model with the following alignment:
+target GSHMGD----LK--------------YSLERLREILERLEENPSEKQIVEAIRAIVENNA
+pdb_id=6n9h, cha... -----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNK
+
+target QIVEAIRAIVENNAQIVENNRAIIEALEAIGVDQKILEEMKKQLKDLKRSLERG
+pdb_id=6n9h, cha... IIVEVLRIILE-------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4909.43)
+No more stereo-chemical problems -> final energy: -2129.53
+
+
+Build model with the following alignment:
+target MAFSDLTSRTVHLYDNWIKDADPRVEDWLLMSSPLPQTILLGFYVYFVTSLGPKLMENRK
+pdb_id=5yq7, cha... ------------------------------------------------------------
+
+target PFELKKAMITYNFFIVLFSVYMCYEFVMSGWGIGYSFRCDIVDYSRSPTALRMARTCWLY
+pdb_id=5yq7, cha... PFEFRTSVVVSTLLGLVMALLI--------------------------------------
+
+target YFSKFIELLDTIFFVLRKKNSQVTFLHVFHHTIMPWTWWFGVKFAAGGLGTFHALLNTAV
+pdb_id=5yq7, cha... ------------------------------------------------------------
+
+target HVVMYSYYGLSALGPAYQKYLWWKKYLTSLQLVQFVIVAIHISQFFFMEDCKYQFPVFAC
+pdb_id=5yq7, cha... ------------------------------------------------------------
+
+target IIMSYSFMFLLLFLHFWYRAYTKGQRLPKTVKNGTCKNKDNAENLYFQ
+pdb_id=5yq7, cha... ------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6509.14)
+No more stereo-chemical problems -> final energy: 3116.78
+
+
+Build model with the following alignment:
+target MIDLIVSQGRVADRAAWMIEGAARTARALEERYGLKGHYVGEPAPHAD---D-DWSVALP
+pdb_id=6dkt, cha... --DLGQ-ARRGVDMGPSAIRYAHLIER-L-SDMGYTVEDLGDIPIN-----------NLN
+
+target QARETLVAVREAATESIKGDNLTVLVNNTCSVSLATLPVVAREHPDAVVLYIDGHGDFNT
+pdb_id=6dkt, cha... SVLAGNEKLAQKVNKVIEEKKFPLVLGGDHSIAIGTLAGTAKHYDNLGVIWYDAHGDLNT
+
+target PETTDTGYLGGMVLSGACGL----WDSGHGA--GLRPEQAVLVGSRDIDEGERELIRKAG
+pdb_id=6dkt, cha... LETSPSGNIHGMPLAVSLGIGHESLVNLEGYAPKIKPENVVIIGARSLDEGERKYIKESG
+
+target VRVIPPGEAT-------AQAVLDAV-KDAPVWIHIDWDVLEPGSIPA-DYTVPDGMLPAQ
+pdb_id=6dkt, cha... MKVYTMHEIDRLGMTKVIEETLDYLSACDGVHLSLDLDGLDPNDAPGVGTPVVGGISYRE
+
+target IRAVFEAIPAE-RLIGVELAELNAPADSERAEQAVAVILDMVAPAFDAAAARPLEHHHHH
+pdb_id=6dkt, cha... SHLAMEMLYDAGIITSAEFVEVNPILDHKNK--TGKTAVELVESLLGK------------
+
+target H
+pdb_id=6dkt, cha... -
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.VAL188-()-A.LYS189 by relaxing A.ALA187-(VKDA)-A.PRO192
+Closed: A.ALA209-()-A.ASP210 by relaxing A.PRO208-(AD)-A.TYR211
+Trying to merge 9 gap(s) with distance 0.
+Merged gap A.ARG27-(A)-A.LEU29 and A.LEU29-(E)-A.GLU31 into A.ARG27-(ALE)-A.GLU31
+Trying to fill 8 gap(s) by database.
+Resolved A.VAL6-(S)-A.GLN8 by filling A.ASP3-(LIVS)-A.GLN8 (40 candidates, BB_DB)
+Resolved A.ARG27-(ALE)-A.GLU31 by filling A.ARG27-(ALEERYG)-A.LEU35 (124 candidates, BB_DB)
+Resolved A.HIS46-(ADDDWSV)-A.ALA54 by filling A.HIS46-(ADDDWSV)-A.ALA54 (85 candidates, BB_DB)
+Resolved A.LEU136-()-A.TRP137 by filling A.SER131-(GACGL)-A.TRP137 (60 candidates, BB_DB)
+Resolved A.ALA143-()-A.GLY144 by filling A.GLY140-(HGAG)-A.LEU145 (74 candidates, BB_DB)
+Resolved A.THR180-()-A.ALA181 by filling A.GLY177-(EAT)-A.ALA181 (49 candidates, BB_DB)
+Resolved A.GLU232-()-A.ARG233 by filling A.ALA231-(ERLI)-A.GLY236 (41 candidates, BB_DB)
+Resolved A.ALA251-(EQ)-A.ALA254 by filling A.ASP247-(SERAEQ)-A.ALA254 (108 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.00254e+21)
+Perform energy minimization (iteration 2, energy: 17322.6)
+No more stereo-chemical problems -> final energy: 13323.4
+
+
+Build model with the following alignment:
+target PETTVLSGRDRLKRHREEVAGKVPIPDSWGKEGLLMGWMDFSTFDAAFTSSQIVSARAAL
+pdb_id=3h0w, cha... -----------------------------GTEKLLEVWFSRQQP----------------
+
+target MADSGHHHHHH
+pdb_id=3h0w, cha... -----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6425.74)
+No more stereo-chemical problems -> final energy: 2646.33
+
+
+Build model with the following alignment:
+target MCELYSKRDTLGLRKKHIGPSCKVFFA-----SDPIKIVRAQRQYMFDENGEQYLDCINN
+pdb_id=5kr3, cha... -----SLDQLFEMDRAHFMHPSTHAHDHASGALPGRIITGGKGIRIEDHEGREYIDAFAG
+
+target VA--HVGHCHPGVVKAALKQMELL-NTNS--RFLHDNIVEYAKRLS-ATLPEKLSVCYFT
+pdb_id=5kr3, cha... LYCVNIGYGRTEVADAIYEQAKQLAYYHTYVGHSTDAIIELSSRIIRDWAPAGMKKVYYG
+
+target NSGSEANDLALRLARQF------RGHQDVITLDHAYHGHLSSLIEISPYKFQK-GKDVKK
+pdb_id=5kr3, cha... MSGSDANETQIKLVWYYNNVLGRPNKKKIISRERGYHGSGIVTGSLTGLPSFHQHFDLPI
+
+target EFVHVAPTPDTYRGKYREDHADSASAYADEVKKIIEDAHNSGRKIAAFIAESMQSCGGQI
+pdb_id=5kr3, cha... DRVKHTVCPHWYRAP--MSEAQFVAYCVEELEKLIA--REGADTIAAFIAEPVMGTGGII
+
+target IPPAGYFQKVAEYVHGAGGVFIADEVQVGFGRVGKHFWSFQMYGEDFVPDIVTMGKPMGN
+pdb_id=5kr3, cha... PPPQGYWEAIQAVLRKHDILLIADEVVCGFGRLGS-KMGSQHYG--IKPDLITVAKGLTS
+
+target G-HPVACVVTTKEIAEAFSSS-----GMEYFNTYGGNPVSCAVGLAVLDIIENEDLQGNA
+pdb_id=5kr3, cha... AYAPLSGVIVGEKVWDVIEKGSQEHGPMGHGWTYSGHPICAAAALANLDILERENLTGNA
+
+target KRVGNYLTELLKKQKAKHTLIGDIRGIGLFIGIDLVKDHLKRTPATA---EAQHIIYKMK
+pdb_id=5kr3, cha... ADVGAYLQQRLHEAFGAHPLVGEVRGVGMLAALEFMADKDARTPFDPALKVGPKVSAAAL
+
+target EKRVLLSADGPHRNVLKIKPPMCFTEEDAKFMVDQLDRILTVLEEAMGTKTESVTSENTP
+pdb_id=5kr3, cha... EDGMIARAMP-HGDILGFAPPLVTTRAEVDEIVGIAKQAVDEVAD---------------
+
+target CKTKMLKEAHIELLRDSTTDSKENPSRKRNGMCTDTHSLLSKRLKT
+pdb_id=5kr3, cha... ----------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA27-()-A.SER28 by relaxing A.PHE26-(AS)-A.ASP29
+Closed: A.LEU77-()-A.ASN78 by relaxing A.LEU77-(N)-A.THR79
+Closed: A.SER96-()-A.ALA97 by relaxing A.ARG94-(LSA)-A.THR98
+Closed: A.LYS156-()-A.GLY157 by relaxing A.LYS156-(GK)-A.ASP159
+Trying to merge 11 gap(s) with distance 0.
+Trying to fill 11 gap(s) by database.
+Resolved A.ALA57-()-A.HIS58 by filling A.ALA57-(HVGHCH)-A.PRO64 (109 candidates, BB_DB)
+Resolved A.SER81-()-A.ARG82 by filling A.ASN78-(TNSRF)-A.LEU84 (47 candidates, BB_DB)
+Resolved A.PHE126-()-A.ARG127 by filling A.GLN125-(FRGH)-A.GLN130 (59 candidates, BB_DB)
+Resolved A.LYS177-(YR)-A.GLU180 by filling A.ARG175-(GKYR)-A.GLU180 (225 candidates, BB_DB)
+Resolved A.GLU198-(DA)-A.HIS201 by filling A.GLU198-(DAHNSG)-A.ARG205 (67 candidates, BB_DB)
+Resolved A.LYS257-(H)-A.PHE259 by filling A.ARG254-(VGKHFW)-A.SER261 (47 candidates, BB_DB)
+Resolved A.GLY266-(ED)-A.PHE269 by filling A.TYR265-(GEDF)-A.VAL270 (146 candidates, BB_DB)
+Resolved A.GLY283-()-A.HIS284 by filling A.ASN282-(GHP)-A.VAL286 (43 candidates, BB_DB)
+Resolved A.SER302-()-A.GLY303 by filling A.SER301-(SGMEY)-A.PHE307 (91 candidates, BB_DB)
+Resolved A.ALA383-()-A.GLU384 by filling A.THR379-(PATA)-A.GLU384 (41 candidates, BB_DB)
+Resolved A.GLY403-(P)-A.HIS405 by filling A.ALA401-(DGPH)-A.ARG406 (59 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.98181e+22)
+Perform energy minimization (iteration 2, energy: 28348.8)
+No more stereo-chemical problems -> final energy: 23898.8
+
+
+Build model with the following alignment:
+target AASSPLLIGDSVMVDIGNVFTKKIPNAQIDGKVGRQLVDATPIVKSQYKDYAAAGQKVVV
+pdb_id=5ug1, cha... -ADGTMLIGDSVALRANTALQTALPGAQINAQVSVTTKTANEIML-NNSQNKFLPKTVVI
+
+target ELGTN-GAFTKDQLNELLDSFG-KADIYLVSIRVPRDYE------GRINKLIYEAAEKRS
+pdb_id=5ug1, cha... ATGVNNPENYKDDWDSIVKNLPKGHHMILVTPYEGDKTKETYAIVEKAAAYMRELAEKTP
+
+target NVHLVDWYKASAGHPE-YFAYDGIHLEYA------GSKALTDLIVKTMETHATN
+pdb_id=5ug1, cha... YITIADWNQVAKEHPEIWAGTDQVHFGSESSTIEAGAKLYADTIATALQTAQD-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.ASN65-()-A.GLY66 by relaxing A.THR64-(NG)-A.ALA67
+Closed: A.GLY81-()-A.LYS82 by relaxing A.SER79-(FGKA)-A.ASP84
+Closed: A.GLU128-()-A.TYR129 by relaxing A.PRO127-(EY)-A.PHE130
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.LYS45-(S)-A.GLN47 by filling A.VAL44-(KSQ)-A.TYR48 (72 candidates, BB_DB)
+Resolved A.GLU97-()-A.GLY98 by filling A.VAL92-(PRDYE)-A.GLY98 (215 candidates, BB_DB)
+Resolved A.ALA140-()-A.GLY141 by filling A.ILE135-(HLEYA)-A.GLY141 (41 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.36639e+15)
+Perform energy minimization (iteration 2, energy: 14293.4)
+No more stereo-chemical problems -> final energy: 11935
+
+
+Build model with the following alignment:
+target DLQLLHQKVEEQAAKYKHRVPKKCCYDGARENKYETCEQRVARVTIGPHCIRAFNECCTI
+pdb_id=4p3a, cha... NLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTI
+
+target ADKIRKNISHKFAPAAR
+pdb_id=4p3a, cha... ANKIRKES---------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7732.57)
+Perform energy minimization (iteration 2, energy: -1548.27)
+No more stereo-chemical problems -> final energy: -1722.46
+
+
+Build model with the following alignment:
+target GSSGKNDESGIPIANAKLDDVADLLGGALFLPLYKWMNEYGPIYRLAAGPRNFVIVSDPA
+pdb_id=6j94, cha... ------------------------RNEAFFIPLYELFLTYGGIFRLTFGPKSFLIVSDPS
+
+target IAKHVLRNYPK-YAKGLVAEVSEFLFGSGFAIAEGPLWTARRRAVVPSLHRRYLSVIVER
+pdb_id=6j94, cha... IAKHILKDNAKAYSKGILAEILDFVMGKGLIPADGEIWRRRRRAIVPALHQKYVAAMIS-
+
+target VFCKCAERLVEKLQPYAEDGSAVNMEAKFSQMTLDVIGLSLFNYNFDSLTTDSPVIEAVY
+pdb_id=6j94, cha... LFGEASDRLCQKLDAAALKGEEVEMESLFSRLTLDIIGKAVFNYDFDSLTNDTGVIEAVY
+
+target TALKEAELRSTDLLPYWKIDALCKIVPRQVKAEKAVTLIRETVEDLIAKCKEIVEREGER
+pdb_id=6j94, cha... TVLREAEDRSVSPIPVWDIPIWKDISPRQRKVATSLKLINDTLDDLIATCKRMVEEEELQ
+
+target INDEEYVNDADPSILRFLLASREEVSSVQLRDDLLSMLVAGHETTGSVLTWTLYLLSKNS
+pdb_id=6j94, cha... F-HEEYMNERDPSILHFLLASGDDVSSKQLRDDLMTMLIAGHETSAAVLTWTFYLLTTEP
+
+target SALRKAQEEVDRVLEGRNPAFEDIKELKYITRCINESMRLYPHPPVLIRRAQVPDILPGN
+pdb_id=6j94, cha... SVVAKLQEEVDSVIGDRFPTIQDMKKLKYTTRVMNESLRLYPQPPVLIRRS-IDNDILGE
+
+target YKVNTGQDIMISVYNIHRSSEVWEKAEEFLPERFDIDGAIPNETNTDFKFIPFSGGPRKC
+pdb_id=6j94, cha... YPIKRGEDIFISVWNLHRSPLHWDDAEKFNPERWPLDGPNPNETNQNFSYLPFGGGPRKC
+
+target VGDQFALMEAIVALAVFLQRLNVELVPDQT-ISMTTGATIHTTNGLYMKVSQR
+pdb_id=6j94, cha... IGDMFASFENVVAIAMLIRRFNFQIAPGAPPVKMTTGATIHTTEGLKLTVTKR
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.LYS71-()-A.TYR72 by relaxing A.PRO70-(K)-A.TYR72
+Closed: A.THR449-()-A.ILE450 by relaxing A.ASP447-(QT)-A.ILE450
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLU118-(R)-A.VAL120 by filling A.ILE116-(VER)-A.VAL120 (92 candidates, BB_DB)
+Resolved A.ILE240-(N)-A.ASP242 by filling A.ARG239-(IND)-A.GLU243 (51 candidates, BB_DB)
+Resolved A.ALA350-(Q)-A.VAL352 by filling A.ALA350-(QVPD)-A.ILE355 (126 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.53531e+09)
+Perform energy minimization (iteration 2, energy: 9282.51)
+Perform energy minimization (iteration 3, energy: 6645.58)
+Perform energy minimization (iteration 4, energy: 5507.11)
+No more stereo-chemical problems -> final energy: 4899.91
+
+
+Build model with the following alignment:
+target PTLEVYLPQGHAVERKASLIQGLTQATVDAIGAPAESVRILLSELPATNIGLGG-----T
+pdb_id=2aaj, cha... -LLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYG
+
+target LTPSALPVIIAILIAGRTDAQKKALIAQLSETIAAVLDAPLQSTRVMIKDIPNTDFGIGG
+pdb_id=2aaj, cha... RSS-AVVLLTV-ISRPRSESQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGR
+
+target QTARALGR
+pdb_id=2aaj, cha... GRA-----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLY54-()-A.THR55 by filling A.LEU52-(GGTL)-A.THR57 (43 candidates, BB_DB)
+Resolved A.PRO58-(S)-A.ALA60 by filling A.THR57-(PSA)-A.LEU61 (55 candidates, BB_DB)
+Resolved A.ALA66-(I)-A.LEU68 by filling A.ALA66-(ILIA)-A.GLY71 (103 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.26655e+11)
+No more stereo-chemical problems -> final energy: 9460.42
+
+
+Build model with the following alignment:
+target MFRRSLNRFCAGEEKRVGTRTVFVGNHPVSETEAYIAQRFCDNRIVSSKYTLWNFLPKNL
+pdb_id=6roh, cha... ------------------PRVIHINDSLAN-----SSFGYSDNHISTTKYNFATFLPKFL
+
+target FEQFRRIANFYFLIIFLVQVTVD-TPTSPVTSGLPLFFVITVTAIKQGYEDWLRHRADNE
+pdb_id=6roh, cha... FQEFSKYANLFFLCTSAIQQVPHVSPTNRYTTIGTLLVVLIVSAMKECIEDIKRANSDKE
+
+target VNKSTVYIIENAK--RVRKESEKIKVGDVVEVQADETFPCDLILLSSCTTDGTCYVTTAS
+pdb_id=6roh, cha... LNNSTAEIFSEAHDDFVEKRWIDIRVGDIIRVKSEEPIPADTIILSSSEPEGLCYIETAN
+
+target LDGESNCKTHYAVRDTIALCTAESIDTLRAAIECEQPQPDLYKFVGRINIYSNSLEAVAR
+pdb_id=6roh, cha... LDGETNLKIKQSRVETAKFIDVKTLKNMNGKVVSEQPNSSLYTYEGTMTLN-D----RQI
+
+target SLGPENLLLKGATLKNTEKIYGVAVYTGMETKMALNYQGKSQKRSAVEKSINAFLIVYLF
+pdb_id=6roh, cha... PLSPDQMILRGATLRNTAWIFGLVIFTGHETKLLRNATATPIKRTAVEKIINRQIIALFT
+
+target ILLTKAAVCTTLKYVWQSTPYNDEPWYNQKTQKERETLKVLKMFTDFLSFMVLFNFIIPV
+pdb_id=6roh, cha... VLIVLILISSIGNVIMSTADA-KHLSYLYLEGTNK-A---GLFFKDFLTFWILFSNLVPI
+
+target SMYVTVEMQKFLGSFFISWDKDFYDEEINEGALVNTSDLNEELGQVDYVFTDKTGTLTEN
+pdb_id=6roh, cha... SLFVTVELIKYYQAFMIGSDLDLYYEKTDTPTVVRTSSLVEELGQIEYIFSDKTGTLTRN
+
+target SMEFIECCIDGHKYKGVTQEVDG--------LSQTDG-TLTYF-D---KVDKNREELFLR
+pdb_id=6roh, cha... IMEFKSCSIAGHCYIDKIPEDKTATVEDGIEVGYRKFDDLKKKLNDPSDEDSPIINDFLT
+
+target ALCLCHTVEIKTNDAVDGATESAELTYISSSPDEIALVKGAKRYGFTFLGNRNGYMRVEN
+pdb_id=6roh, cha... LLATCHTVIPEFQSD-------GSIKYQAASPDEGALVQGGADLGYKFIIRKPNSVTVLL
+
+target -QRKEIEEYELLHTLNFDAVRRRMSVIVKTQEGDILLFCKGADSAVFPRV-QNH--EIEL
+pdb_id=6roh, cha... EETGEEKEYQLLNICEFNSTRKRMSAIFRFPDGSIKLFCKGADTVILERLDDEANQYVEA
+
+target TKVHVERNAMDGYRTLCVAFKEIAPDDYERINRQLIEAKMALQDREEKMEKVFDDIETNM
+pdb_id=6roh, cha... TMRHLEDYASEGLRTLCLAMRDISEGEYEEWNSIYNEAATTLDNRAEKLDEAANLIEKNL
+
+target NLIGATAVEDKLQDQAAETIEALHAAGLKVWVLTGDKMETAKSTCYACRLFQTNTELLEL
+pdb_id=6roh, cha... ILIGATAIEDKLQDGVPETIHTLQEAGIKIWVLTGDRQETAINIGMSCRLLSEDMNLLII
+
+target TTKTIEESERKEDRLHELLIEYRKKLLHEFPKSTRSFKKAWTEHQEYGLIIDGSTLSLIL
+pdb_id=6roh, cha... NEETRDDT---ERNLLEKINALNEHQL------------STHDMNTLALVIDGKSLGFAL
+
+target NSSQDSSSNNYKSIFLQICMKCTAVLCCRMAPLQKAQIVRMVKNLKGSPITLSIGDGAND
+pdb_id=6roh, cha... E-------PELEDYLLTVAKLCKAVICCRVSPLQKALVVKMVKRKS-SSLLLAIGDGAND
+
+target VSMILESHVGIGIKGKEGRQAARNSDYSVPKFKHLKKLLLAHGHLYYVRIAHLVQYFFYK
+pdb_id=6roh, cha... VSMIQAAHVGVGISGMEGMQAARSADIAVGQFKFLKKLLLVHGSWSYQRISVAILYSFYK
+
+target NLCFILPQFLYQFFCGFSQQPLYDAAYLTMYNICFTSLPILAYSLLEQHINIDTLTSDPR
+pdb_id=6roh, cha... NTALYMTQFWYVFANAFSGQSIMESWTMSFYNLFFTVWPPFVIGVFDQFVSSRLLERYPQ
+
+target LYMKISGNAMLQLGPFLYWTFLAAFEGTVFFFGTYFLFQTASLEE-NGKVYGNWTFGTIV
+pdb_id=6roh, cha... LYKLGQKGQFFSVYIFWGWIINGFFHSAIVFIGTILIYRYGFALNMHGELADHWSWGVTV
+
+target FTVLVFTVTLKLALDTRFWTWINHFVIWGSLAFYVFFSFFWGGIIWPFLKQQ-RMYFVFA
+pdb_id=6roh, cha... YTTSVIIVLGKAALVTNQWTKFTLIAIPGSLLFWLIFFPIYAS-IFPHANISREYYGVVK
+
+target QMLSSVSTWLAIILLIFISLFPEILLIVLKNVRRRSARRNLSCRRASDSLSARPSVRPLL
+pdb_id=6roh, cha... HTYGSGVFWLTLIVLPIFALVRDFLWKYYKRMYEPETY----------------------
+
+target LRTFSDESNVL
+pdb_id=6roh, cha... -----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 23).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP83-()-A.THR84 by relaxing A.THR81-(VD)-A.THR84
+Closed: A.GLY446-()-A.THR447 by relaxing A.ASP445-(GTL)-A.THR449
+Closed: A.ASN524-()-A.GLN525 by relaxing A.ASN524-(Q)-A.ARG526
+Closed: A.GLN1051-()-A.ARG1052 by relaxing A.GLN1050-(QR)-A.MET1053
+Trying to merge 19 gap(s) with distance 0.
+Merged gap A.TYR228-(S)-A.ASN230 and A.ASN230-(SLEA)-A.VAL235 into A.TYR228-(SNSLEA)-A.VAL235
+Merged gap A.ARG332-(E)-A.THR334 and A.THR334-(LKV)-A.LEU338 into A.ARG332-(ETLKV)-A.LEU338
+Merged gap A.PHE451-()-A.ASP452 and A.ASP452-()-A.LYS453 into A.PHE451-(D)-A.LYS453
+Trying to fill 16 gap(s) by database.
+Resolved A.SER30-(ETEAY)-A.ILE36 by filling A.HIS27-(PVSETEAY)-A.ILE36 (40 candidates, BB_DB)
+Resolved A.LYS132-()-A.ARG133 by filling A.ILE128-(ENAK)-A.ARG133 (58 candidates, BB_DB)
+Resolved A.TYR228-(SNSLEA)-A.VAL235 by filling A.TYR228-(SNSLEAV)-A.ALA236 (60 candidates, BB_DB)
+Resolved A.TYR318-(N)-A.ASP320 by filling A.THR316-(PYN)-A.ASP320 (50 candidates, BB_DB)
+Resolved A.ARG332-(ETLKV)-A.LEU338 by filling A.LYS330-(ERETLKV)-A.LEU338 (49 candidates, BB_DB)
+Resolved A.GLY440-()-A.LEU441 by filling A.ASP439-(GLS)-A.GLN443 (49 candidates, BB_DB)
+Resolved A.PHE451-(D)-A.LYS453 by filling A.TYR450-(FDKV)-A.ASP455 (76 candidates, BB_DB)
+Resolved A.ALA479-(VDGATES)-A.ALA487 by filling A.ASP478-(AVDGATESA)-A.GLU488 (59 candidates, BB_DB)
+Resolved A.VAL573-()-A.GLN574 by filling A.ARG572-(VQNH)-A.GLU577 (50 candidates, BB_DB)
+Resolved A.SER708-(ERK)-A.GLU712 by filling A.SER708-(ERKEDR)-A.LEU715 (45 candidates, BB_DB)
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Resolved A.ASN761-(SSQDSSS)-A.ASN769 by filling A.ASN761-(SSQDSSSNN)-A.TYR771 (42 candidates, BB_DB)
+Resolved A.LYS806-(G)-A.SER808 by filling A.ASN804-(LKGS)-A.PRO809 (76 candidates, BB_DB)
+Resolved A.GLU985-()-A.ASN986 by filling A.GLU985-(NGK)-A.VAL989 (47 candidates, BB_DB)
+Resolved A.GLY1042-(I)-A.ILE1044 by filling A.PHE1038-(FWGGI)-A.ILE1044 (40 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.LEU727-(HEFPKSTRSFKK)-A.ALA740), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.LEU727-(HEFPKSTRSFKK)-A.ALA740 by filling A.LEU727-(HEFPKSTRSFKKA)-A.TRP741 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.37355e+15)
+Perform energy minimization (iteration 2, energy: 64986)
+Perform energy minimization (iteration 3, energy: 53127)
+Perform energy minimization (iteration 4, energy: 47959.3)
+No more stereo-chemical problems -> final energy: 45098.2
+
+
+Build model with the following alignment:
+target NNKYKTKLCKNFARGGTGFCPYGLRCEFVHPTDKE
+pdb_id=2d9m, cha... -PTGYFSICDRYM---NGTCPEGNSCKFAHGNAE-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.ALA13-(RGG)-A.THR17 by filling A.ALA13-(RGGTGF)-A.CYS20 (52 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.04003e+11)
+Perform energy minimization (iteration 2, energy: 3896.33)
+No more stereo-chemical problems -> final energy: 2192.84
+
+
+Build model with the following alignment:
+target MAKSTTFFISLTLPFLLLSVVTATYYQSMSPTVLGFQEEKFTHLHFYFHDVV-TGP---K
+pdb_id=4rev, cha... -------------------------------------YKPCKNLVFYFHDILY-------
+
+target PSMVIVAEPNGKA----KNSLPFGTVVAMDDPLTVGPESDSKLVGKAQGIYTSISQEEMG
+pdb_id=4rev, cha... --------------TKLAPQSHFGNIIVFDDPITLSHSLSSKQVGRAQGFYIYDT----T
+
+target LMMVMTMAFSDGEFNGSTLSILARNMIMSEPVREMAIVGGTGAFRFARGYAQAKFYSVDF
+pdb_id=4rev, cha... SWLSFTFVLNSTHHQG-TITFAGADP---AKTRDISVTGGTGDFFMHRGIATITTDAF--
+
+target TKGDAIVEYDIFVFHYKGELNSKLEGKPIPNPLLGLDSTRTGHHHHHH
+pdb_id=4rev, cha... ---EAYFRLGVYIKFF--------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Resolved A.SER107-(QEEM)-A.GLY112 by filling A.SER107-(QEEM)-A.GLY112 (196 candidates, BB_DB)
+Resolved A.GLY128-(S)-A.THR130 by filling A.GLU125-(FNGS)-A.THR130 (48 candidates, BB_DB)
+Resolved A.MET138-(IMS)-A.GLU142 by filling A.MET138-(IMSE)-A.PRO143 (77 candidates, BB_DB)
+Resolved A.VAL170-(DFTKG)-A.ASP176 by filling A.VAL170-(DFTKG)-A.ASP176 (74 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.VAL52-(TGPKPSMVIVAEPNGKA)-A.LYS70 by filling A.VAL52-(TGPKPSMVIVAEPNGKAK)-A.ASN71 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.73917e+14)
+Perform energy minimization (iteration 2, energy: 16179)
+No more stereo-chemical problems -> final energy: 14945.3
+
+
+Build model with the following alignment:
+target MSVYKGGVDCPLVVKLYATVGLHRYNMLEGTNLYLHKIEKYVVVCTLMPVSYNITLIAED
+pdb_id=4n6u, cha... -----------------ARFAVDEHNKKENALLEFVRVVKAKEQVVA-GTMYYLTLEAKD
+
+target PATSSFVVFETNVDQRSLGQIDFTCYISRPKGIKSEIYPNQFFDAKDLPDKWPSKEAFAD
+pdb_id=4n6u, cha... GGK--KKLYEAKVWVK--------------------------------------------
+
+target QSRFLYKMQKSDWEEHDWIRLYMEISFFNRDRCLDHNMSDLKILDVVVETEENVPRETVL
+pdb_id=4n6u, cha... ------------------------------------------------------------
+
+target KSLRNVLVYIRYDQDLGADGVCKHIAIVRRTVEPTTHCVCLLGESQLVPDSELEHHHHHH
+pdb_id=4n6u, cha... ------------------------------------------------------------
+
+target HH
+pdb_id=4n6u, cha... --
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.LEU47-(M)-A.PRO49 by filling A.CYS45-(TLMP)-A.VAL50 (44 candidates, BB_DB)
+Resolved A.THR63-(SS)-A.PHE66 by filling A.ASP60-(PATSS)-A.PHE66 (98 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 70944.5)
+No more stereo-chemical problems -> final energy: 4290.5
+
+
+Build model with the following alignment:
+target TLKNSDAYVIRPFMPSDEETLYDLCLKSCIENSNGDEIYKREPRIIGDRDLGAYIYLHPE
+pdb_id=3zj0, cha... -----SEVVIRRATAADHGDLCRVCLLTGDSGRDASSREDD-PTLLGMIYAVPYQVGAPD
+
+target YIYVLEDDRDKICGYLCGALDSKQFYERYESEWLTQIRDRHPQPENDIASWTPEEIVANS
+pdb_id=3zj0, cha... FAFVLEDA-EGVCGYLLGAPDTLSFQHFLEKEWLPPLRAGLTDPGPDPAAWQGSDWARDA
+
+target FYNF-TPPTDVSVLYLSHLEARFDSSV-PEKVIKRIIRFILEQLKAKGSYGASMLIDSWR
+pdb_id=3zj0, cha... IHRPPALPPIDLAAYPAHGHIDLLPRAQGRGVGSRAMDHLEAALAAAGAPGMHLQVSPEN
+
+target TNLRRIFTSMGFVDLQEYSWMSEQKCMIAIKLM
+pdb_id=3zj0, cha... PRALGFYEHRGFRELCRSE--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.PHE124-()-A.THR125 by relaxing A.ASN123-(FTP)-A.PRO127
+Closed: A.VAL146-()-A.PRO147 by relaxing A.VAL146-(PE)-A.LYS149
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.ARG41-(E)-A.PRO43 by filling A.ILE38-(YKRE)-A.PRO43 (49 candidates, BB_DB)
+Resolved A.ASP68-(R)-A.ASP70 by filling A.ASP68-(RDK)-A.ILE72 (47 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.05793e+11)
+No more stereo-chemical problems -> final energy: 5873.45
+
+
+Build model with the following alignment:
+target GSHMDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEA
+pdb_id=3hxj, cha... ------------------------------------------------KWEFLIGNSIDS
+
+target SPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLY
+pdb_id=3hxj, cha... SPILAKNGTIYLGSSNKNLYAINTDGSVKWFFKSGEIIECRPSIGKDGTIYFGSDK--VY
+
+target AINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEA
+pdb_id=3hxj, cha... AINPDGTEKWRFDT-----SDFTI-FEDILYVTSMDGHLYAINTDGTEKWRFKTKKAIYA
+
+target SPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLY
+pdb_id=3hxj, cha... TPIVSEDGTIYVGSNDNYLYAINPDGTEKWRFKTNDAITSAASIGKDGTIYFGS--DKVY
+
+target AINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEA
+pdb_id=3hxj, cha... AINPDGTEKWNFYAGYWTVTRPAISEDGTIYVTSLDGHLYAINPDGTEKWRFKTGKRIES
+
+target SPVIGEDGTIYVGSNDGHLYAINPDGTEKWRFKTGKAIEASPVIGEDGTIYVGSNDGHLY
+pdb_id=3hxj, cha... SPVIGNTDTIYFGSYDGHLYAINPDGTEKWNFETGSWIIATPVIDENGTIYFGTRNGKFY
+
+target AINP
+pdb_id=3hxj, cha... AL--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ASP116-(GH)-A.LEU119 by filling A.SER114-(NDGH)-A.LEU119 (72 candidates, BB_DB)
+Resolved A.THR134-(GKAIE)-A.ALA140 by filling A.THR134-(GKAIE)-A.ALA140 (83 candidates, BB_DB)
+Resolved A.ILE144-(G)-A.GLU146 by filling A.ILE144-(GEDG)-A.THR149 (107 candidates, BB_DB)
+Resolved A.SER234-(ND)-A.GLY237 by filling A.GLY233-(SNDGH)-A.LEU239 (52 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.40724e+10)
+Perform energy minimization (iteration 2, energy: 25912)
+No more stereo-chemical problems -> final energy: 23308.6
+
+
+Build model with the following alignment:
+target MKPITFVVLASVMKELSLKASPLRSETAEGIVVVTTWIEKILTD-LKVQH----KRVPC-
+pdb_id=5wu2, cha... ---------------------------LAPFTQLTAALVQVFREALGCHIEQ--------
+
+target ------G--------KEEVSLFLTAIENSWIHLRRKKRERVRQLREVPRA------P-ED
+pdb_id=5wu2, cha... -----------------SASWRCALWHRVWQGRRRARRRLQQQTKEG---------GWLA
+
+target V----IQALEE-K---KGVAGQYLFKCLINVKKEVDDALVEMHWVEG-QNRDLMNQLCTY
+pdb_id=5wu2, cha... TEAQVTQELK----------TEPLLSFVASVSP--ADRMLTVTPLQDPQG--LFPDLHHF
+
+target IRNQIFRLVAVNLEHHHHHH
+pdb_id=5wu2, cha... L-------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP44-()-A.LEU45 by relaxing A.THR43-(DL)-A.LYS46
+Closed: A.PRO91-()-A.GLU92 by relaxing A.PRO91-(ED)-A.VAL94
+Trying to merge 7 gap(s) with distance 0.
+Trying to fill 7 gap(s) by database.
+Resolved A.HIS49-(KRVPCGKE)-A.GLU58 by filling A.HIS49-(KRVPCGKE)-A.GLU58 (334 candidates, BB_DB)
+Resolved A.VAL87-(PRA)-A.PRO91 by filling A.VAL87-(PRAPEDV)-A.ILE95 (50 candidates, BB_DB)
+Resolved A.GLU99-(EKKGVA)-A.GLY106 by filling A.GLU99-(EKKGVAG)-A.GLN107 (147 candidates, BB_DB)
+Resolved A.LYS118-(EV)-A.ASP121 by filling A.LYS118-(EVDD)-A.ALA123 (40 candidates, BB_DB)
+Resolved A.GLY132-()-A.GLN133 by filling A.HIS128-(WVEG)-A.GLN133 (42 candidates, BB_DB)
+Resolved A.ASN134-(RD)-A.LEU137 by filling A.GLY132-(QNRDL)-A.MET138 (119 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.79456e+06)
+No more stereo-chemical problems -> final energy: 3813.96
+
+
+Build model with the following alignment:
+target MKSPIPLRDVPQSNIFRKGDVFVLFGELFGRGYANGLINEARDAGMTIVGITVGRRDENN
+pdb_id=4bkr, cha... ----------------NGPKRVLVIGASTGYGLAARITAAFG-CGADTLGVFF--ER-PG
+
+target ALR------ALTAEELATAEANLGGRIINVPLMAGFDLDAPAGEPTPTDLLADMTLKSWQ
+pdb_id=4bkr, cha... EEGKPGTSGWYNSAAFHKFAAQKGLYAKSING----------------DA----------
+
+target DDKLDWAHIEKCRAVGVQRFKDGVAKVMAELDGMIPDGANAFFAHTMAGGIPKVKV-FLA
+pdb_id=4bkr, cha... ---FSDEIKQ---------------LTIDAIKQDL--GQVDQVIYSLAS-PRRTHPKTGE
+
+target IANRIYKGRGERFLSSSALLNSDLGKLILMNFDEVTANTFL-----HL------------
+pdb_id=4bkr, cha... VFNSALKPIGNAV--N--------LRGLDTDKEVIKESVLQPATQSEIDSTVAVMGGEDW
+
+target ---IEGS--AAIRARLEKSGGQVRYSAYGYHGTEILIDDKYQWQTYTSYTQGKAKMRLER
+pdb_id=4bkr, cha... QMWIDALLDAGVL----AE--GAQTTAFTYLGEKIT------HDIYWNGSIGAAKKDLDQ
+
+target IAEDAW----KQ-GIKATVYNCPEIRTNSSDIFVGVELSLFPLLKALKKENGGAWAEAQW
+pdb_id=4bkr, cha... KVLAIRESLAAHGGGDARVSVLKAVVTQASSAIPMMPLYLSLLFKVMKEKGTH---EGCI
+
+target QACREVLSEGHTLESLLQKIDDYNASDVMKGFRNFEAWPMPNTAELADIMIGTSDEITKM
+pdb_id=4bkr, cha... EQVYSLYKD---------------------------------------------------
+
+target HKSRDALVTDVLSALVLEGTGPLMFHESSNPAGPVLWLSHDVIAKQLNLMHRLEHHHHHH
+pdb_id=4bkr, cha... ------------------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 21).
+Initialized default backbone scoring for modelling.
+Closed: A.VAL170-()-A.PHE171 by relaxing A.VAL168-(KV)-A.PHE171
+Trying to merge 20 gap(s) with distance 0.
+Merged gap A.PHE186-(LS)-A.SER189 and A.SER189-(SALLNSDL)-A.GLY198 into A.PHE186-(LSSSALLNSDL)-A.GLY198
+Trying to fill 19 gap(s) by database.
+Resolved A.ARG42-(D)-A.ALA44 by filling A.ARG42-(DAGM)-A.THR47 (61 candidates, BB_DB)
+Resolved A.VAL53-(GR)-A.ARG56 by filling A.ILE51-(TVGRR)-A.ASP57 (65 candidates, BB_DB)
+Resolved A.ASP57-(E)-A.ASN59 by filling A.ARG56-(DEN)-A.ASN60 (49 candidates, BB_DB)
+Resolved A.ARG63-()-A.ALA64 by filling A.ASP57-(ENNALR)-A.ALA64 (66 candidates, BB_DB)
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPT)-A.ASP103), only 0 candidates
+Failed at loop insertion (A.LEU104-(LADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Resolved A.ILE149-(PD)-A.GLY152 by filling A.MET148-(IPDGA)-A.ASN154 (43 candidates, BB_DB)
+Resolved A.GLY163-(G)-A.ILE165 by filling A.ALA162-(GGI)-A.PRO166 (43 candidates, BB_DB)
+Failed at loop insertion (A.PHE186-(LSSSALLNSDL)-A.GLY198), only 16 candidates
+Failed at loop insertion (A.LEU214-()-A.HIS215), only 0 candidates
+Failed at loop insertion (A.LEU216-()-A.ILE217), only 0 candidates
+Resolved A.SER220-()-A.ALA221 by filling A.GLY219-(SAA)-A.ILE223 (63 candidates, BB_DB)
+Resolved A.ARG224-(ARLE)-A.LYS229 by filling A.GLY219-(SAAIRARLE)-A.LYS229 (40 candidates, BB_DB)
+Resolved A.SER230-(GG)-A.GLN233 by filling A.ALA225-(RLEKSGG)-A.GLN233 (184 candidates, BB_DB)
+Resolved A.LEU247-(IDDKYQ)-A.TRP254 by filling A.GLU245-(ILIDDKYQWQ)-A.THR256 (50 candidates, BB_DB)
+Resolved A.TRP277-()-A.LYS278 by filling A.TRP277-(KQGIK)-A.ALA283 (44 candidates, BB_DB)
+Resolved A.GLY319-(AWA)-A.GLU323 by filling A.ASN317-(GGAWA)-A.GLU323 (40 candidates, BB_DB)
+Trying to merge 6 gap(s) with distance 1.
+Merged gap A.LEU86-(MAGFDLDAPAGEPTPT)-A.ASP103 and A.LEU104-(LADMTLKSWQDDK)-A.LEU118 into A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118
+Merged gap A.LEU214-()-A.HIS215 and A.LEU216-()-A.ILE217 into A.LEU214-(HL)-A.ILE217
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Failed at loop insertion (A.PHE186-(LSSSALLNSDL)-A.GLY198), only 4 candidates
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217), only 0 candidates
+Trying to merge 4 gap(s) with distance 2.
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Failed at loop insertion (A.PHE186-(LSSSALLNSDL)-A.GLY198), only 4 candidates
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217), only 0 candidates
+Trying to merge 4 gap(s) with distance 3.
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Failed at loop insertion (A.PHE186-(LSSSALLNSDL)-A.GLY198), only 4 candidates
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217), only 0 candidates
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Failed at loop insertion (A.PHE186-(LSSSALLNSDL)-A.GLY198), only 4 candidates
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217), only 0 candidates
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118), only 0 candidates
+Failed at loop insertion (A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140), only 0 candidates
+Resolved A.PHE186-(LSSSALLNSDL)-A.GLY198 by filling A.PHE186-(LSSSALLNSDLG)-A.LYS199 (63 candidates, BB_DB)
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217), only 0 candidates
+Trying to fill 3 gap(s) by Monte Carlo.
+Resolved A.LEU86-(MAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118 by filling A.PRO85-(LMAGFDLDAPAGEPTPTDLLADMTLKSWQDDK)-A.LEU118 (6 candidates, BB)
+Resolved A.GLU124-(KCRAVGVQRFKDGVA)-A.LYS140 by filling A.GLU124-(KCRAVGVQRFKDGVAK)-A.VAL141 (6 candidates, BB)
+Failed at loop insertion (A.LEU214-(HL)-A.ILE217)
+Trying to resolve large deletions (1 gap(s) left) by sampling a linker region.
+Resolved A.LEU214-(HL)-A.ILE217 by sampling A.PHE213-(LHLIEGSA)-A.ALA222 as linker
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.64763e+27)
+Perform energy minimization (iteration 2, energy: 24582.5)
+Perform energy minimization (iteration 3, energy: 17669.5)
+No more stereo-chemical problems -> final energy: 15847.2
+
+
+Build model with the following alignment:
+target MIRTLLRLVPAEKRGAVAGYAVLTLLSVLLRAVGAVLLIPLLAALFSD-TPSDAWLWLGW
+pdb_id=5u1d, cha... -VRRLLGCLG-SETRRLSLFLVLVVLSSLGEMAIPFFTGRLTDWILQDGSADTFTRNLTL
+
+target LTAVTLAGWVTDTNTARLGFDLGFAVLSRTQHDMADRLPNVAMSWFTPDNTATARQAIAA
+pdb_id=5u1d, cha... MSILTIASAVLEFVGDGIYNNTMGHVHSHLQGEVFGAVLRQETEFFQQNQTGNIMSRVTE
+
+target TGPELAGLVVNLLTPLIGAALLPAAIGVALLFVSVPLGLAALAGVAVLFGALALSGRLSR
+pdb_id=5u1d, cha... DTSTLSDSLSENLSLFLWYLVRGLCLLGIMLW--VSLTMVTLITLPLLFLLPKKVGKWYQ
+
+target AADKVAGETNSAFTERIIEFARTQQALRAARRVEPARSQVGSALAAQHGAGLRLLTMQIP
+pdb_id=5u1d, cha... LLEVQVRESLAKSSQVAIEALSAMPTVRSFANEEGEAQKFREKLQEIKTLNQKEAVAYAV
+
+target GQVLFSLAGQVALIGFAGMAVWLTVRGQLGVPEAIALIVVLVRYLEPFAAIADLAPALET
+pdb_id=5u1d, cha... NSWTTSISGMLLKVGILYIGGQLVTSGAVSSGNLVTFVLYQMQFTQAVEVLLSIYPRVQK
+
+target TRATLNRIQAVLDAPTLPAGRRR-L-DRTGAAPSIEFDDVRFSYGD---EVVLDGVSFTL
+pdb_id=5u1d, cha... AVGSSEKIFEYLDR-------GLLTPLHLE-G-LVQFQDVSFAYPNRPDVLVLQGLTFTL
+
+target RPGNTTAIVGPSGSGKTTILSLIAGLQQPASGRVLLDGVDVTTLDPEARRAAVSVVFQHP
+pdb_id=5u1d, cha... RPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGKPLPQYEHRYLHRQVAAVGQEP
+
+target YLFDGTLRDNVLVGDP-EADPDDVTAAMRLARVDELLDRLPDGDATVVGEGGTALSGGER
+pdb_id=5u1d, cha... QVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVDEAGSQLSGGQR
+
+target QRVSIARALLKPAPVLLVDEATSALDNANEAAVVDALTADP--RPRTRVIVAHRLASIRH
+pdb_id=5u1d, cha... QAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLSLVEQ
+
+target ADRVLFVEAGRVVEDGAIDELLAAGGRFAQFWAQQQAASEWAIGSTARALEVLFQ
+pdb_id=5u1d, cha... ADHILFLEGGAIREGGTHQQLMEKKGCYWAMVQA---------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP343-()-A.GLU344 by relaxing A.TYR341-(GDE)-A.VAL345
+Closed: A.PRO430-()-A.GLU431 by relaxing A.ASP429-(PE)-A.ALA432
+Trying to merge 9 gap(s) with distance 0.
+Merged gap A.ARG322-()-A.LEU323 and A.LEU323-()-A.ASP324 into A.ARG322-(L)-A.ASP324
+Merged gap A.GLY327-(A)-A.ALA329 and A.ALA329-(P)-A.SER331 into A.GLY327-(AAP)-A.SER331
+Trying to fill 7 gap(s) by database.
+Resolved A.PRO10-(A)-A.GLU12 by filling A.PRO10-(AEKR)-A.GLY15 (103 candidates, BB_DB)
+Resolved A.ASP48-()-A.THR49 by filling A.LEU45-(FSDT)-A.PRO50 (78 candidates, BB_DB)
+Resolved A.PHE151-(VS)-A.VAL154 by filling A.ALA148-(LLFVS)-A.VAL154 (121 candidates, BB_DB)
+Resolved A.ALA313-(PTLPAGR)-A.ARG321 by filling A.ALA313-(PTLPAGR)-A.ARG321 (562 candidates, BB_DB)
+Failed at loop insertion (A.ARG322-(L)-A.ASP324), only 4 candidates
+Resolved A.GLY327-(AAP)-A.SER331 by filling A.ARG325-(TGAAP)-A.SER331 (126 candidates, BB_DB)
+Resolved A.PRO514-()-A.ARG515 by filling A.PRO514-(RPR)-A.THR518 (78 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Resolved A.ARG322-(L)-A.ASP324 by filling A.ARG322-(LDRT)-A.GLY327 (105 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.2741e+21)
+Perform energy minimization (iteration 2, energy: 13317.7)
+No more stereo-chemical problems -> final energy: 7680
+
+
+Build model with the following alignment:
+target MDRRKFIKTSLFSALGFSVGGLSLLSCGGGGTTGSSSGQGSGTLSKQSLNIPGYFLFPDG
+pdb_id=5b7e, cha... -----------------------------------RA-VFA--AERPTLPIPDLLTTDAR
+
+target QRVSITAKWTTLEVIPGKSTDMLVYEIDNEYNPVIFLRKGQTFSADFVNNSGEDSIIHWH
+pdb_id=5b7e, cha... NRIQLTIGAGQSTF-GGKTATTWGYN-GNLLGPAVKLQRGKAVTVDIYNQLTEETTLHWH
+
+target GFRAPWKSDGHPYYAVKDGETYSYPDFTIIDRSGTYFYHPHPHGRTGYQVYYGLAGMIII
+pdb_id=5b7e, cha... GLEVPGEVDGGPQGIIPPGGKRS-VTLNVDQPAATCWFHPHQHGKTGRQVAMGLAGLVVI
+
+target EDEDEDNLKQALDLEYGVIDIPLIIQDKTFDSSGQLVYNP---MGHMGFWGDTILVNLTP
+pdb_id=5b7e, cha... EDDEILKL--MLPKQWGIDDVPVIVQDKKFSADGQIDYQLDVMTAAVGWFGDTLLTNGAI
+
+target NPYMDVERKIYRFRILNGSNARPYRLALLRGNQRMRFWVIGVEGGLLDTPKEVNEILVAP
+pdb_id=5b7e, cha... YPQHAAPRGWLRLRLLNGCNARSLNFATS---DNRPLYVIASDGGLLPEPVKVSELPVLM
+
+target GERIDILVDFRDASVNDVIKLYNFPHNLIGMGMIGMRMGMGMERGMGMGNGMNMDMGMAD
+pdb_id=5b7e, cha... GERFEVLVEVND---NKPFDLVTLPVSQMGMA------------------------IAPF
+
+target NSEFEVMEFRVTKDSAYDKSIPQRLSEVTP---INTDGAQVQRITLGM------------
+pdb_id=5b7e, cha... DKPHPVMRIQPIAI-SASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLDMMGMQMLME
+
+target ----------R--------------------R----MVFTINGETWEDGYANPQDINNPK
+pdb_id=5b7e, cha... KYGDQAMAG------------------------DFHHANKINGQAFD--------MNKPM
+
+target VLFEQNNGDVVIIEYVNNT-GMYHPMHIHGFQFQVLERSLGPLRATDLGWKDTVIVAPME
+pdb_id=5b7e, cha... FA--AAKGQYERWVISGVGDMMLHPFHIHGTQFRILSENGKPPAAHRAGWKDTVKVE-GN
+
+target TVRIAVDM----SHPYNEHQIYLLHCHILEHHDEGMMVNYRVNA
+pdb_id=5b7e, cha... VSEVLVKFNHDAPKEH----AYMAHCHLLEHEDTGMMLGFTV--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 19).
+Initialized default backbone scoring for modelling.
+Trying to merge 19 gap(s) with distance 0.
+Trying to fill 19 gap(s) by database.
+Failed at loop insertion (A.SER37-(G)-A.GLN39), only 9 candidates
+Resolved A.SER41-(GT)-A.LEU44 by filling A.GLN39-(GSGTL)-A.SER45 (76 candidates, BB_DB)
+Resolved A.VAL74-(I)-A.PRO76 by filling A.GLU73-(VIPG)-A.LYS78 (67 candidates, BB_DB)
+Failed at loop insertion (A.GLU86-(I)-A.ASP88), only 37 candidates
+Resolved A.SER143-(Y)-A.PRO145 by filling A.GLU140-(TYSY)-A.PRO145 (81 candidates, BB_DB)
+Resolved A.LEU188-(KQ)-A.ALA191 by filling A.LEU188-(KQALDL)-A.GLU195 (253 candidates, BB_DB)
+Resolved A.PRO220-()-A.MET221 by filling A.VAL217-(YNPM)-A.GLY222 (104 candidates, BB_DB)
+Resolved A.LEU266-(RGN)-A.GLN270 by filling A.LEU266-(RGNQR)-A.MET272 (78 candidates, BB_DB)
+Resolved A.ASP309-(ASV)-A.ASN313 by filling A.ARG308-(DASVN)-A.ASP314 (56 candidates, BB_DB)
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Resolved A.ASP371-(S)-A.ALA373 by filling A.THR369-(KDS)-A.ALA373 (41 candidates, BB_DB)
+Resolved A.PRO387-()-A.ILE388 by filling A.VAL385-(TPINTD)-A.GLY392 (114 candidates, BB_DB)
+Resolved A.MET402-(RR)-A.MET405 by filling A.MET402-(RRMV)-A.PHE407 (46 candidates, BB_DB)
+Resolved A.GLU415-(DGYANPQD)-A.ILE424 by filling A.TRP414-(EDGYANPQDIN)-A.ASN426 (63 candidates, BB_DB)
+Resolved A.LEU430-(FE)-A.GLN433 by filling A.LEU430-(FEQN)-A.ASN435 (52 candidates, BB_DB)
+Resolved A.THR447-()-A.GLY448 by filling A.ASN445-(NT)-A.GLY448 (90 candidates, BB_DB)
+Resolved A.ALA484-(P)-A.MET486 by filling A.VAL483-(APME)-A.THR488 (59 candidates, BB_DB)
+Failed at loop insertion (A.MET495-()-A.SER496), only 0 candidates
+Resolved A.TYR499-(NEHQ)-A.ILE504 by filling A.HIS497-(PYNEHQ)-A.ILE504 (53 candidates, BB_DB)
+Trying to merge 4 gap(s) with distance 1.
+Trying to fill 4 gap(s) by database.
+Resolved A.SER37-(G)-A.GLN39 by filling A.SER37-(GQGS)-A.GLY42 (67 candidates, BB_DB)
+Failed at loop insertion (A.GLU86-(I)-A.ASP88), only 37 candidates
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Failed at loop insertion (A.MET495-()-A.SER496), only 0 candidates
+Trying to merge 3 gap(s) with distance 2.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU86-(I)-A.ASP88), only 37 candidates
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Failed at loop insertion (A.MET495-()-A.SER496), only 0 candidates
+Trying to merge 3 gap(s) with distance 3.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.GLU86-(I)-A.ASP88), only 37 candidates
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Failed at loop insertion (A.MET495-()-A.SER496), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Resolved A.GLU86-(I)-A.ASP88 by filling A.GLU86-(IDNEY)-A.ASN92 (49 candidates, BB_DB)
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Resolved A.MET495-()-A.SER496 by filling A.MET495-(SHPYNEH)-A.GLN503 (73 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDM)-A.GLY354 by filling A.GLY329-(MIGMRMGMGMERGMGMGNGMNMDMG)-A.MET355 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.1368e+31)
+Perform energy minimization (iteration 2, energy: 29376.5)
+Perform energy minimization (iteration 3, energy: 18081.6)
+Perform energy minimization (iteration 4, energy: 15063.4)
+Perform energy minimization (iteration 5, energy: 13471.4)
+Perform energy minimization (iteration 6, energy: 12127.5)
+Perform energy minimization (iteration 7, energy: 11341.7)
+Perform energy minimization (iteration 8, energy: 10803.4)
+Perform energy minimization (iteration 9, energy: 10198.3)
+Perform energy minimization (iteration 10, energy: 9816.04)
+Perform energy minimization (iteration 11, energy: 9354.98)
+Perform energy minimization (iteration 12, energy: 8878.75)
+Stereo-chemical problem in sidechain of residue A.TYR505
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMTQTNLDFLLQTDPTISGMMQKELQRQREHLELIASENFT
+pdb_id=1cj0, cha... ----------------------------LKDSDAEVYDIIKKESNRQRVGLELIASENFA
+
+target SPAVMATQGSVLTNKYAEGLPKKRYYGGCEFIDEIEQVAIDRAKELFGAAS----ANVQP
+pdb_id=1cj0, cha... SRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQP
+
+target HSGAQANFAVFLTLLKPGDKIMGMDLSHGGHLTHG-----SPANVSGKWFEAVHYGVSQE
+pdb_id=1cj0, cha... YSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPD
+
+target TEQLDYDHILEVARQERPKLIICGYSAYPRIINFEKFRAIADEVGAYLLADIAHIAGLVA
+pdb_id=1cj0, cha... TGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVV
+
+target SGHHPNPVPHCDVVTTTTHKTLRGPRGGLILTRDP--------------ELGKKFNKSVF
+pdb_id=1cj0, cha... AGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVD------ILYNLESLINSAVF
+
+target PGTQGGPLEHVIAGKAVAFGEALKPEFKAYSGQVIANAQAMAQQLQNRGFKIVSGGTDNH
+pdb_id=1cj0, cha... PGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNH
+
+target LMLVDLRSVNLTGKQADQLVSDVNITANKNTVPFDPESPFVTSGLRLGSPAMTTRGLGTE
+pdb_id=1cj0, cha... LILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDK-SALRPSGLRLGTPALTSRGLLEK
+
+target DFAEIANIIADRLQN---P-----E-------------D---EQVKQACVQRVAALCERF
+pdb_id=1cj0, cha... DFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALF
+
+target PLYPHLNAPVPAMA
+pdb_id=1cj0, cha... PLP-GLP-------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.PRO266-()-A.GLU267 by relaxing A.ASP265-(PE)-A.LEU268
+Trying to merge 8 gap(s) with distance 0.
+Merged gap A.ASN412-()-A.PRO413 and A.PRO413-()-A.GLU414 into A.ASN412-(P)-A.GLU414
+Merged gap A.ASN412-(P)-A.GLU414 and A.GLU414-()-A.ASP415 into A.ASN412-(PE)-A.ASP415
+Merged gap A.ASN412-(PE)-A.ASP415 and A.ASP415-()-A.GLU416 into A.ASN412-(PED)-A.GLU416
+Trying to fill 5 gap(s) by database.
+Resolved A.SER111-()-A.ALA112 by filling A.GLU105-(LFGAAS)-A.ALA112 (80 candidates, BB_DB)
+Resolved A.GLY151-()-A.SER152 by filling A.GLY151-(SPA)-A.ASN155 (42 candidates, BB_DB)
+Resolved A.PRO373-(E)-A.SER375 by filling A.PHE371-(DPES)-A.PRO376 (63 candidates, BB_DB)
+Resolved A.ASN412-(PED)-A.GLU416 by filling A.GLN411-(NPED)-A.GLU416 (54 candidates, BB_DB)
+Resolved A.TYR436-(P)-A.HIS438 by filling A.TYR436-(PHL)-A.ASN440 (76 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.42141e+09)
+No more stereo-chemical problems -> final energy: 19837.6
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMLPWELARFSIVKDEVLPHFATNEDLDLANEIISLFKAGK
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target KLGEIDEEIEYLEKIYDHKLVRAFVKLLTRLCEFELDSPIPPIQIRRELFKYGPVLDEKE
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target REDIIQKVSKKLGADIMRFVFSDLDEEKKIIKAPTISAEDLIRWYNLSLLQTLLFKAYKL
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target TVYVSSNWKEIIRRAKWLGLMYFAYDKPLRFEFLGPATLVKLTEKYGRNLAVLLQFIISS
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target QNWKIEAELVLGKKFKRVYKLKLANFKELKELVIDEKRFDSSVEEKFYKDFTNVIKGWKI
+pdb_id=1m0d, cha... ----------------------------------------SGLEDKVSKQLESKGIKFEY
+
+target IREPEPLV--VDNRVFIPDFLVEKGNLKVYVEIVGFWTKEYIKEKLDKLKKVKYPILILL
+pdb_id=1m0d, cha... EEWKVPYVIPASNHTYTPDFLLP-NG--IFVETKGLWESDD-RKKHLLIREQ--------
+
+target NEELGKEKFNGMNVITYKRKIDISLVYKWLRELENKYLNEVKVDYTISGDIISLNEIASK
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target LSLPVEVIRKNIKIFPGYIFLKNYYVSEKFLEKLRNENFDNKSLKELVSAYGDYIVEVLE
+pdb_id=1m0d, cha... ------------------------------------------------------------
+
+target FLGYKLKWQGISDAIVIKDKKVN
+pdb_id=1m0d, cha... -----------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.VAL308-()-A.VAL309), only 0 candidates
+Resolved A.GLU321-(K)-A.GLY323 by filling A.VAL320-(EKG)-A.ASN324 (65 candidates, BB_DB)
+Resolved A.ASN324-(LK)-A.VAL327 by filling A.GLU321-(KGNLK)-A.VAL327 (121 candidates, BB_DB)
+Resolved A.TYR339-(I)-A.LYS341 by filling A.THR336-(KEYI)-A.LYS341 (49 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL308-()-A.VAL309), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL308-()-A.VAL309), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.VAL308-()-A.VAL309), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.VAL308-()-A.VAL309 by filling A.LYS299-(IIREPEPLV)-A.VAL309 (55 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 18659.2)
+No more stereo-chemical problems -> final energy: 7374.82
+
+
+Build model with the following alignment:
+target EDVPQPPVSQFYIQGQVYCDTCRA-RFITELSEFIPGAGVRLQCKDGENGKITFTEVGYT
+pdb_id=4z8w, cha... --------AKFHVEGEVYCNVCHSRNLINELSERMAGAQVQLDCKD-DSKKVIYSIGGET
+
+target RAEGLYSMLIERDHKNEFCEITLLSSSRKDCDEIP--IEGWVKPS-LKFMLNTVNG-TTR
+pdb_id=4z8w, cha... DQDGVYRLPVVGYHED--CEIKLVKSSRPDCSEIPKLAKGTIQTSKVDLSKNTTITEKTR
+
+target TINPLGFFKKEALPKCPQVFNKLGMYPPNM
+pdb_id=4z8w, cha... HVKPLSFRAKTDAPGC--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA24-()-A.ARG25 by relaxing A.CYS22-(RA)-A.ARG25
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.ASP45-(G)-A.GLU47 by filling A.ASP45-(GE)-A.ASN48 (50 candidates, BB_DB)
+Resolved A.ASN75-(EF)-A.CYS78 by filling A.ASP72-(HKNEF)-A.CYS78 (137 candidates, BB_DB)
+Resolved A.PRO94-()-A.ILE95 by filling A.PRO94-(IEGW)-A.VAL99 (46 candidates, BB_DB)
+Resolved A.SER102-()-A.LEU103 by filling A.SER102-(LKFMLN)-A.THR109 (96 candidates, BB_DB)
+Resolved A.GLY112-()-A.THR113 by filling A.LEU107-(NTVNG)-A.THR113 (40 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.60858e+13)
+Perform energy minimization (iteration 2, energy: 6116.89)
+No more stereo-chemical problems -> final energy: 4944.91
+
+
+Build model with the following alignment:
+target MAHHHHHHMSEATDTPPVDENKLIAERREKLKALRGQGIAYPNDFRREDFAGRLQEEFAD
+pdb_id=1lyl, cha... -------------------FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDA
+
+target AETWTAEALEGNGRQVKMAGRLMAKRIMGKASFAQIQDESGRIQLFLQGAVLGD-AYTA-
+pdb_id=1lyl, cha... KD---NQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQ
+
+target FKGWDVGDIIAVEGGLTRTKTGELSVKAESIRLLTKSLRPLPDKWHGLADVEQRYRQRYV
+pdb_id=1lyl, cha... FKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLP-------DQEVRYRQRYL
+
+target DLIVTPESRAVFIKRSKIIRAMRAWLDNRDFLEVETPMMHYIPGGAAAKPFTTHHNALDL
+pdb_id=1lyl, cha... DLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDL
+
+target DLYLRVAPELYLKRLTVGGLERVYEINRNFRNEGVSTRHNPEFTMMELYEAYATYNEIMD
+pdb_id=1lyl, cha... DMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIE
+
+target LTEGVIRDVAKAVNGGTEVEWDGAKIDLGPAFRRWRMDEAVRHHNPEISAADCTDRDALL
+pdb_id=1lyl, cha... LTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAK
+
+target RHCERLKIRVKPSYGWGKLLLEIFEATVEHTLIQPTFITDHPVEVSPLARANDNDPGYTD
+pdb_id=1lyl, cha... ALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITD
+
+target RFELFVNGKELANGFSELNDPEDQAQRFQAQVAAKEGGDDEAMHYDADYIRALEYGMAPT
+pdb_id=1lyl, cha... RFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPT
+
+target GGLGIGVDRLVMLLTGSSSIRDVLLFPYMRPEQ
+pdb_id=1lyl, cha... AGLGIGIDRMIMLFTNSHTIRDVILFPAMRP--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA118-()-A.PHE119 by relaxing A.ALA115-(YTA)-A.PHE119
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLU62-(TWT)-A.ALA66 by filling A.ASP60-(AETWT)-A.ALA66 (103 candidates, BB_DB)
+Resolved A.ASP114-()-A.ALA115 by filling A.GLY109-(AVLGD)-A.ALA115 (92 candidates, BB_DB)
+Resolved A.PRO160-(DKWHGLA)-A.ASP168 by filling A.PRO160-(DKWHGLAD)-A.VAL169 (106 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.35004e+11)
+No more stereo-chemical problems -> final energy: -5912.78
+
+
+Build model with the following alignment:
+target GGHHHHHHELEYFTLQIRGRERFEEFREKNEALELKDAQAGTSCFN
+pdb_id=2mw4, cha... -----------VYTLNIRGKRKFEKVKEYKEALDLLDYVQPDV---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3302.29)
+No more stereo-chemical problems -> final energy: -1134.5
+
+
+Build model with the following alignment:
+target ANHKNFILMLIILFLMEFARGMYILSYINFLPTVTSIAVAITSLAFSIHFIADASTNFVI
+pdb_id=6oom, cha... ---------------------DMIQPGMLAVVEQYQAGIDWVPTSMTAYLAGGMFLQWLL
+
+target GFLLKKFGTKIVLTTGFILAFTSLFLVIWFPASPFVIIFSAMMLGIAVSPIWVIMLSSVE
+pdb_id=6oom, cha... GPLSDRIGRRPVMLAGVVWFIVTCLAIL-LAQNIEQFTLLRFLQGISLCFIGAVGYAAIQ
+
+target ----EDKRGKQMGYVYFSWLLGLLVGMVFMNLLIK-VHPTRFAFMMSLVVLIAWILY-YF
+pdb_id=6oom, cha... ESFEEAVCIKITALMANVALIAPLLGPLVGAAWIHVLPWEGMFVLFAALAAISFFGLQRA
+
+target VDVKLTNYNTR-PV---KAQLRQIVDVTKRHLLLFPGILLQGAAIAALVPILPTYATKVI
+pdb_id=6oom, cha... MPETATRIGEKLSLKELGRDYKLVLKNG-RFVAGALALGFVSLPLLAWTAQSPIIIITGE
+
+target NVSTIEYTVAIIIGGIGCAVSMLFLSKLIDNRSRNFMYGVILSGFILYMILIFTLSMI--
+pdb_id=6oom, cha... QLSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSL---IIMGGWPIMIGLLVAAAATV
+
+target ---VNIHILWIIALAIGLMYGILLPAWNTFMARFIKSDEQEETWGVFNSIQGFGSMIGPL
+pdb_id=6oom, cha... ISSHAYLWMTAGLSIYAFGIGLANAGLVRLTL-FASDMSKGTVSAAMEMLQMLIFTVGIE
+
+target FGGLITQFTNNLNNTFYFSALIFLVLAVFYGSY
+pdb_id=6oom, cha... ISKHAWLNGGN-GLFNLFNLVN-----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.TYR172-()-A.TYR173 by relaxing A.LEU171-(YY)-A.PHE174
+Closed: A.ILE288-()-A.VAL289 by relaxing A.ILE288-(VN)-A.ILE291
+Trying to merge 9 gap(s) with distance 0.
+Trying to fill 9 gap(s) by database.
+Resolved A.ILE88-(W)-A.PHE90 by filling A.ILE88-(WFPAS)-A.PRO94 (60 candidates, BB_DB)
+Resolved A.GLU120-()-A.GLU121 by filling A.VAL119-(EEDK)-A.ARG124 (49 candidates, BB_DB)
+Resolved A.LYS151-()-A.VAL152 by filling A.LEU149-(IKV)-A.HIS153 (43 candidates, BB_DB)
+Resolved A.ARG185-()-A.PRO186 by filling A.ASN181-(YNTR)-A.PRO186 (89 candidates, BB_DB)
+Resolved A.VAL187-()-A.LYS188 by filling A.ASN181-(YNTRPV)-A.LYS188 (128 candidates, BB_DB)
+Resolved A.THR198-(K)-A.ARG200 by filling A.ASP196-(VTKR)-A.HIS201 (75 candidates, BB_DB)
+Resolved A.MET267-(YGV)-A.ILE271 by filling A.MET267-(YGVILS)-A.GLY274 (51 candidates, BB_DB)
+Resolved A.ALA317-(R)-A.PHE319 by filling A.ALA317-(RFIKS)-A.ASP323 (42 candidates, BB_DB)
+Resolved A.ASN356-(L)-A.ASN358 by filling A.PHE353-(TNNL)-A.ASN358 (62 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.37568e+21)
+Perform energy minimization (iteration 2, energy: 41731.8)
+Perform energy minimization (iteration 3, energy: 35473)
+No more stereo-chemical problems -> final energy: 33661.7
+
+
+Build model with the following alignment:
+target MKKYHISMINIPAYGHVNPTLALVEKLCEKGHRVTYATTEEFAPAVQQAGGEALIYHTSL
+pdb_id=3ia7, cha... -RQRHILFANVQGHGHVYPSLGLVSELARRGHRITYVTTPLFADEVKAAGAEVVLYKSEF
+
+target NIDPKQIREMMEKNDA-P-LSLLKESLSILPQLEELYKDDQPDLIIYDFVAL-AGKLFAE
+pdb_id=3ia7, cha... DTFHVPEVVKQEDAETQLHLVYVRENVAILRAAEEALGDNPPDLVVYDVFPFIAGRLLAA
+
+target KLNVPVIKLCSSYAQNESFQLGN--EDM----LKKIRE-AEAEFKAYLEQEKLPAVSFEQ
+pdb_id=3ia7, cha... RWDRPAVRLTGGFAANEHYSLFKELWKSNGQRHPADVEAVHSVLVDLLGKYGVDTPVKEY
+
+target LAVPEALNIVFMPKSFQIQHETFDDRFCFVGPSLGERKEKESLLIDKDDRPLMLISLGTA
+pdb_id=3ia7, cha... WDEIEGLTIVFLPKSFQPFAETFDERFAFVGPTLTG----PGWQPPRPDAPVLLVSLGNQ
+
+target FNAWPEFYKMCIKAFRDSSWQVIMSVGKTIDPESLEDIPANFTIRQSVPQLEVLEKADLF
+pdb_id=3ia7, cha... FNEHPEFFRACAQAFADTPWHVVMAIGGFLDPAVLGPLPPNVEAHQWIPFHSVLAHARAC
+
+target ISHGGMNSTMEAMNAGVPLVVIPQ-MYEQELTANRVDELGLGVYLPKEEVTVSSLQEAVQ
+pdb_id=3ia7, cha... LTHGTTGAVLEAFAAGVPLVLVPHFATEAAPSAERVIELGLGSVLRPDQLEPASIREAVE
+
+target AVSSDQELLSRVKNMQKDVKEAGGAERAAAEIEAFMKKSAVPQ
+pdb_id=3ia7, cha... RLAADSAVRERVRRMQRDILSSGGPARAADEVEAYLGR-----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 8).
+Initialized default backbone scoring for modelling.
+Closed: A.GLU149-()-A.ALA150 by relaxing A.ILE147-(REA)-A.GLU151
+Trying to merge 7 gap(s) with distance 0.
+Merged gap A.ALA76-()-A.PRO77 and A.PRO77-()-A.LEU78 into A.ALA76-(P)-A.LEU78
+Trying to fill 6 gap(s) by database.
+Resolved A.ALA76-(P)-A.LEU78 by filling A.ASN74-(DAP)-A.LEU78 (43 candidates, BB_DB)
+Resolved A.LEU110-()-A.ALA111 by filling A.ASP106-(FVAL)-A.ALA111 (58 candidates, BB_DB)
+Resolved A.ASN140-()-A.GLU141 by filling A.GLY139-(NED)-A.MET143 (52 candidates, BB_DB)
+Resolved A.MET143-()-A.LEU144 by filling A.GLY139-(NEDML)-A.LYS145 (116 candidates, BB_DB)
+Resolved A.GLU206-(RKEK)-A.GLU211 by filling A.GLU206-(RKEK)-A.GLU211 (122 candidates, BB_DB)
+Resolved A.GLN314-()-A.MET315 by filling A.ILE312-(PQM)-A.TYR316 (61 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.28294e+11)
+Perform energy minimization (iteration 2, energy: 30724.3)
+No more stereo-chemical problems -> final energy: 27792.6
+
+
+Build model with the following alignment:
+target NAKGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALV
+pdb_id=6oml, cha... ---KSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCDGECSFPLNAHMNATNHAIVQTLV
+
+target HLKNSQKASKACCVPTKLEPISILYLDK-GVVTYKFKYEGMAVSECGCR
+pdb_id=6oml, cha... HLMNPEYVPKPCCAPTELSAISMLYLDENEKVVLK-NYQDMVVEGCGCR
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.LYS88-()-A.GLY89 by relaxing A.LEU86-(DK)-A.GLY89
+Trying to fill 1 gap(s) by database.
+Resolved A.LYS94-(F)-A.LYS96 by filling A.VAL91-(TYKF)-A.LYS96 (202 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.3737e+21)
+Perform energy minimization (iteration 2, energy: 11070.8)
+No more stereo-chemical problems -> final energy: 10159.4
+
+
+Build model with the following alignment:
+target GSRSFSLGEVSDMAAVEAAELEMTRQVLHAGARQDDAEPGVSGASAHWGQRALQGAQAVA
+pdb_id=4pww, cha... ----------DDLEALLKAAIEMIKQALKFGAT---------------------------
+
+target AAQRLVHAIALMTQFGRAGS
+pdb_id=4pww, cha... --------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2744.06)
+No more stereo-chemical problems -> final energy: 61.335
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMTVPHIPRGPVMADIAAFRLTEEE
+pdb_id=1tr9, cha... --------------------------------------------GPLWLDVAGYELSAED
+
+target KQRLLDPAIGGIILFRRNFQNIEQLKTLTAEIKALRTPELIIAVDHEGGRVQRFIEGFTR
+pdb_id=1tr9, cha... REILQHPTVGGVILFGRNYHDNQQLLALNKAIRQAAKRPILIGVDQEGGRVQRFREGFSR
+
+target LPAMNVLGQIWD-KDGASAAETAAGQVGRVLATELSACGIDLSFTPVLDLDWGNCAVIGN
+pdb_id=1tr9, cha... IPPAQYYARAENGVE-------LAEQGGWLMAAELIAHDVDLSFAPVLDMG-FACKAIGN
+
+target RSFHRNPEAVARLALALQKGLAKGGMKSCGKHFPGHGFVEGDSHLVLPEDGRSLDELEAA
+pdb_id=1tr9, cha... RAFGEDVQTVLKHSSAFLRGMKAVGMATTGKHFPGHGAVIADSHLETPYDER--ETI-AQ
+
+target DLAPFRIMSREG-MAAVMPAHVVYPQVDTKPAGFSEIWLKQILRRDIGFKGVIFSDDLTM
+pdb_id=1tr9, cha... DMAIFRAQIEAGVLDAMMPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSM
+
+target EGACGAGGIKERARISFEAGCDIVLVCNRPDLVDELRDGFTIPDNQDLAGRWQYMENSLG
+pdb_id=1tr9, cha... EGAAVMGGPVERSHQALVAGCDMILICNKREAAVEVLDNLPI---MEVP-QAEALLKKQQ
+
+target HEAVQAVMQTMGFQAAQAFVAGLASPQDTAGGVKVGEAF
+pdb_id=1tr9, cha... -FSYSELKRLERWQQASANMQRLIEQ-------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY251-()-A.MET252 by relaxing A.GLY251-(M)-A.ALA253
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.ASP132-()-A.LYS133 by filling A.GLN129-(IWDK)-A.ASP134 (72 candidates, BB_DB)
+Resolved A.ASP134-(GASAAET)-A.ALA142 by filling A.TRP131-(DKDGASAAET)-A.ALA142 (46 candidates, BB_DB)
+Resolved A.ASP170-(W)-A.GLY172 by filling A.ASP168-(LDW)-A.GLY172 (61 candidates, BB_DB)
+Resolved A.ARG231-(SL)-A.ASP234 by filling A.ASP229-(GRSL)-A.ASP234 (60 candidates, BB_DB)
+Resolved A.LEU236-(E)-A.ALA238 by filling A.ASP234-(ELE)-A.ALA238 (57 candidates, BB_DB)
+Resolved A.ILE340-(PDN)-A.GLN344 by filling A.THR339-(IPDNQ)-A.ASP345 (53 candidates, BB_DB)
+Resolved A.ALA347-(G)-A.ARG349 by filling A.ASN343-(QDLAG)-A.ARG349 (221 candidates, BB_DB)
+Resolved A.GLY358-(H)-A.GLU360 by filling A.ASN355-(SLGH)-A.GLU360 (115 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.60623e+16)
+No more stereo-chemical problems -> final energy: 10665.2
+
+
+Build model with the following alignment:
+target METELKETARGTCPVAHGGQSSVGGCPVHRLAEDFDPFQDAYMADPAQFVRWAREQVPIF
+pdb_id=6gii, cha... ---------------------------VHRLAEDFDPFQDAYMADPAQFVRWAREQVPIF
+
+target YAPKLNYWVVTRYDTIKQIFRDPVTFSPSNVLQSFAQPSAEVRQVLERYGYAFNRTLVNE
+pdb_id=6gii, cha... YAPKLNYWVVTRYDTIKQIFRDPVTFSPSNVLQSFAQPSAEVRQVLERYGYAFNRTLVNE
+
+target DEPMHLERRRVLMEPFASEHLAEHEPMVRELVRRAVNRFIDTGRADLVDQMIWEVPFTVA
+pdb_id=6gii, cha... DEPMHLERRRVLMEPFASEHLAEHEPMVRELVRRAVNRFIDTGRADLVDQMIWEVPFTVA
+
+target LHFLGVDDDDREKMRRFAIAHTVNAFGRPSPEEQLAVAETVGQFWQFCGEVLEKMRRTAD
+pdb_id=6gii, cha... LHFLGVDDDDREKMRRFAIAHTVNAFGRPSPEEQLAVAETVGQFWQFCGEVLEKMRRTAD
+
+target GPGWMRYSIRQQKLYPDVVTDSYLHSMMQAIIVAAHETTVFATTNALKTLLEHETVWREI
+pdb_id=6gii, cha... GPGWMRYSIRQQKLYPDVVTDSYLHSMMQAIIVAAHETTVFATTNALKTLLEHETVWREI
+
+target CADPSLIPAAAEECLRYNGPVAGWRRRTTREVEVEGVRLPVGANILMVVASANHDSAHFD
+pdb_id=6gii, cha... CADPSLIPAAAEECLRYNGPVAGWRRRTTREVEVEGVRLPVGANILMVVASANHDSAHFD
+
+target DPEFFDIGRSNASEHLNFGYGAHQCLGRNLGRMEMQIMIEELSRRLPHMRLAEQRFDYLH
+pdb_id=6gii, cha... DPEFFDIGRSNASEHLNFGYGAHQCLGRNLGRMEMQIMIEELSRRLPHMRLAEQRFDYLH
+
+target NVSFRAPRHLWVEWDPAQNPERRDPDILRLRQPVRIGPPRAKDVVRTMEVAAVERPSEDI
+pdb_id=6gii, cha... NVSFRAPRHLWVEWDPAQNPERR-------------------------------------
+
+target VVLHLTRPDRRPLPRWSPGAHIDIECGEPDRSRQYSLCSDPENRDAWRVAVQRDPASRGG
+pdb_id=6gii, cha... ------------------------------------------------------------
+
+target SRWIHEEVRPGMLLRVRGPRNSFRLDEHAPRYLFLAGGIGITPIMTMAARAKELGTDYEL
+pdb_id=6gii, cha... ------------------------------------------------------------
+
+target HYSVRSRTSLIFVDELRQIHGDRLHVYVSEEGVRNDLAALIRRASAGTQIYACGPQRMLD
+pdb_id=6gii, cha... ------------------------------------------------------------
+
+target TLERLIENRPEVTLRVEHFFGEPSHLDPAKERPFQVVLRNSGLTVEVPADKTLLEVLRAY
+pdb_id=6gii, cha... ------------------------------------------------------------
+
+target NIEVQSDCEEGLCGTCEVSVVEGEVDHRDSVLTRAERRENRRMMCCCSRAKTERLVLDL
+pdb_id=6gii, cha... -----------------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 35393.9)
+No more stereo-chemical problems -> final energy: -18056.7
+
+
+Build model with the following alignment:
+target VSQNQIDDALNGLTTVKVQFDEGIAWVSLNRPDKRNAMSPTLNREMLQVLEALEFDDRCG
+pdb_id=2vsu, cha... ---------EGRWKTVKVEIEDGIAFVILNRPEKRNAMSPTLNREMIDVLETLEQDPAAG
+
+target VVVLTGEGDSFSAGMDLKEYFRETDNAPALIKAQIRRAAGAWQWRKLRFYAKPTIAMVNG
+pdb_id=2vsu, cha... VLVLTGAGEAWTAGMDLKEYFREV--GPEILQEKIRREASQWQWKLLRMYAKPTIAMVNG
+
+target WCFGGAFTPLIACDLAVAADEATFGLSEINWGIIPAGNVTKAVSQVCGERAALYYIMSGE
+pdb_id=2vsu, cha... WCFGGGFAPLVACDLAICADEATFGLSEINYGIPPGNLVSKAMADTVGHRQSLYYIMTGK
+
+target PFGGQKAREIGLVNESVPLAALRERTRELAKTLLGKNPTVLRQAKHALRRVEPMDWDLSE
+pdb_id=2vsu, cha... TFGGQKAAEMGLVNESVPLAQLREVTIELARNLLEKNPVVLRAAKHGFKRCRELTWEQNE
+
+target EYLAAKAEQTAAIDPEKGRTKGMKQFLDDKTIRPGLEGYRRGE
+pdb_id=2vsu, cha... DYLYAKLDQSRLLD-----------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.THR84-(DN)-A.ALA87 by filling A.THR84-(DNA)-A.PRO88 (70 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.42106e+09)
+Perform energy minimization (iteration 2, energy: 4435.81)
+No more stereo-chemical problems -> final energy: 2976.92
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMQEQTAKEDVADSATSVGAIVSIEKAEKNFVITYASGKKA
+pdb_id=6jr6, cha... ---------------------------------LGNCTAYS-VKGNKV--VFSCANNSKI
+
+target QISILNDHLFRYHLDPTGKFEE-YPTPNDPKHVAKITAKTMADYGTQAFEQTNVTDSGNQ
+pdb_id=6jr6, cha... MLQLCSGEVVKIWASADGNFVRNNES------FA------VIEEDLGWKGNVTVKEEPST
+
+target FILENNGLKIIFEKESALMKVLDKKKNQVILEETAPLSFK--NDKATQTLKQSSQENYFG
+pdb_id=6jr6, cha... YEIFTEQLRIRVNKAPFQLQIFDK-YQKLLFSDYAEKGFVNDNGKIRTNKVLRNDEQFFG
+
+target GGTQNGRFTHKGTAIQIVNTNNWVD----GGVASPNPFYWSTAGYGVVRNTWKPGNYDFG
+pdb_id=6jr6, cha... LGEKSGNLNRRGSAYKMWNSDQPCYGVNEDPLYKSIPFFMSSYRYGIFFDNTYKTEFKFG
+
+target SHDPQTTTTTHEGTDFDAFYFFNDSSAGILKDYYELTGKPALMPEYGFYEAHLNAYNRDY
+pdb_id=6jr6, cha... SESNDYYSFEAPAGQMVYYFMFGNDYKEIIQNYIALTGKPIMPPKWALG--F----SQCR
+
+target WVKVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQFSARAVIDRYKKND
+pdb_id=6jr6, cha... GD-----------------YTR-------------ED----------QAREIAAEFRKRK
+
+target MPLGWFLPNDGYGAGYGQTDSLDGDVQNLKEFTDYAQANGVEVGLWTQSNLH--------
+pdb_id=6jr6, cha... IPCDIIYQDIGWTEGLQDFDWRKNNYNNPKGMVKDLSDMGFKMIVSQDPVISQANQQQWK
+
+target ------------------------PADPKNPK---KGERDIA----KEVSVAGVKALKTD
+pdb_id=6jr6, cha... EADALGHLVKDVRTGKSYDMPWPWGGNCGVVDFTKPEVADWWGSYQQKPLNDGVRGFWTD
+
+target VAWVG-------YGYS--------------FGLNGVEDAANVFVKETDGAVRPMIVSLDG
+pdb_id=6jr6, cha... MGEPAWSNEDAVDRLNMKHHLGMHNEIHNVYGFTWDKVVTEQFYKHNPN-KRIFQMTRAA
+
+target WAGTQRHAGIWTGDQ------TGGQWEYIRFHIPTYIGTSLSGQPNVGSDMDGIFGG---
+pdb_id=6jr6, cha... YAGLQRYTFGWSGDSGNGSNVL-DGWKQMANQIPVGLSAGMGLIPFWTCDISGYCGDIKD
+
+target --KNKEVNIRDFQWKTFTPVQLNMDGWGSNPKTPFAFDQEATDLNRAYLKLKSMMMPYNY
+pdb_id=6jr6, cha... YDAMAELYVRWLQFGVFTPLSRAHHEGGN-AVEPWKFGTEAENISRKSIELKYKLFPYLY
+
+target SIAKESV-DGLPMVRAMALEFPNEGTAYTKDSQYQYMWGPNLLVAPIYNGNQDEAGNSIR
+pdb_id=6jr6, cha... TYAREAHDTGLPIMRALLLEYPNDKETFKL--NGQFLVGKELLVAPVVEQGA-----V-T
+
+target DGIYLPDEKQVWVDLFTGEK-YQGGRVLNGVKTPLWKVPVFVKDGSIIPMTNPNNNPKEI
+pdb_id=6jr6, cha... KDVYLPEGE--WIDFNNCKTKYKGEQWI-TVDAPLNTIPVFVKKGSIIPQMPVMQYIDEK
+
+target QRDQRSFLIYP---NGATSFNMYEDDGISTSYEAGQSATTKINSQGPKSNEKGDLTVTIE
+pdb_id=6jr6, cha... KVYPVTFDIFPGNLNKETSFTFYEDDGESRDYERDVFCKTKITSKASN----EEIKITVG
+
+target P-TKGSYKDFVDERSTTLDLLASEAPESVTAMVGGTEVTLK-Q-AANKEEFLAGT-NLYY
+pdb_id=6jr6, cha... EREYKGYS-PAGPRNFILKIHASNKPKDVF--AGGEKLKNVKPHVLEKNIEADFTKINWS
+
+target FDKEFQVNQYLSEASGEKLNQSALSVKLAKQSVTAKDVQITVKGFINKGTVDGGNTTVDD
+pdb_id=6jr6, cha... WNEAENVI----------------------------------------------------
+
+target QLTIPANIAINEEKTTPSSLTLQWDQVTEATSYEVERDGTVFGNIQTNTATFDGFSFLSE
+pdb_id=6jr6, cha... ------------------------------------------------------------
+
+target HTFRVRAVGKNGVSEWSEPIKGKTQDDPYK
+pdb_id=6jr6, cha... ------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 38).
+Initialized default backbone scoring for modelling.
+Closed: A.GLU82-()-A.TYR83 by relaxing A.GLU81-(EY)-A.PRO84
+Closed: A.GLY439-()-A.TYR440 by relaxing A.VAL438-(GY)-A.GLY441
+Closed: A.VAL589-()-A.ASP590 by relaxing A.SER588-(VDG)-A.LEU592
+Closed: A.PRO758-()-A.THR759 by relaxing A.ILE756-(EP)-A.THR759
+Closed: A.LYS797-()-A.GLN798 by relaxing A.LYS797-(QA)-A.ALA800
+Trying to merge 32 gap(s) with distance 0.
+Merged gap A.TYR282-(EA)-A.HIS285 and A.HIS285-(LNAY)-A.ASN290 into A.TYR282-(EAHLNAY)-A.ASN290
+Merged gap A.GLN488-()-A.THR489 and A.THR489-(G)-A.GLY491 into A.GLN488-(TG)-A.GLY491
+Merged gap A.GLN633-(DEAGN)-A.SER639 and A.SER639-(I)-A.ARG641 into A.GLN633-(DEAGNSI)-A.ARG641
+Trying to fill 29 gap(s) by database.
+Resolved A.VAL41-(S)-A.ILE43 by filling A.VAL41-(SIEK)-A.ALA46 (181 candidates, BB_DB)
+Resolved A.LYS48-(NF)-A.VAL51 by filling A.GLU44-(KAEKNF)-A.VAL51 (42 candidates, BB_DB)
+Resolved A.THR85-(PNDPKH)-A.VAL92 by filling A.GLU82-(YPTPNDPKH)-A.VAL92 (97 candidates, BB_DB)
+Resolved A.ALA93-(KITAKT)-A.MET100 by filling A.ALA93-(KITAKTMAD)-A.TYR103 (94 candidates, BB_DB)
+Resolved A.LYS143-(K)-A.LYS145 by filling A.ASP142-(KKKN)-A.GLN147 (93 candidates, BB_DB)
+Resolved A.LYS159-()-A.ASN160 by filling A.LYS159-(NDK)-A.ALA163 (61 candidates, BB_DB)
+Resolved A.ASP202-()-A.GLY203 by filling A.ASN198-(NWVD)-A.GLY203 (127 candidates, BB_DB)
+Failed at loop insertion (A.TYR282-(EAHLNAY)-A.ASN290), only 10 candidates
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNF)-A.TYR313), only 0 candidates
+Failed at loop insertion (A.GLU315-(YQPGDLGNLNGTL)-A.GLU329), only 0 candidates
+Failed at loop insertion (A.SER330-(LNGEKENYQF)-A.SER341), only 9 candidates
+Resolved A.HIS405-()-A.PRO406 by filling A.HIS405-(PADP)-A.LYS410 (62 candidates, BB_DB)
+Resolved A.LYS413-()-A.LYS414 by filling A.PRO412-(KKGE)-A.ARG417 (149 candidates, BB_DB)
+Resolved A.ALA420-()-A.LYS421 by filling A.ARG417-(DIA)-A.LYS421 (212 candidates, BB_DB)
+Resolved A.SER443-()-A.PHE444 by filling A.VAL438-(GYGYSF)-A.GLY445 (100 candidates, BB_DB)
+Resolved A.GLY462-(A)-A.VAL464 by filling A.GLU459-(TDGA)-A.VAL464 (42 candidates, BB_DB)
+Resolved A.GLN488-(TG)-A.GLY491 by filling A.GLN488-(TGGQ)-A.TRP493 (48 candidates, BB_DB)
+Resolved A.GLY524-()-A.LYS525 by filling A.MET518-(DGIFGG)-A.LYS525 (50 candidates, BB_DB)
+Resolved A.SER551-(N)-A.PRO553 by filling A.TRP549-(GSN)-A.PRO553 (50 candidates, BB_DB)
+Resolved A.LYS611-(DS)-A.GLN614 by filling A.THR610-(KDSQ)-A.TYR615 (40 candidates, BB_DB)
+Resolved A.GLN633-(DEAGNSI)-A.ARG641 by filling A.GLY631-(NQDEAGNSI)-A.ARG641 (92 candidates, BB_DB)
+Resolved A.LYS650-(QV)-A.TRP653 by filling A.PRO647-(DEKQV)-A.TRP653 (41 candidates, BB_DB)
+Resolved A.LYS661-()-A.TYR662 by filling A.LEU656-(FTGEK)-A.TYR662 (69 candidates, BB_DB)
+Resolved A.LEU668-(N)-A.GLY670 by filling A.LEU668-(NGV)-A.LYS672 (59 candidates, BB_DB)
+Failed at loop insertion (A.PRO711-()-A.ASN712), only 39 candidates
+Resolved A.LYS745-(SNEK)-A.GLY750 by filling A.PRO744-(KSNEKG)-A.ASP751 (393 candidates, BB_DB)
+Resolved A.LYS764-(D)-A.PHE766 by filling A.SER762-(YKDF)-A.VAL767 (53 candidates, BB_DB)
+Resolved A.THR786-(AM)-A.VAL789 by filling A.GLU783-(SVTAM)-A.VAL789 (154 candidates, BB_DB)
+Resolved A.THR809-()-A.ASN810 by filling A.LEU806-(AGTN)-A.LEU811 (52 candidates, BB_DB)
+Trying to merge 5 gap(s) with distance 1.
+Merged gap A.GLU315-(YQPGDLGNLNGTL)-A.GLU329 and A.SER330-(LNGEKENYQF)-A.SER341 into A.GLU315-(YQPGDLGNLNGTLESLNGEKENYQF)-A.SER341
+Trying to fill 4 gap(s) by database.
+Failed at loop insertion (A.TYR282-(EAHLNAY)-A.ASN290), only 10 candidates
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNF)-A.TYR313), only 0 candidates
+Failed at loop insertion (A.GLU315-(YQPGDLGNLNGTLESLNGEKENYQF)-A.SER341), only 0 candidates
+Failed at loop insertion (A.PRO711-()-A.ASN712), only 39 candidates
+Trying to merge 4 gap(s) with distance 2.
+Merged gap A.VAL295-(KVAEGTAGAVKFEDGNF)-A.TYR313 and A.GLU315-(YQPGDLGNLNGTLESLNGEKENYQF)-A.SER341 into A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.TYR282-(EAHLNAY)-A.ASN290), only 15 candidates
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341), only 0 candidates
+Failed at loop insertion (A.PRO711-()-A.ASN712), only 39 candidates
+Trying to merge 3 gap(s) with distance 3.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.TYR282-(EAHLNAY)-A.ASN290), only 15 candidates
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341), only 0 candidates
+Failed at loop insertion (A.PRO711-()-A.ASN712), only 39 candidates
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.TYR282-(EAHLNAY)-A.ASN290), only 15 candidates
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341), only 0 candidates
+Resolved A.PRO711-()-A.ASN712 by filling A.PHE707-(LIYPNGA)-A.THR715 (44 candidates, BB_DB)
+Trying to fill 2 gap(s) by database.
+Resolved A.TYR282-(EAHLNAY)-A.ASN290 by filling A.TYR282-(EAHLNAYN)-A.ARG291 (89 candidates, BB_DB)
+Failed at loop insertion (A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.VAL295-(KVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341 by filling A.TYR293-(WVKVAEGTAGAVKFEDGNFYKEYQPGDLGNLNGTLESLNGEKENYQF)-A.SER341 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.50559e+28)
+Perform energy minimization (iteration 2, energy: 75923.1)
+Perform energy minimization (iteration 3, energy: 61812.8)
+Perform energy minimization (iteration 4, energy: 56877.1)
+Perform energy minimization (iteration 5, energy: 53990)
+Perform energy minimization (iteration 6, energy: 51467.3)
+Perform energy minimization (iteration 7, energy: 49519.3)
+No more stereo-chemical problems -> final energy: 48621.8
+
+
+Build model with the following alignment:
+target GSHMGTE---------------DLKYSLERLREILERLEENPSEKQIVEAIRAIVENNAQ
+pdb_id=5j0h, cha... ------KYELRRALEELEKALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNKI
+
+target IVEAIRAIVEILALIVENNRAIIEALEAIGGGTKILEEMKKQLKDLKRALERG
+pdb_id=5j0h, cha... IVEVLRIIAEVLKI---------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6060.43)
+No more stereo-chemical problems -> final energy: -1383.99
+
+
+Build model with the following alignment:
+target MTDALGIDKELNLKKKQRAPKVKLDDQRLLSEKGIPKLRKMA-PRLKFKGKGHEFSDTAR
+pdb_id=6skl, cha... ---------------RKRRPQVKLTAEKLLSDKGLPYVLKNAHKRIRISSKKNSYDNLSN
+
+target LLSFYQEWLDDLFPKATFLDALAMVEKAGHKTT-VRNARLKWIDELRPKASFE
+pdb_id=6skl, cha... IIQFYQLWAHELFPKAKFKDFMKICQTVGKTDPVLREYRVSLFRDE-------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA42-()-A.PRO43 by relaxing A.MET41-(A)-A.PRO43
+Closed: A.THR92-()-A.VAL93 by relaxing A.THR91-(TVR)-A.ASN95
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 86557.3)
+No more stereo-chemical problems -> final energy: 2472.16
+
+
+Build model with the following alignment:
+target MMNAQTT-KIALLLAASAVTMALTGCGGSDGNDGNPGEPGGEPAPAIQILNFTFDKSVIT
+pdb_id=4lm8, cha... ---------------------------------------------SIQTLNLDITKVSYE
+
+target NGVPSVEFTVTNENDLPVVGLQKMRFA-AAQLIPQGATGAGNASQWQYFGDETCDVAATC
+pdb_id=4lm8, cha... NGAPMVTVFATNEADMPVIGLANLEIKKALQLIPEGATGPGNSANWQGLGSSK-------
+
+target PGTFVDQKNGHYSYTFNMNLTANAKITYNDQLAQRVLIRAYNTPLPDGTQVPNSNAFVDF
+pdb_id=4lm8, cha... --SYVDNKNGSYTFKFDA-FD--SNKVFNAQLTQRFNVVSAAGKLADGTTVPVAEMVEDF
+
+target TADTGAAPTYSRKIVATESCNTCHQDLANVKHGGAYSDVNYCATCHTAGKV----GVGKE
+pdb_id=4lm8, cha... DGQ-GNAPQYTKNIVSHEVCASCHVEGEKIYHQ--ATEVETCISCHTQEFADGRGKPHVA
+
+target FNVLVHAKHKDLT-------------LGSLESCQSCHAANDAAPDWGNWSRIPTAATCGS
+pdb_id=4lm8, cha... FSHLIHNVHNANKAWGKDNKIPTVAQNIVQDNCQVCHVESDMLTEAKNWSRIPTMEVCSS
+
+target CHSTVDFAAGKGHSQQLDNSNCIACHNSDWTAELHTGKTADKKAVIAQLGMQATLVGQT-
+pdb_id=4lm8, cha... CHVDIDFAAGKGHSQQLDNSNCIACHNSDWTAELHTAKTTATKNLINQYGIETTSTINTE
+
+target DDTAVLTVSILDKDGNAIDAATVQDKIKRLETVTNVGPNFPIMGYNKSPGSGAAKIAKDL
+pdb_id=4lm8, cha... TKAATISVQVVDANGTAVDLKTILPKVQRLEIITNVGPNNATLGYSGK-----DS--IFA
+
+target VKDGALQAGVTLVD-GKLV-FTTPALPFGTG--DTDTAFTFIGLEMCSTGTSLTACTV--
+pdb_id=4lm8, cha... IKNGALDPKATINDAGKLVYTTTKDLKLGQNGADSDTAFSFVGWSMCSSEGKFVDCADPA
+
+target --DSAT---TSMKAELAFGTKSGNAPSMRHVNSVNFSTCQGCHSDTFEIHK-GHHSGFVM
+pdb_id=4lm8, cha... FDGVDVTKYTGMKADLAFATLSGKAPSTRHVDSVNMTACANCHTAEFEIHKGKQHAGFVM
+
+target TEQVSHAKDANGKAIVGVDGCVACHTPDGTYASGANKGAFEMKLHVIH--GEQGVIK-EC
+pdb_id=4lm8, cha... TEQLSHTQDANGKAIVGLDACVTCHTPDGTY-SFANRGALELKLHKKHVEDAYGLIGGNC
+
+target TQCHNDFNLDAFKVKGALAT-----SAGKYTTPITATCTSCHAPES-----IGHGLENMG
+pdb_id=4lm8, cha... ASCHSDFNLESFKKKGALNTAAAADKTGLYSTPITATCTTCHTVGSQYMVHTKETLESFG
+
+target AIVNGDYVQANQAAQSETCFYCHKPTPTDHTQVKM
+pdb_id=4lm8, cha... AVVDGTKDDATSAAQSETCFYCHTPTVADHTKVK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 22).
+Initialized default backbone scoring for modelling.
+Closed: A.THR340-()-A.ASP341 by relaxing A.GLN339-(TD)-A.ASP342
+Closed: A.ASP414-()-A.GLY415 by relaxing A.VAL413-(D)-A.GLY415
+Closed: A.LYS500-()-A.GLY501 by relaxing A.LYS500-(GH)-A.HIS503
+Trying to merge 19 gap(s) with distance 0.
+Trying to fill 19 gap(s) by database.
+Resolved A.ALA86-()-A.ALA87 by filling A.ARG84-(FAAA)-A.GLN89 (41 candidates, BB_DB)
+Resolved A.THR111-(CDVAATCPG)-A.THR121 by filling A.ASP109-(ETCDVAATCPGT)-A.PHE122 (57 candidates, BB_DB)
+Resolved A.MET136-(N)-A.LEU138 by filling A.PHE134-(NMN)-A.LEU138 (139 candidates, BB_DB)
+Resolved A.THR139-(AN)-A.ALA142 by filling A.LEU138-(TANA)-A.LYS143 (123 candidates, BB_DB)
+Resolved A.ASP181-(T)-A.GLY183 by filling A.THR179-(ADTG)-A.ALA184 (66 candidates, BB_DB)
+Resolved A.GLY211-(GA)-A.TYR214 by filling A.VAL208-(KHGGA)-A.TYR214 (65 candidates, BB_DB)
+Resolved A.VAL229-()-A.GLY230 by filling A.GLY227-(KVGV)-A.GLY232 (110 candidates, BB_DB)
+Resolved A.THR247-()-A.LEU248 by filling A.LYS242-(HKDLT)-A.LEU248 (265 candidates, BB_DB)
+Resolved A.SER388-(PGSGA)-A.ALA394 by filling A.GLY384-(YNKSPGSGA)-A.ALA394 (54 candidates, BB_DB)
+Resolved A.LYS395-(IA)-A.LYS398 by filling A.GLY392-(AAKIA)-A.LYS398 (44 candidates, BB_DB)
+Resolved A.VAL418-()-A.PHE419 by filling A.VAL418-(FTTPAL)-A.PRO425 (234 candidates, BB_DB)
+Resolved A.GLY429-()-A.ASP430 by filling A.PHE426-(GTG)-A.ASP430 (40 candidates, BB_DB)
+Resolved A.VAL454-()-A.ASP455 by filling A.ALA451-(CTVD)-A.SER456 (51 candidates, BB_DB)
+Resolved A.THR458-()-A.THR459 by filling A.THR453-(VDSAT)-A.THR459 (40 candidates, BB_DB)
+Resolved A.TYR539-(A)-A.SER541 by filling A.THR538-(YASG)-A.ALA543 (47 candidates, BB_DB)
+Resolved A.HIS556-()-A.GLY557 by filling A.HIS556-(GEQG)-A.VAL561 (100 candidates, BB_DB)
+Resolved A.LYS563-()-A.GLU564 by filling A.GLN559-(GVIK)-A.GLU564 (57 candidates, BB_DB)
+Resolved A.THR585-()-A.SER586 by filling A.THR585-(SAG)-A.LYS589 (52 candidates, BB_DB)
+Resolved A.SER606-()-A.ILE607 by filling A.ALA603-(PESI)-A.GLY608 (46 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.56938e+20)
+Perform energy minimization (iteration 2, energy: 56734.5)
+No more stereo-chemical problems -> final energy: 51647.9
+
+
+Build model with the following alignment:
+target QVQLAETGGGLVQPGGARTLSCAASESISSFYFMGWYRQAPGKPRELVAEISNYGRTDYG
+pdb_id=6mxt, cha... QVQLQESGGGLVQPGGSLRLSCAASGFAFSSYELRWYRQAPGKQHELVAGITTGGNTYYA
+
+target DSLKGRFTISRDNAANTVNLQMNNLAPEDTALYYCNARKWERSVLEDYWGQGTQVTVSS
+pdb_id=6mxt, cha... DSVKGRFTISRDNAKNTVYLQMSNLRPEDTAVYACNANWD---LLSDYWGQGTQVTVS-
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.TRP100-(ERS)-A.VAL104 by filling A.LYS99-(WERSV)-A.LEU105 (93 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 533235)
+No more stereo-chemical problems -> final energy: 1127.82
+
+
+Build model with the following alignment:
+target MDRAKLLLLLLLLLLPQAQAVGNLWVTVYYGVPVWKGATTTLFCASDAKAYETEVHNVWA
+pdb_id=4r4h, cha... ------------------------------------EATTTLFCASDAKAYDTEVHNVWA
+
+target THACVPADPNPQEMVLENVTENFNMWKNDMVNQMQEDVISLWDQSLKPCVKLTGGSAITQ
+pdb_id=4r4h, cha... THACVPTDPNPQEVVLGNVTENFNMWKNNMVDQMHEDIISLWDESLKPCVKLTGGSVITQ
+
+target ACPKVTFDPIPIHYCTPAGYAILKCNDKIFNGTGPCHNVSTVQCTHGIKPVVSTQLLLNG
+pdb_id=4r4h, cha... ACPKVSFQPIPIHYCVPAGFAILKCNNKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNG
+
+target SLAEGEIIIRSENLTNNVKTIIVHLNQSVEIVCTRPGNG--------------------G
+pdb_id=4r4h, cha... SLAEEDIVIRSEDFTDNVKTIIVQLNESVVINCTRPN-----------------------
+
+target DIRQAHCNISEDKWNETLQRVSKKLAEHFQNKTIKFASSSGGDLEVTTHSFNCRGEFFYC
+pdb_id=4r4h, cha... -IRQAHCNISRAKWNNTLQQIVIKLREKFRNKTIAFNQSSGGDPEIVMHSFNCGGEFFYC
+
+target NTSGLFNGAYTPNG-TK-SNSSSIITIPCRIKQIINMWQEVGRAMYAPPIKGNITCKSNI
+pdb_id=4r4h, cha... NTAQLFNSTWNV---TNGTEGNDIITLQCRIKQIINMWQKVGKAMYAPPITGQIRCSSNI
+
+target TGLLLVRDGGTEPN-DTETFRPGGGDMRNNWRSELYKYKVVEIKPLGVAPTTTKR
+pdb_id=4r4h, cha... TGLLLTRDGGNSTETETEIFRPGGGDMRDNWRSELYKYKV---------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.GLY217-(NGGD)-A.ILE222 by filling A.ARG215-(PGNGGD)-A.ILE222 (223 candidates, BB_DB)
+Resolved A.PRO292-(NG)-A.THR295 by filling A.THR291-(PNGT)-A.LYS296 (74 candidates, BB_DB)
+Resolved A.LYS296-()-A.SER297 by filling A.GLY294-(TKS)-A.ASN298 (87 candidates, BB_DB)
+Resolved A.ASN352-()-A.ASP353 by filling A.GLY348-(TEPN)-A.ASP353 (87 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 85736.2)
+No more stereo-chemical problems -> final energy: 19888
+
+
+Build model with the following alignment:
+target CSVVVGENYSIKCDATKCTIEDKNRGIIKTVTGSRCEELAKAVQKAQ
+pdb_id=6oe4, cha... --------IVSCYGKTKCTASNKNRGIIKTF-SNGC-----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.VAL31-(T)-A.GLY33 by filling A.THR30-(VTGS)-A.ARG35 (51 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 64296.7)
+No more stereo-chemical problems -> final energy: 1321.46
+
+
+Build model with the following alignment:
+target TPELALDWRQSAEEVIVKLRVGVGP-LQLEDVDAAFTDTDCVVRFAGGQ-QWGGVFYAEI
+pdb_id=2cr0, cha... ----NYRWTQTLAELDLAVPFRVSFRLKGKDVVVDIQRRHLRVGLKGQPPVVDGELYNEV
+
+target KSSCAKVQTRKGSLLHLTLPKKVPMLTWPSLLVE
+pdb_id=2cr0, cha... KVEESSWLIEDGKVVTVHLEKINKMEWWNRLVT-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.GLN48-()-A.GLN49 by relaxing A.ALA45-(GGQ)-A.GLN49
+Trying to fill 1 gap(s) by database.
+Resolved A.PRO25-()-A.LEU26 by filling A.GLY22-(VGPL)-A.GLN27 (58 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.86502e+24)
+Perform energy minimization (iteration 2, energy: 7614.36)
+No more stereo-chemical problems -> final energy: 6445.21
+
+
+Build model with the following alignment:
+target MTVVPENFVPGLDGVVAFTTEIAEPDKDGGALRYRGVDIEDLVSQRVTFGDVWALLVDGN
+pdb_id=4xgh, cha... ------TYDPGFMSTASCNSAITYIDGDKGELLYRGYPIDNLAQ-NADFLESCYLLLKGE
+
+target FGSGLPPAEPF----------------------PLPIHSGDVRVDVQAGLAMLAPIWGYA
+pdb_id=4xgh, cha... ----LPNAAQKKEFVATVTKHTMVHEQMQFFFRGFRR-DAHPMAILVAAVGALSAFYHDS
+
+target -P--LLDIDDATARQQLARASVMALSYVAQSARGIYQPAVPQRIIDECSTVTARFMTRWQ
+pdb_id=4xgh, cha... ----DPRHREVSAIRMIAKLPTL-VAMAYKYSIG-QPFVYPRNDL----SYSANFMRMMF
+
+target G------EPDPRHIEAIDAYWVSAAEHGMNASTFTARVIASTGADVAAALSGAIGAMSGP
+pdb_id=4xgh, cha... ANPCEEYKVNDVLVRALDRILILHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGP
+
+target LHGGAPARVLPMLDEVERAGDARSVVKGILDR--GEKLMGFGHRVYRAEDPRARVLRAAA
+pdb_id=4xgh, cha... --GGANEAALNMLEQIGTPDNIPEFIK---------------------YDPRAKLMRETC
+
+target ERL----G---APRYEVAVAVEQAALSELRERRPDRAIETNVEFWAAVVLDFARVPANMM
+pdb_id=4xgh, cha... YEVLNELGLHDDPLFKLAMQLEK--------------LYPNVDFYSGIVQRALGIPTSMF
+
+target PAMFTCGRTAGWCAHILEQKRL--GKLVRPSAIYVGPGPRSPESVDGWERVLTTAGHHHH
+pdb_id=4xgh, cha... TCIFAMARTVGWIAQWNEMIADPEQKIGRPRQLFIGETPRAAKPIDQ-------------
+
+target HH
+pdb_id=4xgh, cha... --
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Trying to merge 15 gap(s) with distance 0.
+Merged gap A.LEU270-()-A.GLY271 and A.GLY271-()-A.ALA272 into A.LEU270-(G)-A.ALA272
+Trying to fill 14 gap(s) by database.
+Resolved A.SER44-(Q)-A.ARG46 by filling A.SER44-(QRVT)-A.PHE49 (101 candidates, BB_DB)
+Resolved A.ASN60-(FGSG)-A.LEU65 by filling A.GLY59-(NFGSGL)-A.PRO66 (87 candidates, BB_DB)
+Failed at loop insertion (A.PHE71-()-A.PRO72), only 0 candidates
+Resolved A.ILE75-(H)-A.SER77 by filling A.PRO74-(IHS)-A.GLY78 (44 candidates, BB_DB)
+Resolved A.ALA98-(P)-A.LEU100 by filling A.TRP95-(GYAPL)-A.LEU101 (91 candidates, BB_DB)
+Resolved A.MET118-(A)-A.LEU120 by filling A.MET118-(ALS)-A.TYR122 (46 candidates, BB_DB)
+Resolved A.GLY129-(I)-A.TYR131 by filling A.ARG128-(GIYQ)-A.PRO133 (60 candidates, BB_DB)
+Resolved A.ILE140-(DECS)-A.THR145 by filling A.GLN137-(RIIDECS)-A.THR145 (44 candidates, BB_DB)
+Resolved A.GLY156-()-A.GLU157 by filling A.ARG153-(WQGEP)-A.ASP159 (110 candidates, BB_DB)
+Resolved A.PRO209-(LH)-A.GLY212 by filling A.SER207-(GPLHG)-A.GLY213 (41 candidates, BB_DB)
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Resolved A.LEU270-(G)-A.ALA272 by filling A.LEU270-(GAPR)-A.TYR275 (94 candidates, BB_DB)
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Resolved A.LEU342-()-A.GLY343 by filling A.ARG341-(LGKLV)-A.ARG347 (63 candidates, BB_DB)
+Trying to merge 3 gap(s) with distance 1.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.PHE71-()-A.PRO72), only 0 candidates
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Trying to merge 3 gap(s) with distance 2.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.PHE71-()-A.PRO72), only 0 candidates
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Trying to merge 3 gap(s) with distance 3.
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.PHE71-()-A.PRO72), only 0 candidates
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Failed at loop insertion (A.PHE71-()-A.PRO72), only 0 candidates
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Trying to fill 3 gap(s) by database.
+Resolved A.PHE71-()-A.PRO72 by filling A.PRO70-(FPLPIHSGDVR)-A.VAL82 (178 candidates, BB_DB)
+Failed at loop insertion (A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256), only 0 candidates
+Failed at loop insertion (A.GLN283-(AALSELRERRPDRA)-A.ILE298), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.LYS236-(GILDRGEKLMGFGHRVYRA)-A.GLU256 by filling A.VAL235-(KGILDRGEKLMGFGHRVYRA)-A.GLU256 (6 candidates, BB)
+Resolved A.GLN283-(AALSELRERRPDRA)-A.ILE298 by filling A.GLN283-(AALSELRERRPDRA)-A.ILE298 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.38414e+20)
+Perform energy minimization (iteration 2, energy: 18688.4)
+Perform energy minimization (iteration 3, energy: 7212.84)
+Perform energy minimization (iteration 4, energy: 4531.17)
+No more stereo-chemical problems -> final energy: 2974.54
+
+
+Build model with the following alignment:
+target LAGVDSAGQVLPDSYPSAPAEQLPYFLLEPQDAYIVKNKPVELHCRAFPATQIYFKCNGE
+pdb_id=5ftt, cha... -----------------SAPGTLPHFIEEPEDAYIIKSNPIALRCKARPAMQIFFKCNGE
+
+target WVSQNDHVTQESLDEATGLRVREVQIEVSRQQVEELFGLEDYWCQCVAWSSSGTTKSRRA
+pdb_id=5ftt, cha... WVHQNEHVSEESLDESSGLKVREVFINVTRQQVEDFHGPEDYWCQCVAWSHLGTSKSRKA
+
+target YIRIAYLRKNFDQEPLAKEVPLDHEVLLQCRPPEGVPVAEVEWLKNEDVIDPAQDTNFLL
+pdb_id=5ftt, cha... SVRIAYLRKNFEQDPQGREVPIEGMIVLHCRPPEGVPAAEVEWLKNEEPIDSEQDENIDT
+
+target TIDHNLIIRQARLSDTANYTCVAKNIVAKRRSTTATVIVYVNGGWSSWAEWSPCSNRCGR
+pdb_id=5ftt, cha... RADHNLIIRQARLSDSGNYTCMAANIVAKRRSLSATVVVYVNGGWSSWTEWSACNVRCGR
+
+target GWQKRTRTCTNPAPLNGGAFCEGQAFQKTACTTVCPVDGAWTEWSKWSACSTECAHWRSR
+pdb_id=5ftt, cha... GWQKRSRTCTNPAPLNGGAFCEGMSVQKITCTALCPVDG---------------------
+
+target ECMAPPPQNGGRDCSGTLLDSKNCTDGLCVLNQRTLNDPKSHPLETSGDV
+pdb_id=5ftt, cha... --------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.40119e+11)
+No more stereo-chemical problems -> final energy: 8665.22
+
+
+Build model with the following alignment:
+target MAHHHHHHMTSPLRNDRLLRALRREPVDCTPVWLMRQAGRYLPEYRATRAKAGSFLAMAK
+pdb_id=1j93, cha... -------------TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSE
+
+target NPEIACEVTLQPLRRFPLDAAILFSDILTIPDAMGLELYFVEGEGPKFRHPVRDEAAIAR
+pdb_id=1j93, cha... NVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEK
+
+target LAVPDMEQDLGYVMDAVRLIRRELDGQVPLIGFSGSPWTLACYMVEGGGSKDFARIKAMA
+pdb_id=1j93, cha... VREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLA
+
+target LNHPQALHRLLEVTTDAVIAYLGAQRAAGAQALQVFDTWGGVLSPAMYREFSLRYLQRIA
+pdb_id=1j93, cha... FAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIV
+
+target EGLERGEGSERTPLILFGKGTGLHLEALSQTGADALGLDWTLDLDEAMRRTGGRVALQGN
+pdb_id=1j93, cha... DSVKLTH--PNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGN
+
+target LDPTTLYASPDAIAAAAARVLDTYAAGNGGSREGHVFNLGHGMSPDMDPAHVQVLVDAVH
+pdb_id=1j93, cha... VDPGVLFGSKEFITNRINDTVKKA--G---K-GKHILNLGHGIKVGTPEENFAHFFEIAK
+
+target AHSQR
+pdb_id=1j93, cha... GLR--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Merged gap A.TYR324-(AA)-A.GLY327 and A.GLY327-(NGG)-A.SER331 into A.TYR324-(AAGNGG)-A.SER331
+Merged gap A.TYR324-(AAGNGG)-A.SER331 and A.SER331-(R)-A.GLU333 into A.TYR324-(AAGNGGSR)-A.GLU333
+Trying to fill 2 gap(s) by database.
+Resolved A.GLU247-(GS)-A.GLU250 by filling A.GLU247-(GSERT)-A.PRO253 (99 candidates, BB_DB)
+Resolved A.TYR324-(AAGNGGSR)-A.GLU333 by filling A.TYR324-(AAGNGGSREG)-A.HIS335 (68 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.49853e+16)
+Perform energy minimization (iteration 2, energy: 3528.43)
+Perform energy minimization (iteration 3, energy: -89.1991)
+No more stereo-chemical problems -> final energy: -1724.13
+
+
+Build model with the following alignment:
+target NLTKQKDAVSDTGTAAVVKVVESQAELYELKNTNEKASLSKLVSSGNISQKQADSYKAYY
+pdb_id=5nca, cha... --TKQKEAVNDKGKAAVVKVVESQAELYSLEK-NEDASLRKLQADGRITEEQAKAYKEYN
+
+target GKHSGETQTVAN
+pdb_id=5nca, cha... DKNGGANRKVND
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.ASN32-(T)-A.ASN34 by filling A.ASN32-(TNEK)-A.ALA37 (66 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 17852.1)
+No more stereo-chemical problems -> final energy: 8590.07
+
+
+Build model with the following alignment:
+target MTSRIRFLMCPPDHYDVDYVINPWMEGNIHKSSRDRAVEQWQGLYQILKEHAIVDLVTPQ
+pdb_id=6juy, cha... --DDIRILMCPPD------------------SSQERAVEQWKKLHQTIKECAIVDLVKPA
+
+target KGWPDLVFTANAGLVLGDNVVLSRFLHKERQGEEPYFKEWFEGNGYTVYELPKDLPFEGA
+pdb_id=6juy, cha... KGWPDMVFTANAGLVLGENVVLSRFYHKERQGEEPYFKAWFEENGFTVYELPQDLPFEGA
+
+target GDALLDREGRWLWAGYGFRSELDSHPYLAKWLDIEVLSLRLIDERFYHLDTCFCPLANGY
+pdb_id=6juy, cha... GDALFDREGRWLWAGYGFRSELDSHPYIAKWLDTEVVSLRLIDERFYHLDTCFCPLSGGY
+
+target LLYYPGAFDSYSNRLIEMRVAPEKRIAIAEADAVNFACNTVNVESIVIMNKASDALKQSL
+pdb_id=6juy, cha... LLYYPPAFDAYSNRVIEMRIPPEKRIIVEELDAVNFACNAVNVNDIIIMNLVSRTLKEKL
+
+target TGVGFQVLETPLTEFLKAGGAAKCLTLRVTEPVRDEVHANVYVESRIIRIEGHLLDSGLI
+pdb_id=6juy, cha... AEAGFKVRETPLTEFLKAGGAAKCLTLRVTEPILPDVHATVSIESRVIRMEGHLLDAGIL
+
+target NRALDMIVDTGGSFQVLNFNLGEQRQSTSAAEVKVSAPSHEVMEEIISLLIDLGAVDLPQ
+pdb_id=6juy, cha... NQALDLVVENSGSFRVLNFNLGVERNSTSSAEVRVSAPSHQIMEEIMTELIDLGAVPPPQ
+
+target DERDAKLEPVIQDGVAPDDFYVSTIYPTEVRINGQWIKVENQRMDGAIAITQTPNGLLAQ
+pdb_id=6juy, cha... ELCDINTETVTQGGVAPDDFYVSTIYPTEVRVNCEWVQVTGQRMDAAIVVTSNP--PSAR
+
+target CKILRDLKAGEQVIVDVLGIRTIRKTESREQ--R-NTQEFSFMSGGVSSERRVELVVEQV
+pdb_id=6juy, cha... CVLLRDLQVGDRVMVGVEGIRTI-------------------------SERRVELLVEQI
+
+target AWELRKIRDAGGKVVVTAGPVVIHTGGGEHLSRLIREGYVQALLGGNAIAVHDIEQNMMG
+pdb_id=6juy, cha... AWEMRQIRDQGGKIVVTAGPVVIHTGGAQHLSHLVREGYVHALLGGNAIAVHDIEQATMG
+
+target TSLGVDMKRGVAVRGGHRHHLKVINTIRRHGSIAKGVESGIIRSGVMYECVRNQIPFVLA
+pdb_id=6juy, cha... TSLGVDM--------GHRHHLKIINSVRRYGGIRQAVEAGFISKGVMYECVKNNIPYCLA
+
+target GSIRDDGPLPDTQMDLIKAQEEYAKHLEGAEMILMLSSMLHSIGVGNMTPAGVKMVCVDI
+pdb_id=6juy, cha... GSIRDDGPLPDTEMNLVRAQSRYSELIQGADMILMLSSMLHSIGVGNMTPSGVKMVCVDI
+
+target NPAVVTKLSDRGSIESVGVVTDVGLFLSLLTQQLDKLTSPY-VSKVG
+pdb_id=6juy, cha... NPAVVTKL-----VESVGVVTDVGLFLSLLVRQLQQLTR--------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Resolved A.PRO414-(NG)-A.LEU417 by filling A.GLN412-(TPNGL)-A.LEU418 (56 candidates, BB_DB)
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Resolved A.MET544-(KRGVAVRG)-A.GLY553 by filling A.ASP543-(MKRGVAVRGG)-A.HIS554 (50 candidates, BB_DB)
+Resolved A.LEU665-(SDRGS)-A.ILE671 by filling A.LEU665-(SDRGS)-A.ILE671 (65 candidates, BB_DB)
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32), only 0 candidates
+Failed at loop insertion (A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.ASP13-(HYDVDYVINPWMEGNIHK)-A.SER32 by filling A.PRO12-(DHYDVDYVINPWMEGNIHK)-A.SER32 (6 candidates, BB)
+Resolved A.ILE443-(RKTESREQRNTQEFSFMSGGVS)-A.SER466 by filling A.ILE443-(RKTESREQRNTQEFSFMSGGVSS)-A.GLU467 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.93339e+17)
+Perform energy minimization (iteration 2, energy: 22103.4)
+No more stereo-chemical problems -> final energy: 13584
+
+
+Build model with the following alignment:
+target HTSPLLAPVRQIHAFGDSYSDNGESQRLTREMLAKGIAG-AQALPGEVYWQGRWSNGPTA
+pdb_id=5xtu, cha... ------AEFDRITNFGDSLSDIGNKHMITVDMNQATSGKIGI-RADKPNFDGRFSNGPVW
+
+target VEVLARQLGAQ---------------------------------LADHAVGGAKSGADNY
+pdb_id=5xtu, cha... TEYLAGFLAKPAPVRGHGEIDSQVVLKDQAGKQITYHYHHNALPGTNWAVGGAMSGLGNF
+
+target Y------GWMS--AYRHTGLAGQVDAYLATLDGKPVDGQALHFIFVSANDFFEHEDFAGE
+pdb_id=5xtu, cha... LDIDAANGFTAKSGLDVLTNTGQQIKLRIANKG-QFTGNELVSYMSGTNNLWFTLFGD--
+
+target QPLEQLAGSSVANIRAAVQRLGEAGARRFLVVSSTDLSVVPAVVAGNRVERAQRYLQAVN
+pdb_id=5xtu, cha... --LDQTGNKAAGFALTDIETLIDAGAKQVLAANIPDFVDAPWFA--GQQKKTTRFIQSHN
+
+target ASLPIQLAALRKTR-GLELSWFDHLTFSRHLRRNPARYG----------LVELDAPCQPT
+pdb_id=5xtu, cha... QALKAGLDQLAAAHPDVEIYYFDAFDLFNKVSNEVKTKGKYQDKELAITLTNVTGEAYSY
+
+target QPSVRPACANPDQYYFWDEWHPTRRVHQLAGEAMAARYAR
+pdb_id=5xtu, cha... AT--GKVIAQPNRNLFWDGLHPTTAMHKIMAKEAASLVI-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.ARG212-()-A.GLY213 by relaxing A.ARG212-(G)-A.LEU214
+Trying to merge 10 gap(s) with distance 0.
+Trying to fill 10 gap(s) by database.
+Resolved A.GLY39-()-A.ALA40 by filling A.LYS35-(GIAG)-A.ALA40 (98 candidates, BB_DB)
+Resolved A.GLN41-(A)-A.LEU43 by filling A.GLN41-(ALPG)-A.GLU46 (44 candidates, BB_DB)
+Resolved A.GLN70-()-A.LEU71 by filling A.GLY68-(AQLAD)-A.HIS74 (52 candidates, BB_DB)
+Resolved A.TYR87-()-A.GLY88 by filling A.TYR87-(GWMSAY)-A.ARG94 (418 candidates, BB_DB)
+Resolved A.GLY111-(K)-A.PRO113 by filling A.ASP110-(GKPV)-A.ASP115 (55 candidates, BB_DB)
+Resolved A.ALA136-(GEQP)-A.LEU141 by filling A.ASP134-(FAGEQP)-A.LEU141 (43 candidates, BB_DB)
+Resolved A.VAL182-(AG)-A.ASN185 by filling A.VAL181-(VAGN)-A.ARG186 (98 candidates, BB_DB)
+Resolved A.GLY236-()-A.LEU237 by filling A.TYR235-(GLV)-A.GLU239 (64 candidates, BB_DB)
+Resolved A.PRO249-(SV)-A.ARG252 by filling A.THR247-(QPSVR)-A.PRO253 (46 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.26964e+15)
+Perform energy minimization (iteration 2, energy: 1739.08)
+No more stereo-chemical problems -> final energy: -446.555
+
+
+Build model with the following alignment:
+target SSPCPQAWGPPGVQYGQPGRSVKLCCPGVTA--GDPVSWFRDGEPKLL-QGPDSGLGHEL
+pdb_id=1n26, cha... --RCPAQEVARGVLTSLPGDSVTLTCPGVEPEDNATVHWVLRKPAAGSHPSRWAGMGRRL
+
+target VLAQADSTDEGTYICQTLDGALGGTVTLQLGYPPARPVVSCQAADY-ENFSCTWSPSQIS
+pdb_id=1n26, cha... LLRSVQLHDSGNYSCYR-AGRPAGTVHLLVDVPPEEPQLSCFRKSPLSNVVCEWGPRSTP
+
+target GLPTRYLTSYRKKTVLGADSQRRSPSTGPWPCPQD-PLGAARCVVHGAE-FWSQYRINVT
+pdb_id=1n26, cha... SLTTKAVLLVRKFQNSPA-------EDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMC
+
+target EVNPLGAS-TRLLDVSLQSILRPDPPQGLRVESVPGYPRRLRASWTYPASWPSQPHFLLK
+pdb_id=1n26, cha... VASSVGSKFSKTQTFQGCGILQPDPPANITVTAVARNPRWLSVTWQDPHSWN-SSFYRLR
+
+target FRLQYRPAQHPAWSTVEP--AGLEEVITDAVAGLPHAVRVSARDFLDAGTWSTWSPEAWG
+pdb_id=1n26, cha... FELRYRAERSKTFTTWMVKDLQHHCVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMG
+
+target TPSTGTIPKEIPAWGQLHTQPEVEPQVDSPAPPRPSLQPHPRLLDHRDSVHHHHHHHH
+pdb_id=1n26, cha... TPWTES----------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA31-()-A.GLY32 by relaxing A.THR30-(AG)-A.ASP33
+Closed: A.TYR103-()-A.GLU104 by relaxing A.ASP102-(Y)-A.GLU104
+Closed: A.ASP151-()-A.PRO152 by relaxing A.ASP151-(P)-A.LEU153
+Closed: A.PRO251-()-A.ALA252 by relaxing A.GLU250-(PA)-A.GLY253
+Trying to merge 6 gap(s) with distance 0.
+Trying to fill 6 gap(s) by database.
+Resolved A.LEU46-()-A.GLN47 by filling A.GLU42-(PKLL)-A.GLN47 (113 candidates, BB_DB)
+Resolved A.THR74-(L)-A.ASP76 by filling A.THR74-(LDGAL)-A.GLY80 (75 candidates, BB_DB)
+Resolved A.ALA134-(DSQRRSP)-A.SER142 by filling A.VAL131-(LGADSQRRSP)-A.SER142 (110 candidates, BB_DB)
+Resolved A.GLU164-()-A.PHE165 by filling A.HIS161-(GAEF)-A.TRP166 (72 candidates, BB_DB)
+Failed at loop insertion (A.SER182-()-A.THR183), only 11 candidates
+Resolved A.PRO225-(S)-A.GLN227 by filling A.ALA222-(SWPS)-A.GLN227 (136 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER182-()-A.THR183), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER182-()-A.THR183), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER182-()-A.THR183), only 11 candidates
+Trying to fill 1 gap(s) by database.
+Resolved A.SER182-()-A.THR183 by filling A.ALA181-(STRLL)-A.ASP187 (40 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.34541e+29)
+Perform energy minimization (iteration 2, energy: 16550.4)
+No more stereo-chemical problems -> final energy: 13488.5
+
+
+Build model with the following alignment:
+target GSHMASMKKKGSVAIVGRIILSGDTAYAQQTRGEEGAQEVSQTGRDKNEAEGEVQVLSTA
+pdb_id=3suf, cha... ----------GSVVIVGRINLSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTA
+
+target TQTFLGTCINGVMWTVFHGAGAKTLAGPKGPVVQMYTNVDKDLVGWPTPPGTRSLTPCTC
+pdb_id=3suf, cha... TQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTC
+
+target GSADLYLVTRHADVVPARRRGDTRASLLSPRPISYLKGSSGGPVMCPSGHVVGVFRAAVC
+pdb_id=3suf, cha... GSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVC
+
+target TRGVAKALDFIPVENLETTMRSP
+pdb_id=3suf, cha... TRGVAKAVAFIPVESLETTM---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 32517.4)
+No more stereo-chemical problems -> final energy: 7157.82
+
+
+Build model with the following alignment:
+target MEMKKSGLGTTAIHAGT-LKNLYGTLAMPIYQTSTFIFDSAEQGGRRFALE-EAGYIYTR
+pdb_id=1cl2, cha... ------KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGR
+
+target LGNPTTTVLENKIAALEEGEAGIAMSSGMGAISSTLWTVLKAGDHVVTDKTLYGCTFALM
+pdb_id=1cl2, cha... RGTLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFC
+
+target NHGLTRFGVEVTFVDTSNLEEVKNAMKKNTRVVYLETPANPNLKIVDLEALSKIAHT--N
+pdb_id=1cl2, cha... SKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVP
+
+target PNTLVIVDNTFATPYMQKPLKLGVDIVVHSATKYLNGHGDVIAGLVVTRQELADQIRFVG
+pdb_id=1cl2, cha... -DAIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRE--
+
+target LKDMTGAVLGPQEAYYIIRGLKTFEIRMERHCKNARTIVDFLNKHPKVEKVYYPGLETHP
+pdb_id=1cl2, cha... NAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSK
+
+target GYEIAKKQMKDFGAMISFELKGG--FEAGKTLLNNLKLCSLAVSLGDTETLIQHPASMTH
+pdb_id=1cl2, cha... GHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLIL-ANQPEH
+
+target SPYTKEEREV--AGITDGLVRLSVGLENVEDIIADLEQGLEKI
+pdb_id=1cl2, cha... ---IAAIRPQGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARI
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Closed: A.THR17-()-A.LEU18 by relaxing A.THR17-(LK)-A.ASN20
+Closed: A.GLU50-()-A.GLU51 by relaxing A.LEU49-(E)-A.GLU51
+Trying to merge 7 gap(s) with distance 0.
+Merged gap A.THR175-()-A.ASN176 and A.ASN176-(P)-A.ASN178 into A.THR175-(NP)-A.ASN178
+Trying to fill 6 gap(s) by database.
+Resolved A.THR175-(NP)-A.ASN178 by filling A.THR175-(NPNT)-A.LEU180 (50 candidates, BB_DB)
+Resolved A.PHE234-(VG)-A.LEU237 by filling A.PHE234-(VGLKDM)-A.THR241 (43 candidates, BB_DB)
+Resolved A.GLY319-()-A.PHE320 by filling A.LYS317-(GGFEA)-A.GLY323 (117 candidates, BB_DB)
+Resolved A.GLN347-(H)-A.PRO349 by filling A.GLN347-(HPAS)-A.MET352 (60 candidates, BB_DB)
+Resolved A.HIS354-(SPY)-A.THR358 by filling A.MET352-(THSPYT)-A.LYS359 (40 candidates, BB_DB)
+Resolved A.VAL364-()-A.ALA365 by filling A.GLU361-(REVA)-A.GLY366 (212 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.42807e+15)
+Perform energy minimization (iteration 2, energy: 36313.2)
+No more stereo-chemical problems -> final energy: 26842.2
+
+
+Build model with the following alignment:
+target SVLQSGALPSVGVDELDKIDLSYETTESGDTAVSEDSYDKYASQNTNKEY-VCDFTDQ--
+pdb_id=2ymo, cha... --------------------------------------------------LTCDFNDVYK
+
+target --LKPTESGPKVKKCEVKVNEPLIKVKIICPLKGSVEKLYDNIEYVPKKSPYVVLTKEET
+pdb_id=2ymo, cha... LEFHPNQQTSVTKLCNL-TPNVLEKVTIKCGSDKL------NYNLYPPTCFE--------
+
+target KLKEKLLSKLIYGLLISPTVNEKE-NNFKEGVIEFTLPPVVHKATVFYFICDNSKTEDDN
+pdb_id=2ymo, cha... -----------------------------INEVSFRIPPNMMPEKPIYCFCENKK-----
+
+target K-KG---------NRGIVEVYVEPYGNKING
+pdb_id=2ymo, cha... ----------DIINRGIVEIIIPSLNEKVKG
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.GLN57-()-A.LEU58 by filling A.PHE54-(TDQ)-A.LEU58 (87 candidates, BB_DB)
+Resolved A.VAL72-(K)-A.VAL74 by filling A.VAL72-(KVN)-A.GLU76 (100 candidates, BB_DB)
+Resolved A.SER90-(VEKLYD)-A.ASN97 by filling A.LYS88-(GSVEKLYD)-A.ASN97 (155 candidates, BB_DB)
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Resolved A.LYS169-(TEDDNKKG)-A.ASN178 by filling A.LYS169-(TEDDNKKG)-A.ASN178 (709 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFK)-A.GLU144 by filling A.TYR107-(VVLTKEETKLKEKLLSKLIYGLLISPTVNEKENNFKE)-A.GLY145 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.8652e+11)
+Perform energy minimization (iteration 2, energy: 20621.7)
+No more stereo-chemical problems -> final energy: 17766.3
+
+
+Build model with the following alignment:
+target MSSFTSKFADELIANAAYIGTPGKGILAADESTGTIGKRLASINVENVESNRRALRELLF
+pdb_id=1qo5, cha... FPALTQEQKKELSEIAQSIVANGKGILAADESVGTMGNRLQRIKVENTEENRRQFREILF
+
+target TTPG-ALPCLSGVILFEETLYQKSSDGTPFVDMLKSAGVLPGIKVDKGTVELAGTNGETT
+pdb_id=1qo5, cha... SVDSSINQSIGGVILFHETLYQKDSQGKLFRNILKEKGIVVGIKLDQGGAPLAGTNKETT
+
+target TQGLDGLGDRCKKYYEAGARFAKWRAVLKIGVNEPSQLAIHENAYGLARYAVICQENGLV
+pdb_id=1qo5, cha... IQGLDGLSERCAQYKKDGVDFGKWRAVLRIADQCPSSLAIQENANALARYASICQQNGLV
+
+target PIVEPEILVDGSHDIQKCAAVTERVLAACYKALSDHHVLLEGTLLKPNMVTPGSESA-KV
+pdb_id=1qo5, cha... PIVEPEVIPDGDHDLEHCQYVTEKVLAAVYKALNDHHVYLEGTLLKPNMVTAGHACTKKY
+
+target APEVIAEHTVRALQRTVPAAVPAIVFLSGGQSEEEATRNLNAMNQLKTKKPWSLSFSFGR
+pdb_id=1qo5, cha... TPEQVAMATVTALHRTVPAAVPGICFLSGGMSEEDATLNLNAINLCPLPKPWKLSFSYGR
+
+target ALQQSTLKTWGGKEENVKKAQEAFLVRCKANSEATLGAYKGDAKLGEGAAESLHVKDYKY
+pdb_id=1qo5, cha... ALQASALAAWGGKAANKEATQEAFMKRAMANCQAAKGQYVHTGSSGAASTQSLFTAC---
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY64-()-A.ALA65 by relaxing A.PRO63-(GA)-A.LEU66
+Closed: A.ALA236-()-A.LYS237 by relaxing A.GLU234-(SA)-A.LYS237
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.61266e+29)
+Perform energy minimization (iteration 2, energy: 21528.8)
+No more stereo-chemical problems -> final energy: 18801.1
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPRGSHMGENQELVLSDHYISLKRYLSATSRDGNPKPPPNKARDKL
+pdb_id=2k76, cha... ------------------------PVEDLIRFYNDLQQYLN-------------------
+
+target QRLTEVQFLELSTDVYDELKRREQVARRGPNAPPETAPPDFLLPQDNFHPKRNQARQKLS
+pdb_id=2k76, cha... ------------------------------------------------------------
+
+target SLGPPRFRDLATDVFCELERRYPNFANLEMPLNAS
+pdb_id=2k76, cha... -----------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3721.58)
+No more stereo-chemical problems -> final energy: 1026.4
+
+
+Build model with the following alignment:
+target MKSIHIKIVLALCISIFTIMGLQPLNQHSTVAAANHKSSTKQTPLTFVLIHGSWATAGFW
+pdb_id=3stx, cha... -----------------------------------------FVKKHFVLVHTAFHGAWCW
+
+target DETASELRKLGHTVYTPEYAGHGADK---NNNVTHEQITKSVVDYIKQKDL-KDFILLGH
+pdb_id=3stx, cha... YKIVALMRSSGHNVTALDLGASGINPKQALQIPNFSDYLSPLMEFMASLPANEKIILVGH
+
+target SFGGSVIQTVSQQVPDRIKRIVFFDAFAPLDGQSVADQFPAESL---KSFEQLRDASG--
+pdb_id=3stx, cha... ALGGLAISKAMETFPEKISVAVFLSGLMPGPNIDATTVCTKAGSAVLGQLDNCVTYENGP
+
+target NNTI---TLPFPLFRDTFVNTASLAQAQAFYKQAPPEPATP---LFEKLDLKKFYSLQIP
+pdb_id=3stx, cha... TNPPTTLIAGPKFLATNVYHLSPIEDLALATALVRPLYLYLAEDISKEVVLSSKRYGSVK
+
+target KSYLYLTEDTAIPQGPYGFHPTQSSHLGVFRFIEGK-GDHMTTVRTEPKMMAELMVKAGR
+pdb_id=3stx, cha... RVFIVATENDALKKE--FLKLMIEKNPP-DEVKEIEGSDAVTMM-SKPQQLFTTLLSIAN
+
+target D
+pdb_id=3stx, cha... K
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY171-()-A.ASN172 by relaxing A.GLY171-(NN)-A.THR174
+Closed: A.LYS261-()-A.GLY262 by relaxing A.GLY260-(K)-A.GLY262
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.LYS86-()-A.ASN87 by filling A.ALA80-(GHGADK)-A.ASN87 (221 candidates, BB_DB)
+Resolved A.LEU108-()-A.LYS109 by filling A.LYS106-(DLK)-A.ASP110 (85 candidates, BB_DB)
+Resolved A.LEU160-()-A.LYS161 by filling A.LEU160-(KSFEQ)-A.LEU166 (65 candidates, BB_DB)
+Resolved A.ILE175-()-A.THR176 by filling A.ALA169-(SGNNTI)-A.THR176 (129 candidates, BB_DB)
+Resolved A.PRO209-()-A.LEU210 by filling A.PRO206-(ATPL)-A.PHE211 (154 candidates, BB_DB)
+Resolved A.GLY240-(PY)-A.GLY243 by filling A.PRO238-(QGPYG)-A.PHE244 (60 candidates, BB_DB)
+Resolved A.GLY253-(V)-A.PHE255 by filling A.SER250-(HLGV)-A.PHE255 (90 candidates, BB_DB)
+Resolved A.VAL268-(R)-A.THR270 by filling A.VAL268-(RTEP)-A.LYS273 (43 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.63421e+13)
+No more stereo-chemical problems -> final energy: 19508
+
+
+Build model with the following alignment:
+target MKHHHHHHSAGLEVLFQGPMEDGEVNDVVHPQVRAHINSLVSALGGI---SIDDDGGYKL
+pdb_id=6skl, cha... ----------------------------SLTVLRARIALLATAIGGPDYT-----PPYKL
+
+target GDDALEVLRDLKKWIRFYDEKTNRMDVARCLAEANIVSTDLLHILALWTP----------
+pdb_id=6skl, cha... GDDCLACLKDLKRWFKLVDDQQKRWDVAMAVAEYRILTDDLLPILIDWENKCSLAAKLA-
+
+target --N----ENSNKYKARIALACFELMVPLTWPIEKDRETMTINHHRHIPVLQLAQLGYKRA
+pdb_id=6skl, cha... ---------NKAYYDKIALNCLQLLVLMTWPLIVTEQ-SSSNQITLYGELKKHQLVYKKT
+
+target IINYDAAPILSTAVRVALPAMAMPIGERTARDQGIIKLILYFLRNIAMITPPPG------
+pdb_id=6skl, cha... ILSMESGKVLRAAIRLALDVIKIDRLSRTPRDNMVLKLVLNFFRNVIAIEPGEFTINTKK
+
+target ------------VKYEGDESQISRSALIDAFSYQDIFLTLLTIASNMGEDFR--TEDVIV
+pdb_id=6skl, cha... SMPKKGITSIDTLPPNVSMDDISLNTVISSFHKNKVFGFLLTLTSSLS-----DFINIPL
+
+target MEIIFHLVKRVDPK----------------------------------------------
+pdb_id=6skl, cha... LEIMFYFTKDVNQELLFPR-----------------------TSAGFELSKLLQKEHQMR
+
+target --------------G---------------------------------------------
+pdb_id=6skl, cha... KNVIKHTSARHSRFGGLLSIQTPDKTRLTVSGSQALVDEKIALQKLDDSKKWNKRIIKK-
+
+target ----------------------------QQLGSFVSDFLDSGFNPLFSHIRKSLEREAPH
+pdb_id=6skl, cha... -----EGLPNSLLNSQTGKAIFFTESNGKHFKEFINNFIDSGFNILLHSVTNYFTTEQDR
+
+target VLHYHQSQFFYLVAWFLEAERARR-----SSFNLIASVLTQEMFIALNRALDRAYGDKDW
+pdb_id=6skl, cha... MVTLEQVEYLLFFAWFVKYQLLRSKIDNSADIKQVSEALKEVTFILVSSLLRSAYDLKNW
+
+target RLLTSAMRCFTQILLTVQEMFDSGNDEDQEIADNILSRLFYEESTHDAVANIVRTYKDQG
+pdb_id=6skl, cha... TVTHAGMIAFNELLNLVSRTKAAQ------DIEFIVSRLFSD-ERIQLLSNLPKIGSKYS
+
+target FEYLDACTELAHTFLRILEAYSKQNVDLQVRS---------------G-----S----AD
+pdb_id=6skl, cha... LQFMKSCIELTHSVLKVLEQYS--------------------------------------
+
+target DEKMAEKTSQERKFDFKRFAARFTPQGVVDTFVTFTKYYRDLDDSQLKRAHRYFYRVAFK
+pdb_id=6skl, cha... -------------VNFQKVQANYMTEPVIETYINFLERFRELEDDSIKKVFSFFHRVFVQ
+
+target QEMSVMLFRLDIIHLFYNMIKGPEPLDKNSPMYKEWEELVRQILKRCIRKLEERPALFTE
+pdb_id=6skl, cha... AKEQALLFRFDLIILLREML-SPDGLDRMSRSRKYVSQFSDYFLARLKKRLKKSPAWFVG
+
+target ILFSKIN--STAYYLEYGFEKQ
+pdb_id=6skl, cha... LLFPPLHNSEVGFYQRYGE---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 13).
+Initialized default backbone scoring for modelling.
+Trying to merge 13 gap(s) with distance 0.
+Merged gap A.LYS275-()-A.GLY276 and A.GLY276-()-A.GLN277 into A.LYS275-(G)-A.GLN277
+Trying to fill 12 gap(s) by database.
+Resolved A.ILE47-(SIDDD)-A.GLY53 by filling A.ILE47-(SIDDDG)-A.GLY54 (95 candidates, BB_DB)
+Resolved A.PRO107-(NEN)-A.SER111 by filling A.PRO107-(NENSN)-A.LYS113 (377 candidates, BB_DB)
+Resolved A.GLU138-(T)-A.MET140 by filling A.ASP136-(RET)-A.MET140 (43 candidates, BB_DB)
+Resolved A.GLY215-()-A.VAL216 by filling A.ILE210-(TPPPG)-A.VAL216 (77 candidates, BB_DB)
+Resolved A.GLY251-(EDFR)-A.THR256 by filling A.GLY251-(EDFR)-A.THR256 (100 candidates, BB_DB)
+Resolved A.LYS275-(G)-A.GLN277 by filling A.ARG271-(VDPKG)-A.GLN277 (142 candidates, BB_DB)
+Resolved A.ARG332-()-A.SER333 by filling A.ARG331-(RSS)-A.PHE335 (43 candidates, BB_DB)
+Resolved A.GLY387-(NDEDQE)-A.ILE394 by filling A.GLY387-(NDEDQE)-A.ILE394 (46 candidates, BB_DB)
+Resolved A.GLU405-(E)-A.SER407 by filling A.ARG401-(LFYEE)-A.SER407 (210 candidates, BB_DB)
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Resolved A.ILE539-(K)-A.GLY541 by filling A.ILE539-(KGPEP)-A.LEU545 (66 candidates, BB_DB)
+Resolved A.ASN586-()-A.SER587 by filling A.SER583-(KINST)-A.ALA589 (69 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERK)-A.PHE473 by filling A.SER445-(KQNVDLQVRSGSADDEKMAEKTSQERKF)-A.ASP474 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.02913e+20)
+Perform energy minimization (iteration 2, energy: 15206)
+Perform energy minimization (iteration 3, energy: 8056.08)
+No more stereo-chemical problems -> final energy: 5669.6
+
+
+Build model with the following alignment:
+target MNKEHILAQKEVLTPIEYEHYVKHLFDIGEITKELYIELSSDL
+pdb_id=3o7m, cha... -------------YGIDCAEKYRNLPFIASVV-----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.35545e+12)
+No more stereo-chemical problems -> final energy: 2881
+
+
+Build model with the following alignment:
+target DNDDYDEKPREECGVVGIYGDSEASRLCYLALHALQHRGQEGAGIVTVSKDKVLQTITGV
+pdb_id=6czf, cha... ------------CGIVGIAGVMPVNQSIYDALTVLQHRGQDAAGIITIDANNCFRLRKAN
+
+target GLVSEVFSESKLDQLPGDIAIGHVRYSTAGSSMLKNVQPFVAGYRFGSVGVAHNGNLVNY
+pdb_id=6czf, cha... GLVSDVFEARHMQRLQGNMGIGHVRYPTAGSSSASEAQPFYVNSPYG-ITLAHNGNLTNA
+
+target TKLRADLEEN-GSIFNTSSDTEVVLHLIAISKA---------RPFFMRIVDACEKLQGAY
+pdb_id=6czf, cha... HELRKKLFEEKRRHINTTSDSEILLNIFASELDNFRHYPLEADNIFAAIAATNRLIRGAY
+
+target SMV-FVTEDKLVAVRDPHGFRPLVMGRRS---N-GAVVFASETCALDLIEATYEREVYPG
+pdb_id=6czf, cha... ACVAMIIGHGMVAFRDPNGIRPLVLGKRDIDENRTEYMVASESVALDTLGFDFLRDVAPG
+
+target EVLVVDKDGV-KCQCLMPHPEPKQCIFEHIYFSLPNSIVFGRSVYESRHVFGEILATES-
+pdb_id=6czf, cha... EAIYITEEGQLFTRQCADNPVSNPCLFEYVYFARPDSFIDKISVYSARVNMGTKLGEKIA
+
+target ----PVDCDVVIAVPDSGVVAALGYAAKAGVAFQQGLIRSHYVGRTFIEPSQKIRDFGVK
+pdb_id=6czf, cha... REWEDLDIDVVIPIPETSCDIALEIARILGKPYRQGFVKNRYVGRTFIMPGQQLRRKSVR
+
+target LKLSPVRGVLEGKRVVVVDDSIVRGTTSSKIVRLLREAGAKEVHMRIASPPIIASCYYGV
+pdb_id=6czf, cha... RKLNANRAEFRDKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLASAAPEIRFPNVYGI
+
+target DTPSSNELISNRMSVDEIRDYIGCDSLAFLSFETLKKHLGED---SRSFCYACFTGDYPV
+pdb_id=6czf, cha... DMPSATELIAHGREVDEIRQIIGADGLIFQDLNDLIDAVRAENPDIQQFECSVFNGVYVT
+
+target K-PTEDKVKRGGDFIDDGLVGGIHNIEGGWVR
+pdb_id=6czf, cha... KDVDQ---------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 9).
+Initialized default backbone scoring for modelling.
+Trying to merge 9 gap(s) with distance 0.
+Merged gap A.SER198-()-A.ASN199 and A.ASN199-()-A.GLY200 into A.SER198-(N)-A.GLY200
+Trying to fill 8 gap(s) by database.
+Resolved A.GLY107-(S)-A.VAL109 by filling A.GLY103-(YRFGS)-A.VAL109 (141 candidates, BB_DB)
+Resolved A.ASN130-()-A.GLY131 by filling A.GLU128-(ENG)-A.SER132 (114 candidates, BB_DB)
+Resolved A.ALA152-()-A.ARG153 by filling A.SER150-(KARPF)-A.PHE156 (99 candidates, BB_DB)
+Resolved A.VAL173-()-A.PHE174 by filling A.VAL173-(FVTED)-A.LYS179 (174 candidates, BB_DB)
+Resolved A.SER198-(N)-A.GLY200 by filling A.ARG196-(RSNG)-A.ALA201 (150 candidates, BB_DB)
+Resolved A.VAL235-()-A.LYS236 by filling A.VAL230-(DKDGV)-A.LYS236 (199 candidates, BB_DB)
+Resolved A.SER283-()-A.PRO284 by filling A.SER283-(PVDC)-A.ASP288 (40 candidates, BB_DB)
+Resolved A.ASP441-()-A.SER442 by filling A.LEU438-(GEDS)-A.ARG443 (44 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.92934e+18)
+Perform energy minimization (iteration 2, energy: 21112.4)
+No more stereo-chemical problems -> final energy: 17365.4
+
+
+Build model with the following alignment:
+target MSTFEDADDEETVTCLQMTIYHPGQ-QSGIFKSIRFSSKEKFPSIEVVKFGRNSNMCQYT
+pdb_id=4ym4, cha... ---------EETVTCLQMTVYHPGQLQCGIFQSISF-NREKLPSSEVVKFGRNSNICHYT
+
+target FQDKQVSRIQFVLQPFKQFNSSVLSFEIKNMSKKTSLMVDNQELGYLNKMDLPYKCMLRF
+pdb_id=4ym4, cha... FQDKQVSRVQFSLQLFKKFNSSVLSFEIKNMSKKTNLIVDSRELGYLNKMDLPYRCMVRF
+
+target GEYQFLLQKEDGESVESFETQFIMSSRPLLQENNWPTQNPIPEDGMYSSYFTHRSSPSEM
+pdb_id=4ym4, cha... GEYQFLMEKEDGESLEFFETQFILSPRSLLQ-----------------------------
+
+target DENELLEHHHHHH
+pdb_id=4ym4, cha... -------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.GLN25-()-A.GLN26 by relaxing A.GLY24-(Q)-A.GLN26
+Trying to fill 1 gap(s) by database.
+Resolved A.PHE35-(S)-A.SER37 by filling A.ARG34-(FSS)-A.LYS38 (62 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 43660.2)
+Perform energy minimization (iteration 2, energy: 9943.97)
+No more stereo-chemical problems -> final energy: 8960.23
+
+
+Build model with the following alignment:
+target QVQLVETGGGGLVQAGGSLRLSCAASGSISSLNAMGWYRQAPGKERELVADISASGRTNY
+pdb_id=6mxt, cha... QVQLQESG-GGLVQPGGSLRLSCAASGFAFSSYELRWYRQAPGKQHELVAGITTGGNTYY
+
+target ADSVKGRFTISRDNAKNTVSLQMNSLKPEDTAVYYCNAVGGTYYYDEYDYWGQGTQVTVS
+pdb_id=6mxt, cha... ADSVKGRFTISRDNAKNTVYLQMSNLRPEDTAVYACNANWD-L---LSDYWGQGTQVTVS
+
+Starting modelling based on a raw model.
+Removed 0 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Merged gap A.GLY101-(T)-A.TYR103 and A.TYR103-(YYD)-A.GLU107 into A.GLY101-(TYYYD)-A.GLU107
+Trying to fill 2 gap(s) by database.
+Resolved A.GLY8-(G)-A.GLY10 by filling A.VAL5-(ETGG)-A.GLY10 (61 candidates, BB_DB)
+Resolved A.GLY101-(TYYYD)-A.GLU107 by filling A.GLY101-(TYYYDE)-A.TYR108 (189 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.26862e+07)
+No more stereo-chemical problems -> final energy: 4573.45
+
+
+Build model with the following alignment:
+target HHHHHHTGLDLGAASSFGALAPQGVANAGATVINGDMG-TTGTSITGFPPGLITGQLHIN
+pdb_id=6eio, cha... ----------LGSANNFAVIAGSSVTNTGATNITGDLGLSPGTSIGGFPPGILNGTLHIN
+
+target DDTSTQAFADSRTAFVAGQALIATVDQA-GTATLGGNTFVAGVYKYDSAVGL-DGVLTLD
+pdb_id=6eio, cha... DAIANQAKLDITTAYNDAAARV-ASDMVTISGNIGGLTLTPGLYKSTSSLAVSSGDVTFD
+
+target GAGDASSVWVFQLATTLVTYASSSIILTNGAKANNVFWIVGSSATLGTYSHLEGNVIANA
+pdb_id=6eio, cha... ALGDPSAIFVIQIASTLTTTPGRKVLLSGGALASNIYWQVSSSASFGTTTSFKGTVIALE
+
+target LIAAQTGATINGALLA-GSAVTLDSNTVTVQNSASKLVRSAKFFKV
+pdb_id=6eio, cha... SITFDTGATLEGRALARNGAVTMEGNTFVLP---------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Trying to merge 5 gap(s) with distance 0.
+Trying to fill 5 gap(s) by database.
+Resolved A.GLY38-()-A.THR39 by filling A.GLY38-(TTG)-A.THR42 (77 candidates, BB_DB)
+Resolved A.ILE81-(A)-A.THR83 by filling A.ALA79-(LIAT)-A.VAL84 (119 candidates, BB_DB)
+Resolved A.ALA87-()-A.GLY88 by filling A.ALA82-(TVDQA)-A.GLY88 (210 candidates, BB_DB)
+Resolved A.LEU110-()-A.ASP111 by filling A.GLY109-(LDGV)-A.LEU114 (42 candidates, BB_DB)
+Resolved A.ALA193-()-A.GLY194 by filling A.LEU192-(AGSAV)-A.THR198 (41 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.32501e+11)
+No more stereo-chemical problems -> final energy: 19471.7
+
+
+Build model with the following alignment:
+target MQIFIKTLTGKTITAETEPAETVADLKQKIADKEGVPVDQQRLIFAGKQLEDSKTMADYN
+pdb_id=4pyu, cha... IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYE
+
+target IQKESTLHMVLRLRGG
+pdb_id=4pyu, cha... IHDGMNLELYY-----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 17420.5)
+No more stereo-chemical problems -> final energy: 6131.14
+
+
+Build model with the following alignment:
+target TYFSFWNKFSSNADINTMMLNNNADQLEPFDRADIIQDLPDFTGMNVVDVGAGIGRFTTT
+pdb_id=4krg, cha... -FKTFWDKYSDKPDTNSMMLNQTAQDLEASDRADILSSLPHLTNKDVVDIGAGIGRFTTV
+
+target FAQRAKHVVSSDFIDSFIEKNKERNAAFENITYQVSDALGLQVDPQSTDLVFTNWLLMYL
+pdb_id=4krg, cha... LAETARWVLSTDFIESFIEKNQERNAHMGNISYQIGDAVHLQMDEKSVDLVFTNWLMMYL
+
+target NEQECVRFLMKTMEWLKPGGYLHVRESCTEPSTGKSKTGSMHSDKKANPTHYRYSSVYLQ
+pdb_id=4krg, cha... SDREVIEFLLNAMRWLRADGYIHLRESCSEPSTGRLKTATMHSAVDANPTHYRFSSLYIK
+
+target LLKELRWTDARGMQWRFNVLWAKSVPTYVERVLNWRQVHWLCVKVPAQDGGISNEKALIS
+pdb_id=4krg, cha... LLRAIRYRDSDGKMWKFDVQWSCSVPTYIRRCNNWRQVHWLTKKVPAVGDEETSVDDLLN
+
+target A-MGRWKIIQDH-TEYLLNGKTSWATDVINNVISKVDFANNNLPLYVYSPRVVSPFVFVD
+pdb_id=4krg, cha... LFSQIWPAEQKTWDEKLDNEKYSWTDKIFSNAIDDEV-VPKNSTAYVFTPRQRSPFLHVN
+
+target SHNIAAMTGLSVWAVETNPLFYRHMLNRCVEAKDRRVQYGWNADLQSSINDWGLKKARFG
+pdb_id=4krg, cha... SHLLAEKFTCNVWNVETKEYLYRTSLTKANNQKDQRVRFGWNESLSSSIDYWNQRDASFD
+
+target GVIATELFMANSDTSLMALKEILDDNANIFTIEPALSI--EDFKENVVVPENMEMIAITD
+pdb_id=4krg, cha... CMVATELLATCDDESINSIASIMKPEAKVVLLEPVSGIDETSVRQRMTT-CGFKNITIVD
+
+target VSAYVVCREQKQAFDSPNQPCWLLVHARLL
+pdb_id=4krg, cha... VTQESL-NAEVSFIKDHN------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 6).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA241-()-A.MET242 by relaxing A.SER240-(AMG)-A.ARG244
+Closed: A.HIS251-()-A.THR252 by relaxing A.ASP250-(HT)-A.GLU253
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ASP275-(F)-A.ALA277 by filling A.LYS273-(VDFA)-A.ASN278 (51 candidates, BB_DB)
+Resolved A.ILE396-()-A.GLU397 by filling A.PRO392-(ALSI)-A.GLU397 (169 candidates, BB_DB)
+Resolved A.VAL405-(P)-A.GLU407 by filling A.VAL405-(PENME)-A.MET411 (129 candidates, BB_DB)
+Resolved A.VAL422-(C)-A.ARG424 by filling A.TYR420-(VVCR)-A.GLU425 (41 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.29217e+07)
+Perform energy minimization (iteration 2, energy: 15988.1)
+No more stereo-chemical problems -> final energy: 12828.3
+
+
+Build model with the following alignment:
+target GSSHHHHHHSGDPASMIINNRNESQPRRVVVTGLGVVAPTGVGVNEFWNNIHNGKSGVSK
+pdb_id=4na1, cha... ------------------------DFEPVAIVGISGRFPGAMDIDEFWKNLEEGKDSITE
+
+target Y-----EWG--R-----ERFGFKSGAIGQV-----YGSDGNNKEF-VLKSER----KYLQ
+pdb_id=4na1, cha... VPKDRWDWREHYGNPDTDVNKTDIKWGGFIDGVAEFDPL----FFGISPREADYVDPQQR
+
+target FALDAAEMAMQDANLRPSDIDGRRFGVAIATAIADAAGMEECLLRITKGGKENIHPDLIK
+pdb_id=4na1, cha... LLMTYVWKALEDAGCSPQSLSGTGTGIFIGTGNTGYKDLFH------RAN-LPIEGHAAT
+
+target SEDYDSFDFSSAATSVAKKYGASMSVSNISTGCAAGLDALGIAMEHIRYGRADIMLAGAS
+pdb_id=4na1, cha... ----GHMIPSVGPNRMSYFLNIHGPSEPVETACSSSLVAIHRAVTAMQNGDCEMAIAGGV
+
+target EAPLCPLSIGSFEALGALSSRELENQQAATCPFSLERDGFVIAEGCGILILESYEHAKQR
+pdb_id=4na1, cha... NTILTEEAHISYSKAGMLS------TDGRCKTFSADANGYVRGEGVGMVMLKKLEDAERD
+
+target GAHIYAELAGYASVNNAYHMTDLPADGMAMARCIDMALKDAQISPSTVNYISAHGSSTAQ
+pdb_id=4na1, cha... GNHIYGVIRGTAENHGGRANTLTSPNPKAQADLLVRAYRQADIDPSTVTYIEAHGTGTEL
+
+target NDINESNAIKFVLGES------------AFGIPINSLKSMTGHALAAANAIESVALCLEI
+pdb_id=4na1, cha... GDPIEINGLKAAFKELSNM------DVPDHRCGIGSVKSNIGHLELAAGISGLIKVLLQM
+
+target EKQYVHPTINYQTPDPDCDLD----YIPNQGCSYP----------IKTALKLSSGFSGIH
+pdb_id=4na1, cha... KHKTLVKSLHCETLNPYLQLTDSPFYIVQEKQEWKSVTDRDGNELPRRAGISSFGIGGVN
+
+target SVIVMRAVDNA
+pdb_id=4na1, cha... AHIVIEEY---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 14).
+Initialized default backbone scoring for modelling.
+Trying to merge 14 gap(s) with distance 0.
+Merged gap A.GLY64-()-A.ARG65 and A.ARG65-()-A.GLU66 into A.GLY64-(R)-A.GLU66
+Trying to fill 13 gap(s) by database.
+Resolved A.TYR61-()-A.GLU62 by filling A.SER59-(KYEW)-A.GLY64 (85 candidates, BB_DB)
+Resolved A.GLY64-(R)-A.GLU66 by filling A.GLY64-(RERFG)-A.PHE70 (47 candidates, BB_DB)
+Failed at loop insertion (A.VAL78-()-A.TYR79), only 0 candidates
+Resolved A.ASP82-(GNNK)-A.GLU87 by filling A.ASP82-(GNNKEF)-A.VAL89 (50 candidates, BB_DB)
+Resolved A.ARG94-()-A.LYS95 by filling A.ARG94-(KYLQ)-A.PHE99 (106 candidates, BB_DB)
+Resolved A.GLU139-(CLLRIT)-A.LYS146 by filling A.GLU138-(ECLLRITKG)-A.GLY148 (49 candidates, BB_DB)
+Resolved A.GLY148-(K)-A.GLU150 by filling A.GLY148-(KEN)-A.ILE152 (154 candidates, BB_DB)
+Resolved A.LYS158-(SEDY)-A.ASP163 by filling A.LEU156-(IKSEDYD)-A.SER164 (45 candidates, BB_DB)
+Resolved A.SER237-(SRELEN)-A.GLN244 by filling A.SER237-(SRELENQQAA)-A.THR248 (42 candidates, BB_DB)
+Resolved A.SER354-()-A.ALA355 by filling A.LEU351-(GESAF)-A.GLY357 (113 candidates, BB_DB)
+Resolved A.ASP407-()-A.TYR408 by filling A.ASP405-(LDY)-A.ILE409 (73 candidates, BB_DB)
+Resolved A.PRO417-()-A.ILE418 by filling A.SER415-(YPIK)-A.THR420 (230 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Resolved A.VAL78-()-A.TYR79 by filling A.VAL78-(YGSDGN)-A.ASN85 (110 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.7317e+20)
+Perform energy minimization (iteration 2, energy: 40146.7)
+No more stereo-chemical problems -> final energy: 28993.9
+
+
+Build model with the following alignment:
+target MAQSVEESGGRLVTPGTPLTLACTVSGFSL-NTYSMFWVRQA-PGKGLQWIGIISNFGVI
+pdb_id=4p48, cha... ----LTQPSSVSANPGGTVEITCSGGGRYYDGSYYYGWYQQKSPGSAPVTVIYENT----
+
+target YYATWAKGRFTISKTSTTVDLKITSPTTEDTATYFCVRKYGSEWGGDLWGPGTLVTVSSV
+pdb_id=4p48, cha... KRPSNIPSRFSGSKSGSTATLTITGVRAEDEAVYYCGSADDNM-NPTIFGAGTTLTVLG-
+
+target SRGGGGSGGGGSGGGGSELDMTQTPASVSEPVGGTVTIKCQASQSI-S-SYLAWYQQKPG
+pdb_id=4p48, cha... -----------------ALTLDESG-GGLQTPGGALSLVCKASGFTFSSYGMQWVRQAPG
+
+target QRPRLLIYETST-----LASGVPSRFKGS--GSGTEFTLTISDLECADAATYYCQSTYEN
+pdb_id=4p48, cha... KGLEWVAGIQNDDTGTYYGAAVKGRATISRDNGQSTVRLQLNNLRAEDTGTYYCAKDASS
+
+target ------PTYVSFGGGTEVGVKSSSTVSSHHHHHH
+pdb_id=4p48, cha... DGGYGGDSIDAWGHGTEVIVSS------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA41-()-A.PRO42 by relaxing A.GLN40-(AP)-A.GLY43
+Closed: A.ILE164-()-A.SER165 by relaxing A.SER161-(QSI)-A.SER165
+Closed: A.SER165-()-A.SER166 by relaxing A.ILE164-(SSY)-A.LEU168
+Trying to merge 8 gap(s) with distance 0.
+Trying to fill 8 gap(s) by database.
+Resolved A.LEU30-()-A.ASN31 by filling A.PHE28-(SLN)-A.THR32 (47 candidates, BB_DB)
+Resolved A.ASN54-(FGVI)-A.TYR59 by filling A.ILE52-(SNFGVI)-A.TYR59 (50 candidates, BB_DB)
+Resolved A.GLU101-(W)-A.GLY103 by filling A.GLY99-(SEWG)-A.GLY104 (60 candidates, BB_DB)
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Resolved A.PRO143-(A)-A.SER145 by filling A.THR142-(PASV)-A.SER147 (77 candidates, BB_DB)
+Resolved A.THR188-()-A.LEU189 by filling A.TYR184-(ETST)-A.LEU189 (172 candidates, BB_DB)
+Resolved A.SER200-()-A.GLY201 by filling A.SER200-(GSGT)-A.GLU205 (91 candidates, BB_DB)
+Resolved A.ASN229-()-A.PRO230 by filling A.THR226-(YENPT)-A.TYR232 (133 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.SER117-(VSRGGGGSGGGGSGGGGS)-A.GLU136 by filling A.SER117-(VSRGGGGSGGGGSGGGGSE)-A.LEU137 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.82129e+23)
+Perform energy minimization (iteration 2, energy: 33886.5)
+Perform energy minimization (iteration 3, energy: 24168.1)
+No more stereo-chemical problems -> final energy: 21740.5
+
+
+Build model with the following alignment:
+target SEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSA
+pdb_id=1khc, cha... ------------------------------------------------------------
+
+target DKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLE
+pdb_id=1khc, cha... ------------------------------------------------------------
+
+target WAHGGFKPTGIEGLKPNSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSG
+pdb_id=1khc, cha... -----------------TEYQDDKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMPG
+
+target MRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTF
+pdb_id=1khc, cha... MRWVQWFGDGKFSEISADKLVALGLFSQHFNLATFNKLVSYRKAMYHTLEKARVRAGKTF
+
+target PSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPN
+pdb_id=1khc, cha... SSSPGESLEDQLKPMLEWAHGGFKPTGIEGLKPN
+
+residue A.THR4 is missing atoms N, CA, O
+A.THR4 has incomplete backbone. skipping
+residue A.ASN140 is missing atoms CA, C, O
+A.ASN140 has incomplete backbone. skipping
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 26272.9)
+No more stereo-chemical problems -> final energy: 8904.08
+
+
+Build model with the following alignment:
+target MAHHHHHHMNHDQSHALFSRAQQLLPGGVNSPVRAFKSVGGEPFFVERADGAYLYDVDGN
+pdb_id=4zm4, cha... -------------NAESLDGIKSVIAGGVSSSMRAA-AV-PLPLVVRSAGGCLLRDVEDG
+
+target RYIDYVGSWGPMIVGHNHPAVRQAVKKAIDNGLSFGAPCAGEVTMAETITRLVPSCEMVR
+pdb_id=4zm4, cha... EIIDLNMGYGPHLFGYADREVLDAVADQFAKGHMTGLPHELDARAGALIAELVPGVEQVR
+
+target MVNSGTEATLSAIRLARGATGRNRIVKFEGCYHGHGDSFLVKAGSGM------LTLGVPT
+pdb_id=4zm4, cha... FANSGTEAVASALRLARATTGRTLVVTFEGHYHGWSETVLRAG---------RPTDVVPG
+
+target SPGVPAGLSELTLTLPYNDFEAATALFEQQGDDIAGLIIEPVVGNANCIPPREGYLQHLR
+pdb_id=4zm4, cha... ALGMIPEALAHTVQLGWNDPDALRELFARDGDRIAAVIVEPVLANAGVIPPAPGFLQLLR
+
+target ALCTKHGALLIFDEVMTGFRVALGGAQAHYGITPDLTTFGKIIGGGMPVGAYGGRRELMQ
+pdb_id=4zm4, cha... ELTGRSGAMLVFDEVITGFRVARGGAQERYGVEPDLTVLSRVMGGGFPVAAFGGRRHAMR
+
+target QIAPAGPIYQAGTLSGNPVAMAAGLAMLELVQQ-PGFHADLAERTARLCAGLEAAAADAG
+pdb_id=4zm4, cha... MLAS-NEAHHAGVYAGNHAALRAVVAMLGKIRSLPDLYERLEDTGQYMEDTVREVFATEK
+
+target VAVTTTRVGAMFGLFFTS---E---KVETYAQATAC-DIPAFNRFFHAMLEQGVFLAPSA
+pdb_id=4zm4, cha... RPVHINRVGTLMSVALLK-------EPRDLRQLAALVDFPRHRRLQTLAQKEGVYFHPNA
+
+target YEAGFLSSAHDDAVIEATLAAARVAFRAAKG
+pdb_id=4zm4, cha... LEPWFLSTAHTRDVIDKVAGALQRSLVGL--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 7).
+Initialized default backbone scoring for modelling.
+Closed: A.GLN327-()-A.PRO328 by relaxing A.VAL325-(QQ)-A.PRO328
+Trying to merge 6 gap(s) with distance 0.
+Trying to fill 6 gap(s) by database.
+Resolved A.PHE36-(K)-A.SER38 by filling A.VAL33-(RAFKS)-A.VAL39 (96 candidates, BB_DB)
+Resolved A.VAL39-(G)-A.GLY41 by filling A.LYS37-(SVGG)-A.GLU42 (44 candidates, BB_DB)
+Resolved A.ALA163-(GSGM)-A.LEU168 by filling A.VAL161-(KAGSGM)-A.LEU168 (40 candidates, BB_DB)
+Resolved A.PRO298-(A)-A.GLY300 by filling A.PRO298-(AGPIY)-A.GLN304 (96 candidates, BB_DB)
+Resolved A.SER371-(E)-A.LYS373 by filling A.LEU367-(FFTSEK)-A.VAL374 (42 candidates, BB_DB)
+Resolved A.CYS383-()-A.ASP384 by filling A.ALA380-(TAC)-A.ASP384 (83 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.6959e+16)
+Perform energy minimization (iteration 2, energy: 25594.1)
+No more stereo-chemical problems -> final energy: 20906.3
+
+
+Build model with the following alignment:
+target GSMDQPAGLQVDYVFRGVEHAVRVMVSGQVLELEVEDRMTADQWRGEFDAGFIEDLTHKT
+pdb_id=1lbj, cha... ------------------------------------------------------------
+
+target GNFKQFNIFCHMLESALTQSSESVTLDLLTYTDLESLRNRKMGGRPGSLAPRSAQLNSKR
+pdb_id=1lbj, cha... -------------------------VPIFTYGELQRMQEK--------------------
+
+target YLILIYSVEFDRIHYPLPLPYQGKP
+pdb_id=1lbj, cha... -------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 540.412)
+No more stereo-chemical problems -> final energy: -1639.08
+
+
+Build model with the following alignment:
+target MAHHHHHHMNDYRIESDLIGELKVPVNAYYGVQTQRAIDNFKISN--DHLSDHPEFIKAF
+pdb_id=3e04, cha... -----------FRIEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTERM--PTPVIKAF
+
+target AFVKKAAAQTNFELGLLDEIINKNIATACDEIIAGKMHKEFPTDMIQGGAGTSMNMNANE
+pdb_id=3e04, cha... GILKRAAAEVNQDYG-LDPKIANAIMKAADEVAEGKLNDHFPLVVWQTGSGTQTNMNVNE
+
+target VIANRALELMGHQKGEYQFCSPNDHVNLSQSTNDAYPTAIRIALYNLNK-TLVERLELLI
+pdb_id=3e04, cha... VISNRAIEMLGGELGSKIPVHPNDHVNKSQSSNDTFPTAMHIAAAIEVHEVLLPGLQKLH
+
+target QSFRKKADDLKDVIKMGRTQLQDAVPMTMGQEFNAFANTLQEEIARLNTNADLFLETNMG
+pdb_id=3e04, cha... DALDAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVKYAMTRIKAAMPRIYELAAG
+
+target ATAIGTGLNAHPDYAVKCTENLAKISGADVVLASDLVEATPDTGAYVIYSSAMKRMAVKL
+pdb_id=3e04, cha... GTAVGTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSL
+
+target SKICNDLRLLASGPRAGLYEINLPKMQPGSSIMPGKVNPVIPEVVNQVCFKVIGNDLTVT
+pdb_id=3e04, cha... MKIANDIRFLGSGPRSGLGELILPENEPG-----GKVNPTQCEAMTMVAAQVMGNHVAVT
+
+target FAAEAGQLQLNVMEPVLTQSIMESIRFLKNAMDTLREKCIDGITANKEICLNMVKNSIGI
+pdb_id=3e04, cha... VGGSNGHFELNVFKPMMIKNVLHSARLLGDASVSFTENCVVGIQANTERINKLMNESLML
+
+target VTALNPYIGYKNSTKIAKEALDTGKSVYDLVLEHELLSKEKLDEILAPENMLNPHTKF
+pdb_id=3e04, cha... VTALNPHIGYDKAAKIAKTAHKNGSTLKETAIELGYLTAEQFDEWVKPKDMLGP----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.LYS167-()-A.THR168 by relaxing A.ASN166-(KT)-A.LEU169
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ASN45-()-A.ASP46 by filling A.ILE43-(SND)-A.HIS47 (72 candidates, BB_DB)
+Resolved A.LEU48-(SD)-A.HIS51 by filling A.ASP46-(HLSDH)-A.PRO52 (95 candidates, BB_DB)
+Resolved A.GLY73-(L)-A.LEU75 by filling A.LEU72-(GLLD)-A.GLU77 (130 candidates, BB_DB)
+Resolved A.GLY326-(SSIMP)-A.GLY332 by filling A.GLY326-(SSIMP)-A.GLY332 (70 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.04051e+14)
+Perform energy minimization (iteration 2, energy: 29693.8)
+No more stereo-chemical problems -> final energy: 24873
+
+
+Build model with the following alignment:
+target QLINTNGSWHINSTALNCNESLNTGWLAGLFYQHKFDSSGCPKTE---------------
+pdb_id=6mej, cha... QLINTNGSWHLNRTALNCNDSLNTGWLAGLFYHHKFNSSGCPERMASCRPLTDFDQGWGP
+
+target ---------------VHY-PRPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGA
+pdb_id=6mej, cha... ISHANGSGPDQRPYCWHYPPRPCGIVPAKTVCGPVYCFTPSPVVVGTTDRAGAPAYNWGE
+
+target NDTDVFVLNNT----GNWFGCTWMNSTGFTKVCGAPPGG-----------PTD-------
+pdb_id=6mej, cha... NDTDVFVLNNTRPPLGNWFGCTWMNSTGFTKACGAPPCAI-------LYCPTDCFRKHPE
+
+target -----GGSGPWITPRCMVDYPYRLWHYPCTINYTIFKVRMYVGGVEHRLEAACN
+pdb_id=6mej, cha... ATYSRCGSGPWITPRCLVDYPYRLWHYPCTINYTVFKIRMYVGGVEHRLEAACN
+
+Starting modelling based on a raw model.
+Removed 0 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.THR100-()-A.GLY101 by relaxing A.THR100-(G)-A.ASN102
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.GLU45-()-A.VAL46 by filling A.CYS41-(PKTE)-A.VAL46 (78 candidates, BB_DB)
+Resolved A.TYR48-()-A.PRO49 by filling A.THR44-(EVHY)-A.PRO49 (64 candidates, BB_DB)
+Resolved A.GLY124-()-A.PRO125 by filling A.PRO121-(PGGPTD)-A.GLY128 (45 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4.48784e+12)
+Perform energy minimization (iteration 2, energy: 13842.8)
+No more stereo-chemical problems -> final energy: 12923.2
+
+
+Build model with the following alignment:
+target SKDAEKLNDEIISLNIENSLLQDKLTALQAEYDKLIQRWLAKAQSEADAMNQGLA
+pdb_id=3a7p, cha... NKNTERLNAALISGTIENNVLQQKLSDLKKEHSQLVARWLKKTEKETEAM-----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 10434)
+No more stereo-chemical problems -> final energy: 3335.64
+
+
+Build model with the following alignment:
+target EEKDPLWLYKVLLTKGIEVWFDIKLEKYGIKRNNRVDYIAKSSLQQIVFEIIGKTPKNIA
+pdb_id=1tue, cha... ------------------------------------------------------------
+
+target VPTYIGAYEPSKPEKWEEEGIKYINLFKPTPLMKVKPVKEMPEIVKNLLLNLFDYDAKSM
+pdb_id=1tue, cha... --------------------------------------GGDWRPIVQFLRYQQ----IEF
+
+target GLFINWLAFIYQYKERTGVAWIFMGKQGTGKGLLVDLLKKIFEEHMSSNITDANLDSQFN
+pdb_id=1tue, cha... ITFLGALKSFLKGTPKKN-CLVFCGPANTGKSYFGMSFIHFIQGAVISFVN---STSHFW
+
+target -PYLYNKLIVHLNEVSADNRKSRMLVKNRLKTWITDETLYINRKNMKEVEIKNFCNFIIN
+pdb_id=1tue, cha... LEPLTDTKVAMLDDATTT--CWTYF-DTYMRNALDGNPISID----PLIQLK-CPPILLT
+
+target SNETIPVDIEDS----DRRFNVIECNNVLKEQEWWTTESYQEILNNAEGFAKYLAGIKVD
+pdb_id=1tue, cha... TNIHPAK--DNRWPYLESRITVFEFPNAFP------------------------------
+
+target RSKVNEVVMSEKKKAIVETTESVLKQIAKALTDRDIEWFLDNGLEGVVEKNIVNDFQWEE
+pdb_id=1tue, cha... ------------------------------------------------------------
+
+target LQEAITTGVIPNKYLMIIVEQILGDSKTITWIKRNIITPYQVGETTVVKMAGKPIRAIVV
+pdb_id=1tue, cha... ------------------------------------------------------------
+
+target G
+pdb_id=1tue, cha... -
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 10).
+Initialized default backbone scoring for modelling.
+Trying to merge 10 gap(s) with distance 0.
+Trying to fill 10 gap(s) by database.
+Resolved A.PHE113-(DYDA)-A.LYS118 by filling A.LEU112-(FDYDAK)-A.SER119 (47 candidates, BB_DB)
+Resolved A.GLY138-(V)-A.ALA140 by filling A.LYS134-(ERTGV)-A.ALA140 (62 candidates, BB_DB)
+Resolved A.THR171-(DAN)-A.LEU175 by filling A.ILE170-(TDANL)-A.ASP176 (59 candidates, BB_DB)
+Resolved A.ASN180-()-A.PRO181 by filling A.SER177-(QFN)-A.PRO181 (47 candidates, BB_DB)
+Resolved A.ASP197-(NR)-A.LYS200 by filling A.VAL194-(SADNR)-A.LYS200 (48 candidates, BB_DB)
+Resolved A.LEU204-(V)-A.LYS206 by filling A.SER201-(RMLV)-A.LYS206 (53 candidates, BB_DB)
+Resolved A.ASN221-(RKNM)-A.LYS226 by filling A.ASN221-(RKNMK)-A.GLU227 (130 candidates, BB_DB)
+Resolved A.LYS231-(N)-A.PHE233 by filling A.ILE230-(KNFC)-A.ASN235 (44 candidates, BB_DB)
+Resolved A.VAL246-(DI)-A.GLU249 by filling A.PRO245-(VDIED)-A.SER251 (48 candidates, BB_DB)
+Resolved A.SER251-()-A.ASP252 by filling A.GLU249-(DSD)-A.ARG253 (64 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.71641e+14)
+No more stereo-chemical problems -> final energy: 11120.5
+
+
+Build model with the following alignment:
+target MPFTIDSARGIFPETLTADSVPATIARFNQLSAEDQLALIWFAYLEMGKTITIAAPGAAN
+pdb_id=5hgr, cha... --ITIDSARRIFPNTLQADAVPALTARFNQLSAEDQLAWTWFAFLEMGKTITVAAPGAAS
+
+target MVFAENTLNELKQMSFQEQTQVMCDLANRADTPICRTYAIWSVNIKLGFWYRLAEWMEQG
+pdb_id=5hgr, cha... MQFAEGILKQIKEMTFEEQTQVMCDLANHTDTPICRTYATWSPNIKLGFWNQLGEWMEQG
+
+target IVAPIPQGYRLSANAAAVLQAIRELDAGQQITVLRNSVVDMGYDPSKLGSYTKVSEPVAP
+pdb_id=5hgr, cha... AVAPIPAGYQLSANANAVLETLKSLDQGQQITVLRSSVVDMGFDAAKLDGYTRVAEPLVA
+
+target PKEMAKRTPVTIEGIDNPTILSYMDNLNANDFDALIELFTPDGALQPPFQKPIAGKEAVY
+pdb_id=5hgr, cha... PKDISQRVQVTIEGINNSTVLNYMNNLNANDFDELIKLFVEDGALQPPFQRPIVGKDAIL
+
+target RFFREDCQNLKLIPQRGVSEAVEDGYTQIKVTGTVQTPWFGASVGMNMAWRFLLTPENKI
+pdb_id=5hgr, cha... RFFREECQNLNLLPERGVAEPADDGYTQVKVTGKVQTPWFGAAVGMNMAWRFLLNPQGKI
+
+target FFVAIDLLASPKELLNLVRHHHHHHH
+pdb_id=5hgr, cha... FFVAIDLLASPKELLNL---------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 696562)
+No more stereo-chemical problems -> final energy: 13938.9
+
+
+Build model with the following alignment:
+target SSASLLEKQSTGGAIARVGFGYQDAFVLRSLPLWLSQSAFSHIVSEALSDIEVCYFSSEK
+pdb_id=6ohz, cha... ------------------------------------------------------------
+
+target SLHVMYEAKNHSLTATEFWDEIRRFKSLFDTHPKNFIWFNLVCPSYNTAISPLISKIDRL
+pdb_id=6ohz, cha... ------------------------------------------------------------
+
+target RGVGSSYDDDSSVSVNGRSEYLDWCVGKKIDFSLAEFALDYVGFITFNSENSESIFLSEI
+pdb_id=6ohz, cha... --------------------------------------RQSVDIITQNLKDAKTFPLGQL
+
+target QDTINIELLRSQVKQLKDQFKNLISRSSFGPIYRKDFENFICHALEEDRSQWLLDPIKIN
+pdb_id=6ohz, cha... EEEI--------------------------------------------------------
+
+target LSASSSQYQDLNLDISDFNGPDRAQKTSSDWNSLIKKAVSIGDFIHNSGDRRTLLIDGKQ
+pdb_id=6ohz, cha... ------------------------------------------------------------
+
+target RMSTACMLGYVFSATRNFLLEIEHNGLIYRTDDHKQKEGQFFTKIEAVEPQGETEAIVAI
+pdb_id=6ohz, cha... ------------------------------------------------------------
+
+target GFPTAIGKDIDSTINEVKSLPRLNLESSHAIDNMETLNLAVREAKSALVSFKSENKLSKL
+pdb_id=6ohz, cha... ------------------------------------------------------------
+
+target HLFIKAPSVFAMVLGHRLNGICDIQLYDWVDGQYIPTAELNL
+pdb_id=6ohz, cha... ------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6694.61)
+No more stereo-chemical problems -> final energy: 3395.99
+
+
+Build model with the following alignment:
+target MSVYGLQRLYIAGAHADATSGKTFDTFDPATGELLARVQQASADDVDRAVASAREGQREW
+pdb_id=3r31, cha... LKAQPKASHFIDGDYVEDNTGTPFESIFPATGEMIAKLHAATPAIVERAIASAKRAQKEW
+
+target AAMTAMQRSRILRRAVELLRERNDALAELEMRDTGKPIAETRAVDIVTGADVIEYYAGLA
+pdb_id=3r31, cha... AAMSPMARGRILKRAADIMRERNDALSTLETLDTGKPIQETIVADPTSGADAFEFFGGIA
+
+target TA-IEGLQVPLRPESFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSE
+pdb_id=3r31, cha... PSALNGDYIPLG-GDFAYTKRVPLGVCVGIGAWNYPQQIACWKAAPALVAGNAMVFKPSE
+
+target VTPLSALKLAEIYTEAGVPAGVFNVVQGDGSVGALLSAHPGIAKVSFTGGVETGKKVMSL
+pdb_id=3r31, cha... NTPLGALKIAEILIEAGLPKGLFNVIQGDRDTGPLLVNHPDVAKVSLTGSVPTGRKVAAA
+
+target AGASSLKEVTMELGGKSPLIVFDDADLDRAADIAVTANFFSAGQVCTNGTRVFVQQAVKD
+pdb_id=3r31, cha... AAG-HLKHVTMELGGKSPMIVFDDADIESAVGGAMLGNFYSSGQVCSNGTRVFVQKKAKA
+
+target AFVERVLARVARIRVGKPSDSDTNFGPLASAAQLDKVLGYIDSGKAEGAKLLAGGARLVN
+pdb_id=3r31, cha... RFLENLKRRTEAMILGDPLDYATHLGPLVSKAQQEKVLSYIEKGKAEGATLITGGGIPNN
+
+target DHFASGQYVAPTVFGDCRDDMRIVREEIFGPVMSILSFETEDEAIARANATDYGLAAGVV
+pdb_id=3r31, cha... V-AGEGAYVQPTVFADVTDDMTIAREEIFGPVMCVLDFDDEDEVLARANATEFGLAGGVF
+
+target TENLSRAHRAIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQ
+pdb_id=3r31, cha... TADLARAHRVVDGLEAGTLWINTYNLCPVEIPFGGSKQSGFGRENSAAALEHYSELKTVY
+
+target VELGRYQPVFGHHHHHH
+pdb_id=3r31, cha... VST--------------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Trying to merge 4 gap(s) with distance 0.
+Trying to fill 4 gap(s) by database.
+Resolved A.ALA122-()-A.ILE123 by filling A.ALA122-(IE)-A.GLY125 (49 candidates, BB_DB)
+Resolved A.ARG131-(P)-A.GLU133 by filling A.PRO129-(LRPE)-A.SER134 (87 candidates, BB_DB)
+Resolved A.ALA242-(S)-A.SER244 by filling A.ALA242-(SSLK)-A.GLU247 (61 candidates, BB_DB)
+Resolved A.ASP360-(H)-A.PHE362 by filling A.LEU357-(VNDH)-A.PHE362 (48 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.45973e+09)
+Perform energy minimization (iteration 2, energy: 12641.4)
+No more stereo-chemical problems -> final energy: 8875.12
+
+
+Build model with the following alignment:
+target MMGMVFTGLMELIEDEFGYETLDTLLESCELQSEGIYTSVGSYDHQELLQLVVKLSEVSS
+pdb_id=4u9b, cha... MKGIIFNVLEDMVVAQCGMSVWNELLEKHAPK-DRVYVSAKSYAESELFSIVQDVAQRLN
+
+target VPVTELVRLFGKKLFVELIEGHPEIANEMKDSFDLLSKIDSFIHVEVYKLYPQAELPKFT
+pdb_id=4u9b, cha... MPIQDVVKAFGQFLFNGLASRHTDVVDKFDDFTSLVMGIHDVIHLEVNKLYHEPSLPHIN
+
+target CDRLGDNDIRLHYQSKRPFASFAEGLLDGCAEYFKEDFTISRTPETQDSETDVIFNITRA
+pdb_id=4u9b, cha... GQLLPNNQIALRYSSPRRLCFCAEGLLFGAAQHFQQKIQISHDTCMHTGADHCMLIIELQ
+
+target PRGAENLYFQ
+pdb_id=4u9b, cha... N---------
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.GLN32-(S)-A.GLU34 by filling A.CYS29-(ELQS)-A.GLU34 (108 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.86611e+12)
+Perform energy minimization (iteration 2, energy: 13490.1)
+No more stereo-chemical problems -> final energy: 12024.6
+
+
+Build model with the following alignment:
+target MATANVAGAGGSGSEPTRIAILGKEDIIVDHGIWLNFVAHDLLQTLPSSTYVLITDTNLY
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target TTYVPPFQAVFEAAAPRDVRLLTYAIPPGEYSKSRETKAEIEDWMLSHACTRDTVIIALG
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target GGVIGDMIGYVAATFMRGVRFVQVPTTLLAMVDSSIGGKTAIDTPMGKNLIGAFWQPRRI
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target YIDLAFLETLPVREFINGMAEVIKTAAIWNETEFTALEENAAAILEAVRSKASSPAARLA
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target PIRHILKRIVLGSARVKAEVVSADEREGGLRNLLNFGHSIGHAYEAILAPQVLHGECVAI
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target GMVKEAELARYLGVLRPSAVARLTKLIASYDLPTSVHDKRIAKLSAGKECPVDVLLQKMA
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target VDKKNEGRKKKIVLLSAIGKTYEKKATVVDDRAIRLVLSPSVRVTPGVPKGLSVTVTPPG
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target SKSISNRALVLAALGEGTTRIHGLLHSDDVQYMLAAIEQLHGADFSWEDAGEILVVTGKG
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target GKLQASKEPLYLGNAGTASRFLTSVVALCAPSAVSSTVLTGNARMKVRPIGALVDALRAN
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target GVGVKYLEKEKSLPVEVDAAGGFAGGVIELAATVSSQYVSSILMAAPYAHQPVTLRLVGG
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target KPISQPYIDMTIAMMASFGIKVERSAEDPNTYLIPKGVYKNPPEYVVESDASSATYPLAV
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target AAITGTTCTIPNIGSESLQGDARFAVEVLRPMGCAVEQTATSTTVTGPPIGTLKAIPHVD
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target MEPMTDAFLTAAVLAAVADGTTQITGIANQRVKECNRIAAMKDQLAKFGVQCNELEDGIE
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target VIGKPYQELRNPVEGIYCYDDHRVAMSHSVLSTISPHPVLILERECTAKTWPGWWDILSQ
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target FFKVQLDGEEDPTKRTTQSTQQVRKGTDRSIFIVGMRGAGKSTAGRWMSELLKRPLVDLD
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target AELERREGMTIPEIIRGERGWEGFRQAELELLQDVIKNQSKGYIFSCGGGIVETEAARKL
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target LIDYHKNGGPVLLVHRDTDQVVEYLMRDKTRPAYSENIREVYERRKPWFYECSNLQYHSP
+pdb_id=5swv, cha... ------------------------------------------------------------
+
+target HEDGSEALLQPPADFARFVKLIAGQSTHLEDVRAKKHSFFVSLTVPNVADALDIIPRVVV
+pdb_id=5swv, cha... -----------------------------QKFKTKKRSTFLTLNYPRIEDALPTLRDVTV
+
+target GSDAVELRVDLLESYE-------PEFVARQVALLRAAAQVPIVYTVRTQSQGGKFPDEDY
+pdb_id=5swv, cha... GCDAIEVRVDYLKDPKSSNGISSLDFVAEQISLLRCSTTLPIIFTIRTISQGGLFPNDKE
+
+target DLALRLYQTGLRSGVEYLDLEMTMPDHILQAVTDAKGFTSIIASHHDPQCKLSWKSGS-W
+pdb_id=5swv, cha... EEAKELMLSAMRYGCDFVDVELGWSSETINILYQHKGYTKLIMSWHDLSGTWSWARPHEW
+
+target IPFYNKALQYGDVIKLVGVAREMADNFALTNFKAKMLAAHDNKPMIALNMGTAGKLSRVL
+pdb_id=5swv, cha... MQKVELASSYADVIKLVGMANNLNDNLELEEFRTRITNSM-DIPLILFNMGRFGQLSRIL
+
+target NGFLTPVSHPALPSKAAPGQLSATEIRQALSLIGEIEPKSFYLFGKPISASRSPALHNTL
+pdb_id=5swv, cha... NKFMTPVTHPLLPSKAAPGQLTVKQLNEARVLIGEILPEKFFLFGKPIKHSRSPILHSTA
+
+target FYKTGLPHHYSRFETDEASKALESLIRSPDFGGASVTIPLKLDIMPLLDSATDAARTIGA
+pdb_id=5swv, cha... YELLGLPHTYEAFETDTVDE-VQKVLNLPDFGGANVTIPYKLSVMKFMDELSDEARFFGA
+
+target VNTIIPQTRDGSTTTLVGDNTDWRGMVHALLH-SSGSGSVVQRTAAPRGAAMVVGSGGTA
+pdb_id=5swv, cha... VNTIIPIRI-GDKLVLRGDNTDWRGIYDTFANALDGVS---L----RDTNGLVIGAGGTS
+
+target RAAIYALHDLGFAPIWIVARSEERVAELVRGFD-GYDLRRMTSPH---QGKDN-MPSVVI
+pdb_id=5swv, cha... RAAIYSLHRLGVSRIYLLNRTLANSYRVQDVFPPDYNIHIIDSDNIPSEELSSVTLSAVV
+
+target STIPATQPIDPSMREVIVEVLKHGHPSAEGKVLLEMAYQPPRTPLMTLAEDQGWRTVGGL
+pdb_id=5swv, cha... STIPADIELPEKVASVIKALLAN---KADGGVFLDMAYKPLHTPLMAVASDLEWKCCNGL
+
+target EVLAAQGWYQFQLWTGITPLYEEARAAVMGEDSVELEHHHHHH
+pdb_id=5swv, cha... EALVRQGLASFHLWTGMTAPFDAVYQKVI--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 12).
+Initialized default backbone scoring for modelling.
+Closed: A.SER1191-()-A.TRP1192 by relaxing A.GLY1190-(SW)-A.ILE1193
+Closed: A.HIS1404-()-A.SER1405 by relaxing A.LEU1403-(HS)-A.SER1406
+Closed: A.ASP1464-()-A.GLY1465 by relaxing A.ASP1464-(GY)-A.ASP1467
+Trying to merge 9 gap(s) with distance 0.
+Merged gap A.GLY1409-(SVV)-A.GLN1413 and A.GLN1413-(RTAA)-A.PRO1418 into A.GLY1409-(SVVQRTAA)-A.PRO1418
+Trying to fill 8 gap(s) by database.
+Resolved A.GLU1096-()-A.PRO1097 by filling A.LEU1092-(ESYE)-A.PRO1097 (66 candidates, BB_DB)
+Resolved A.HIS1232-(D)-A.ASN1234 by filling A.HIS1232-(DNK)-A.PRO1236 (44 candidates, BB_DB)
+Resolved A.LYS1332-(A)-A.LEU1334 by filling A.GLU1329-(ASKA)-A.LEU1334 (105 candidates, BB_DB)
+Resolved A.ARG1381-(D)-A.GLY1383 by filling A.THR1380-(RDGS)-A.THR1385 (109 candidates, BB_DB)
+Resolved A.GLY1409-(SVVQRTAA)-A.PRO1418 by filling A.SER1408-(GSVVQRTAA)-A.PRO1418 (53 candidates, BB_DB)
+Resolved A.HIS1475-()-A.GLN1476 by filling A.ARG1470-(MTSPH)-A.GLN1476 (147 candidates, BB_DB)
+Resolved A.ASN1480-()-A.MET1481 by filling A.GLY1477-(KDNM)-A.PRO1482 (114 candidates, BB_DB)
+Resolved A.HIS1509-(GHP)-A.SER1513 by filling A.HIS1509-(GHPSA)-A.GLU1515 (40 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.66372e+10)
+Perform energy minimization (iteration 2, energy: 23910.7)
+No more stereo-chemical problems -> final energy: 20389
+
+
+Build model with the following alignment:
+target AIELSTDLINKFKDMNSSGNGRFIQATIVDETINIKAIEQGTSDFDADLD-LVLKYLVEG
+pdb_id=2vac, cha... GIHATEELKEFFAKARA-GSVRLIKVVIEDEQLVLGASQEPVGRWDQDYDRAVLPLLDAQ
+
+target EPSYILFRTETRDDITNGYKWLLLAYIPDRAKVRMKMLYSSTKARFRTTLGGSTFLYEIH
+pdb_id=2vac, cha... QPCYLLYRLDSQNA--QGFEWLFLAWSPDNSPVRLKMLYAATRATVKKEFGGGHIKDELF
+
+target GTVFSDFGKSGYEAFLRHE
+pdb_id=2vac, cha... GTVKDDLSFAGYQKH----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP50-()-A.LEU51 by relaxing A.LEU49-(DL)-A.VAL52
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.SER17-(S)-A.GLY19 by filling A.SER17-(SGNG)-A.ARG22 (65 candidates, BB_DB)
+Resolved A.ASP73-(IT)-A.ASN76 by filling A.ARG71-(DDITN)-A.GLY77 (55 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.41669e+14)
+Perform energy minimization (iteration 2, energy: 6637.3)
+No more stereo-chemical problems -> final energy: 5270.61
+
+
+Build model with the following alignment:
+target PTLEVYLPQGHSDERKASLIDGLTRATVDAIGAPAESVRILLTELPVSNIGLGG----KP
+pdb_id=2aaj, cha... -LLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYG
+
+target TPAALPVIIAILIAGRTEAQKEALIAHLSETSASVLDVSLQSTRVMIKDIPNTDFGLGG-
+pdb_id=2aaj, cha... RSSAVVLLTV-ISRPRSESQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRG
+
+target KTARALGR
+pdb_id=2aaj, cha... RAEFLTG-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Closed: A.GLY115-()-A.LYS116 by relaxing A.GLY114-(GK)-A.THR117
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.GLY54-()-A.LYS55 by filling A.ILE50-(GLGGK)-A.PRO56 (136 candidates, BB_DB)
+Resolved A.ALA66-(I)-A.LEU68 by filling A.ALA66-(ILIA)-A.GLY71 (103 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.31047e+11)
+No more stereo-chemical problems -> final energy: 7684.08
+
+
+Build model with the following alignment:
+target GPLGSRTSLIPTLGNLSNIILSILGKPVQEASAIVTNPASEMGMAFTKVMNMFRMVKDIY
+pdb_id=1hbw, cha... ------------------------------------------------------------
+
+target TEESFIYSSAIGMRTPSQRSTTRRANLAIFLAAVYGALQIGFFHLNENFLEVFAPDESNI
+pdb_id=1hbw, cha... ------------------------------------------------------------
+
+target LTNQGTLYMELKTQAYISAMAQAERPKGDILNDLFPS-DMAHRFLIRRNAKLDDKLTYVE
+pdb_id=1hbw, cha... ------------TRAHLTEVESRLERLEQLFLLIFPREDLDMILK---------------
+
+target KQIIEKCTARKERLANFSPQEALNEVYPWGKFLSEIACYIHNNYSSIS
+pdb_id=1hbw, cha... ------------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.SER157-()-A.ASP158 by filling A.PHE155-(PSDM)-A.ALA160 (71 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.9874e+07)
+No more stereo-chemical problems -> final energy: 1780.4
+
+
+Build model with the following alignment:
+target GSHMGD----LK--------------YSLERLREILERLEENPSEKQIVEAIRAIVENNA
+pdb_id=6n9h, cha... -----DAQDKLKYLVKQLERALRELKKSLDELERSLEELEKNPSEDALVENNRLNVENNK
+
+target QIVEAIRAIVENNAQIVENNRAIIEALEAIGGHNKILEEMKKQLKDLKRSLERG
+pdb_id=6n9h, cha... IIVEVLRIILE-------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 4909.43)
+No more stereo-chemical problems -> final energy: -2129.53
+
+
+Build model with the following alignment:
+target MSTPQDNANTVHRYLEFVAKGQPDEIAALYADDATVEDPVGSEVHIGRQAIRGFYGNLEN
+pdb_id=1w02, cha... LPTAQEVQGLMARFIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGL-
+
+target V-QSRTEVK-TLRALGHEV-AFYWTLSIGGDEGGMTMDIISVMTFNDDGRIKSMKAYWTP
+pdb_id=1w02, cha... --KVRACLTGPVRASHNGCGAMPFRVEMV----PCALDVILVMRFDEHGRIQTMQAYWSE
+
+target ENITQR
+pdb_id=1w02, cha... VNLSV-
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.LYS68-()-A.THR69 by relaxing A.VAL67-(KTL)-A.ARG71
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLU59-(NV)-A.GLN62 by filling A.LEU58-(ENVQ)-A.SER63 (52 candidates, BB_DB)
+Resolved A.VAL77-()-A.ALA78 by filling A.ALA72-(LGHEV)-A.ALA78 (165 candidates, BB_DB)
+Resolved A.GLY86-(GDEG)-A.GLY91 by filling A.ILE85-(GGDEGG)-A.MET92 (95 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.83529e+06)
+No more stereo-chemical problems -> final energy: 4987.54
+
+
+Build model with the following alignment:
+target MGSHHHHHHLVPRGSHMHQCYNGSGMDYRGTASTTKSGHQCQPWALQHPHSHHLSSTDFP
+pdb_id=1pkr, cha... ------------------ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHP
+
+target ELGGGHAYCRNPGGQMEGPWCFTQNKNVRMELCDVPSC
+pdb_id=1pkr, cha... SEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.10965e+06)
+No more stereo-chemical problems -> final energy: 5395.46
+
+
+Build model with the following alignment:
+target MGAVFDRRAFLLTLGSLVFLPAGAARAAGLDAAAAATRLAAIETSLDGRLGLFALNTADG
+pdb_id=6w34, cha... --------------------------------QATHKEFSQLEKKFDARLGVYAIDTGTN
+
+target RTLAHRSDERFAMCSTFKLVLAGAILAQSAQTPGLLERRVAYGPEALVSYSPITQKHAAG
+pdb_id=6w34, cha... QTISYRSNERFAFASTYKALAAGVLLQQNSIDS--LNEVITYTKEDLVDYSPVTEKHVDT
+
+target GMTVAALCAAAVRHSDNTAANLLLDQLDGPAALTTFARTIGDNHFRLDRREPELNTAIPG
+pdb_id=6w34, cha... GMKLGEIAEAAVRSSDNTAGNILFNKIGGPKGYEKALRHMGDRITMSDRFETELNEAIPG
+
+target DPRDTTTPAAMGRSLQRLALGRALPAEGRALLCAWLRGCVTGAARIRAGVPAGWVVGDKT
+pdb_id=6w34, cha... DIRDTSTAKAIATNLKAFTVGNALPAEKRKILTEWMKGNATGDKLIRAGVPTDWVVGDKS
+
+target GTGAYGVANDVAVLWPAAGAPPVLLAIYTARRQKDAAPRNDVIVAAAKVVAEWLGAAA
+pdb_id=6w34, cha... GAGSYGTRNDIAIVWPPN-RTPIIIAILSSKDEKEATYDNQLIAEATEVIVKAL----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.PRO93-(GL)-A.LEU96 by filling A.SER89-(AQTPGL)-A.LEU96 (75 candidates, BB_DB)
+Resolved A.ALA258-(G)-A.ALA260 by filling A.TRP255-(PAAG)-A.ALA260 (44 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.43056e+11)
+No more stereo-chemical problems -> final energy: -1657.56
+
+
+Build model with the following alignment:
+target GPHMAQVQLVESGGRLVQAGDSLRLSCAASGRTFSTSAMAWFRQAPGREREFVAAITWTV
+pdb_id=6xw4, cha... -----QVQLQESGGGLVQAGGSLRLSCAKSGRTFRAYAMGWFRQAPGKEREFVAAIDWSA
+
+target GNTILGDSVKGRFTISRDRAKNTVDLQMDNLEPEDTAVYYCSARSRGYVLSVLRSVDSYD
+pdb_id=6xw4, cha... AITNYADSVKGRFTILRDKGMNTAYLQMNSLEPEDTAVYYCAATYSTI-AP--R--TSYD
+
+target YWGQGTQVTVS
+pdb_id=6xw4, cha... FWGQGTQVTVS
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Merged gap A.SER111-(VL)-A.ARG114 and A.ARG114-(SV)-A.ASP117 into A.SER111-(VLRSV)-A.ASP117
+Trying to fill 2 gap(s) by database.
+Resolved A.TYR108-(V)-A.LEU110 by filling A.ARG106-(GYV)-A.LEU110 (48 candidates, BB_DB)
+Resolved A.SER111-(VLRSV)-A.ASP117 by filling A.LEU110-(SVLRSVD)-A.SER118 (80 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.19881e+13)
+Perform energy minimization (iteration 2, energy: -1501.96)
+No more stereo-chemical problems -> final energy: -2449.98
+
+
+Build model with the following alignment:
+target MGSSHHHHHHSSGLVPAGSHMAGTKKGVSAAAFSGVTAALGDVGARWFYTWAADPQGITA
+pdb_id=5u22, cha... ------------------------------------------------------------
+
+target PAGTEFVPMIWGRDSVTADQLQRAKAAGSTLLAFNEPDLAGQANMSVETA-LDLWPQLQ-
+pdb_id=5u22, cha... --------------------------------IWNEPDVTWK--DSNGLSFNQMWKQTYD
+
+target -----ATGMRLGAPAVAYGGDTPGGWLDRFMSGAAARGYRVDFIPLHWYGGDFSAAATGQ
+pdb_id=5u22, cha... LLRQIDPNEKIIGPSFSWY---EENKMKNFLQFSKQNNCLPDIIAWHELSGI------DG
+
+target LQSYLQA---VYNRYH---RPIWLTEYALTDFSGSTPRYPSAAEQADFVSRSTAMLNGLS
+pdb_id=5u22, cha... VSSHFRSYRNLEKSLGISERPITINEYCDENHDLE----GQPGSSARFIGR----FERYK
+
+target FV-ERYAWFS-LSTSTTPTGLYT-GTTPNSSGVAYRAAG
+pdb_id=5u22, cha... VDSGMITWWFVPHPG-RLGSLLASDTQKGAGWYFYK---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 13).
+Initialized default backbone scoring for modelling.
+Closed: A.ALA110-()-A.LEU111 by relaxing A.ALA110-(L)-A.ASP112
+Closed: A.ALA180-()-A.VAL181 by relaxing A.GLN179-(AV)-A.TYR182
+Closed: A.SER236-()-A.LEU237 by relaxing A.SER236-(L)-A.SER238
+Closed: A.THR248-()-A.GLY249 by relaxing A.TYR247-(TG)-A.THR250
+Trying to merge 9 gap(s) with distance 0.
+Trying to fill 9 gap(s) by database.
+Resolved A.GLN102-(AN)-A.MET105 by filling A.LEU99-(AGQAN)-A.MET105 (120 candidates, BB_DB)
+Resolved A.GLN118-()-A.ALA119 by filling A.GLN118-(ATGMRL)-A.GLY125 (461 candidates, BB_DB)
+Resolved A.GLY132-(GDT)-A.PRO136 by filling A.TYR131-(GGDTP)-A.GLY137 (131 candidates, BB_DB)
+Resolved A.ASP165-(FSAAAT)-A.GLY172 by filling A.GLY163-(GDFSAAATG)-A.GLN173 (48 candidates, BB_DB)
+Resolved A.HIS186-()-A.ARG187 by filling A.TYR182-(NRYH)-A.ARG187 (61 candidates, BB_DB)
+Resolved A.SER202-(TPRY)-A.PRO207 by filling A.SER200-(GSTPRYPS)-A.ALA209 (127 candidates, BB_DB)
+Resolved A.ARG218-(STAM)-A.LEU223 by filling A.ARG218-(STAMLNG)-A.LEU226 (45 candidates, BB_DB)
+Resolved A.VAL229-()-A.GLU230 by filling A.ASN224-(GLSFV)-A.GLU230 (53 candidates, BB_DB)
+Resolved A.SER240-(T)-A.THR242 by filling A.LEU237-(STST)-A.THR242 (121 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.88161e+17)
+Perform energy minimization (iteration 2, energy: 12100.4)
+No more stereo-chemical problems -> final energy: 9248.72
+
+
+Build model with the following alignment:
+target MEEQSLKLDSLEPRLQRELERLQAALRQTEAREIEWREKAQDL-ALSLAQTKASVSSLQE
+pdb_id=3ibp, cha... -------------ALRQEQEQLQSRIQSLMQRAPVWLA-AQNSLNQLSEQCGEEFTSSQD
+
+target VAMFLQASVLERDSEQQRLQDELELTRRALEK--ERLHSPG
+pdb_id=3ibp, cha... VTEYLQQL-LEREREAIVERDEVGARKNAVDEEIERLSQPG
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.LEU43-()-A.ALA44 by relaxing A.ASP42-(LAL)-A.SER46
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLU38-(K)-A.ALA40 by filling A.TRP36-(REK)-A.ALA40 (61 candidates, BB_DB)
+Resolved A.SER67-(V)-A.LEU69 by filling A.LEU64-(QASV)-A.LEU69 (85 candidates, BB_DB)
+Resolved A.LYS91-()-A.GLU92 by filling A.ALA88-(LEK)-A.GLU92 (88 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 8342.21)
+No more stereo-chemical problems -> final energy: -4129.18
+
+
+Build model with the following alignment:
+target GSSMSRAAQLLPGTWQVTMTNEDGQTSQGQWHFQPRSPYTMDIVAQGTISDGRPIVGYGK
+pdb_id=6czi, cha... ----SRAAQLLPGTWQVTMTNEDGQTSQGQWHFQPRSPYTLDIVAQGTISDGRPITGYGK
+
+target ATVKTPDTLDIDITYPSLGNIKAQGQITMDSPTQFKWDAHYKGDKDGDGYISAAEAAAQG
+pdb_id=6czi, cha... ATVKTDDTLHANLTYPSLGNIKAQGQITYDSPTQFTWNSTTS---DG-----------KK
+
+target LTGTLQRQE
+pdb_id=6czi, cha... LTGTLQR--
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Resolved A.LYS102-(GDK)-A.ASP106 by filling A.ALA99-(HYKGDKD)-A.GLY107 (130 candidates, BB_DB)
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.GLY107-(DGYISAAEAAA)-A.GLN119), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.GLY107-(DGYISAAEAAA)-A.GLN119 by filling A.GLY107-(DGYISAAEAAAQ)-A.GLY120 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.5401e+17)
+No more stereo-chemical problems -> final energy: 8351.87
+
+
+Build model with the following alignment:
+target ATVKLTYQGEEKQVDISKIKRVARYGQNIYFSYDEGGGAYDYGAVSEKDAPKELLQMLEK
+pdb_id=1sso, cha... ATVKFKYKGEEKQVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEK
+
+target Q
+pdb_id=1sso, cha... Q
+
+Starting modelling based on a raw model.
+Removed 0 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 15080)
+No more stereo-chemical problems -> final energy: 5578.2
+
+
+Build model with the following alignment:
+target DVQLVESGGGLVQAGGSLRLSCTASGFTFDDYTMGWFRQAPGKEREGVSYTGWSGSMSGS
+pdb_id=6xw4, cha... QVQLQESGGGLVQAGGSLRLSCAKSGRTFRAYAMGWFRQAPGKEREFVAAIDWS----AA
+
+target TTYYTDSVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAARYRGIGSQVRWTDFIYW
+pdb_id=6xw4, cha... ITNYADSVKGRFTILRDKGMNTAYLQMNSLEPEDTAVYYCAATYSTI-AP---RTSYDFW
+
+target GQGTQVTVSS
+pdb_id=6xw4, cha... GQGTQVTVS-
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.SER54-(GSMS)-A.GLY59 by filling A.TRP53-(SGSMSGS)-A.THR61 (42 candidates, BB_DB)
+Resolved A.GLY107-(I)-A.GLY109 by filling A.TYR105-(RGIG)-A.SER110 (47 candidates, BB_DB)
+Resolved A.SER110-(QVR)-A.TRP114 by filling A.GLY107-(IGSQVR)-A.TRP114 (291 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.1512e+18)
+No more stereo-chemical problems -> final energy: 4100.79
+
+
+Build model with the following alignment:
+target MPILQVQVTAGRSQQQKTAFLQNATKVIEQTLNAALPSIRISLHEIEQQDSIVAGQVG--
+pdb_id=2aaj, cha... --LLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGY
+
+target ---AEFVNIVAFLLAGRNDEVKANFLAAINKTAVTTLDVSDSCIRTMLIDIAPEHMGVQE
+pdb_id=2aaj, cha... GRSSAVVLLTV-ISRPRSESQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSF-G
+
+target GLSAAAFRARSAG
+pdb_id=2aaj, cha... RGRAE--------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 3).
+Initialized default backbone scoring for modelling.
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.GLY58-()-A.ALA59 by filling A.ALA54-(GQVGA)-A.GLU60 (46 candidates, BB_DB)
+Resolved A.ALA66-(F)-A.LEU68 by filling A.ALA66-(FLLA)-A.GLY71 (52 candidates, BB_DB)
+Resolved A.VAL113-(Q)-A.GLU115 by filling A.MET111-(GVQE)-A.GLY116 (55 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 3.09778e+19)
+No more stereo-chemical problems -> final energy: 8312.96
+
+
+Build model with the following alignment:
+target AHMNAGWVIGVDPDTSGALALLKPNQPPQVFDSPHLKVLVGKGVRKRLDAKAIVQLLKSF
+pdb_id=6is9, cha... -----GWVIGVDPDIGGAIAVLSPDGSSQVFDNPFVHIVVSEVIRKRLDTKSIIQLLRGL
+
+target EAPIGTTVYVEQSTPYPQDGKQGWWSGGFGYGMWIGILVASGFSVIPVPSSAWKSEFQLT
+pdb_id=6is9, cha... DAPPGTTAYIEKSSPFPTDGKQGWWSTGFSYGLWIASLVASGFSVVPIASQTWKAYFGLM
+
+target KERSNKDYSRQVASQLFPSLSSLLKRKKDHGRAEALLIAAYGKGIKINSDS
+pdb_id=6is9, cha... RSETPKDDSRQAASILFPDKDQSLKLKKHHGRAEALLLAAYGKGLVLPSG-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.73125e+08)
+No more stereo-chemical problems -> final energy: 12828.9
+
+
+Build model with the following alignment:
+target MSLLAPAQVPGSQSSHALWSAPMSAPAAPPLTGPLKVTTFNVNGLRSALRK---GLADWV
+pdb_id=2j63, cha... ------------------------------PSRMYKFITWNVAGLRGLLKKNASALRAFM
+
+target ESNQPDVLLLQEVRAEPM-P---DA---LPGYHSAWFPA-QKAGYSGVAILSRLP-----
+pdb_id=2j63, cha... EAEKPDVLCLQETKLNVDEADANATLGVVDGYSFVDHPCAFKRGYSGTRTYMKNSTTVKG
+
+target LKDV-RLGMPH-----------------DEMDAEGRVVSAVVA----------GVRFVSV
+pdb_id=2j63, cha... LHARCTRGFALPSE-----------LVEGAGDEEGRVLTTFLSPDPD----SSRIALVNT
+
+target YLPSGSSGEARQGFKDR-VLADYQAWVSELLAA------------------GEPVVIGGD
+pdb_id=2j63, cha... YVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWATENAA----------SSPHGFIWAGD
+
+target YNIAHREIDLK---NWRSNQKNSGFLPHERTWMTAHLA-AGLVDCHRDCLGEEAE-YTWW
+pdb_id=2j63, cha... LNVAERDYDRYYAGTFKSMQECSGFAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSFW
+
+target SNRANAYANNVGWRIDYLL-SAG--VRVSGVRSDRSVRLSDHAPLTGWVELESE
+pdb_id=2j63, cha... SQRINGRPRNLGWRLDYFVVSSRLASYVVDCFPMPTVMGSDHCPFQMWMRH---
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 16).
+Initialized default backbone scoring for modelling.
+Closed: A.MET75-()-A.PRO76 by relaxing A.PRO74-(M)-A.PRO76
+Closed: A.ARG153-()-A.VAL154 by relaxing A.ASP152-(RV)-A.LEU155
+Closed: A.ALA212-()-A.ALA213 by relaxing A.LEU211-(AAG)-A.LEU215
+Trying to merge 13 gap(s) with distance 0.
+Trying to fill 13 gap(s) by database.
+Resolved A.LYS51-()-A.GLY52 by filling A.LYS51-(GLAD)-A.TRP56 (92 candidates, BB_DB)
+Resolved A.PRO76-()-A.ASP77 by filling A.ARG71-(AEPMP)-A.ASP77 (91 candidates, BB_DB)
+Resolved A.ALA78-()-A.LEU79 by filling A.MET75-(PDALP)-A.GLY81 (48 candidates, BB_DB)
+Resolved A.ALA89-()-A.GLN90 by filling A.ALA89-(QKAG)-A.TYR94 (47 candidates, BB_DB)
+Resolved A.PRO104-()-A.LEU105 by filling A.LEU103-(PLKD)-A.VAL108 (40 candidates, BB_DB)
+Resolved A.VAL108-()-A.ARG109 by filling A.VAL108-(RLGMP)-A.HIS114 (91 candidates, BB_DB)
+Resolved A.HIS114-()-A.ASP115 by filling A.GLY111-(MPHD)-A.GLU116 (71 candidates, BB_DB)
+Resolved A.ALA129-()-A.GLY130 by filling A.VAL128-(AGV)-A.ARG132 (117 candidates, BB_DB)
+Resolved A.ALA168-()-A.GLY169 by filling A.ALA167-(AGEP)-A.VAL172 (113 candidates, BB_DB)
+Resolved A.LYS188-()-A.ASN189 by filling A.ARG183-(EIDLK)-A.ASN189 (93 candidates, BB_DB)
+Resolved A.GLU228-()-A.TYR229 by filling A.GLU225-(EAE)-A.TYR229 (66 candidates, BB_DB)
+Resolved A.LEU251-()-A.SER252 by filling A.LEU251-(SAGV)-A.ARG256 (87 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.63651e+11)
+Perform energy minimization (iteration 2, energy: 5674.49)
+No more stereo-chemical problems -> final energy: 3752.34
+
+
+Build model with the following alignment:
+target SNAMNLFTR-HRNNIRLTTAGEKLLPYAETLMNTWQAARKEVAHSS--RHNEFSIGASAS
+pdb_id=3fzv, cha... SF-VQLF---------LTPAGARFYRKAQELLRMAHEFEQN-LADNDVIAGQIDIGCFET
+
+target LWECMLNGWLGTLYSAPYNLQFEARIAQRQSLVKQLHERQLDLLITTESPKMDELSSQLL
+pdb_id=3fzv, cha... VAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPL
+
+target -GNFTLALYCASPA----------KNRNELNYLRLEWGPDFQQNEVGLIGSD---DVPLL
+pdb_id=3fzv, cha... MPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQP-SRTYFVSLFEELGLTPNIAF
+
+target TTSSAELIYQQLSRLNGCCWLPARWAK---EKHG-LHTVM-DSATLSRPLYAIWLQNSDK
+pdb_id=3fzv, cha... SSPSIEMVRGMVGQGFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQL
+
+target QAQIHEILKNPILE
+pdb_id=3fzv, cha... TKPARLFVD-----
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 11).
+Initialized default backbone scoring for modelling.
+Closed: A.MET199-()-A.ASP200 by relaxing A.MET199-(DS)-A.ALA202
+Trying to merge 10 gap(s) with distance 0.
+Trying to fill 10 gap(s) by database.
+Resolved A.ASN2-(A)-A.MET4 by filling A.ASN2-(AM)-A.ASN5 (64 candidates, BB_DB)
+Resolved A.PHE7-(TRHRNNIR)-A.LEU16 by filling A.PHE7-(TRHRNNIR)-A.LEU16 (198 candidates, BB_DB)
+Resolved A.GLU40-(V)-A.ALA42 by filling A.LYS39-(EV)-A.ALA42 (84 candidates, BB_DB)
+Resolved A.SER45-()-A.ARG46 by filling A.GLU40-(VAHSS)-A.ARG46 (65 candidates, BB_DB)
+Resolved A.LEU117-()-A.GLY118 by filling A.GLN115-(LLG)-A.ASN119 (48 candidates, BB_DB)
+Resolved A.ALA130-()-A.LYS131 by filling A.SER128-(PAKNR)-A.ASN134 (47 candidates, BB_DB)
+Resolved A.PRO145-(D)-A.PHE147 by filling A.GLU142-(WGPD)-A.PHE147 (40 candidates, BB_DB)
+Resolved A.ASP158-()-A.ASP159 by filling A.ILE155-(GSDD)-A.VAL160 (123 candidates, BB_DB)
+Resolved A.LYS190-()-A.GLU191 by filling A.LYS190-(EKHG)-A.LEU195 (44 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.50232e+14)
+Perform energy minimization (iteration 2, energy: 11149)
+No more stereo-chemical problems -> final energy: 8724.7
+
+
+Build model with the following alignment:
+target EEVVVEIRIRVQREEKVRRLIKR---ILEEVKRESNSVEVHVETRKRNGEVEVHVRIRHD
+pdb_id=6nuk, cha... --VRIEIRFTNMRREEVQKELEKFKERLKELEKRTG-SEIRIEIEERDGEVRVEVEIRNS
+
+target DKETIERLVERILREIKKLDKNSEVEVRTTTKR
+pdb_id=6nuk, cha... HEEEVRQIIEEIERWVRKMGGE-----------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Closed: A.ARG23-()-A.ILE24 by relaxing A.LYS22-(RI)-A.LEU25
+Trying to fill 1 gap(s) by database.
+Resolved A.ASN33-(S)-A.VAL35 by filling A.SER32-(NSV)-A.GLU36 (45 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 15787.2)
+No more stereo-chemical problems -> final energy: -9485.67
+
+
+Build model with the following alignment:
+target GSEKKLDALLAMPVKETKVFVESNEEPLFVMLKSSLSEETDETVGKPVVSEKTAEPGQDN
+pdb_id=6ok3, cha... ------------------------------------------------------------
+
+target DGETGGAWMQQLRHQADQGDAKSAFWLGRFTVEDSRDGKTIDEGIRLIRRSAEGGFVRAQ
+pdb_id=6ok3, cha... ---DYQEAVFWYRKSALQGDELGQYNLGVAYYYGRGIKKDFSEAVSWYKKSAEQDYAQAQ
+
+target LYLGTLYANGTHVKADPHEAEKWLSRAAGQGSPMVQLYLGLMYGHGKGVPRDLNKSLFWV
+pdb_id=6ok3, cha... HNLGVTYYEGEGIKKDYAKAVYWWKKAAEQGIPQSQYNLGIAYEEGWGAEKNPENAVFWY
+
+target EKAADRGLPHAQLARGLFASFSHYYPRDDEKAVLYLTKAAKQGMPMAQFYLALMYQRGRG
+pdb_id=6ok3, cha... RKAAEQGHADAQNRLGIAYRYGTGVRKNPALSVKWLEKAAKQGLARAQFNLGKTFYIGAG
+
+target VEQSNEQALHWNMLAAEQGYPDAEYAMSRMAELGIGVTADKAWSMMWLDRAAHHGMPLAQ
+pdb_id=6ok3, cha... INKNTDKAVYWFIKAANQGFTEAQAYIGMIYFKGKYVAKNEKKGFYWLKKAAEKDSAKAQ
+
+target YLMGMAYLEGKSVPQDLPVAAAWFYKAAMQGNADAQLRLGYMYARGIGVPVDKP------
+pdb_id=6ok3, cha... AFLGALYIAGNEVKPNIKEGVALTKKAALQGNYEAQTLLGFCYENGLEVKKDLIAAYALY
+
+target ------------KAVAWLEKAASAGNTVAGQWLKQLD
+pdb_id=6ok3, cha... LSASPHFDFAEKARLDLERKLSEQEIAKAISV-----
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.PRO354-()-A.LYS355 by filling A.PRO354-(KAVAW)-A.LEU360 (63 candidates, BB_DB)
+Rebuilding sidechains.
+Trying to fix 1 ring punch(es).
+Trying to fill 1 gap(s) by database.
+Resolved A.THR131-(H)-A.VAL133 by filling A.ASN129-(GTHV)-A.LYS134 (49 candidates, BB_DB)
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 2.74744e+21)
+Perform energy minimization (iteration 2, energy: 14889)
+Perform energy minimization (iteration 3, energy: 11095)
+No more stereo-chemical problems -> final energy: 9888.49
+
+
+Build model with the following alignment:
+target MALKLLGFNQDATCFSVISSNKGVTIYNCDPFGKCFELEKSTSNDEELDFLVEMLFSTSL
+pdb_id=5ltd, cha... -NINFANFNQDFSCVSVGY-SNGYKIYNCEPFGQCYSK------SDGSIGIVEMLFSSSL
+
+target IAVVDKT-IGASKRKKLKIVNTKRKATICELTFPHEIMDVIMNRKIICVVLKSDQIFVYD
+pdb_id=5ltd, cha... LAIVGMGEQHSLSPRRLKIINTKRQTTICELTFPGAILAVKLNRERLVVLL-EETIYIYD
+
+target ISCMKLLRTIDVRGEKLKSTSKFRNSEAVGDIGVRVSLST-DNNSILCYSSYSKSD----
+pdb_id=5ltd, cha... INNMRLLHTIETP--------SNPN--------GLIALSPSSENNYLAYPSP--------
+
+target --------KENAPLNDIVVFDALKCIQINVLPAVHQSNIVCIACSPDGMLMATASEKGTI
+pdb_id=5ltd, cha... -------------NGDVIIFDAKTLQPTSVIEA-HRTSLAAIALSKDGLLLATASDKGTI
+
+target IRVFKTIDTENDEPILVNEFRRGSRPSRISEMKFNHDNTLLACVGESDTIHIFALPVTTT
+pdb_id=5ltd, cha... IRVFSVATG-----IKLYQFRRGTYPTKIYSLAFSPDNRFVIASSATETVHIFRLG----
+
+target -----------------E----------------A--------DA---N--E------DD
+pdb_id=5ltd, cha... ------------------------------------------------------------
+
+target T---------------------------------LQQSSHSL-SSSINGLQYISKGLANR
+pdb_id=5ltd, cha... ------------------------------------------------------------
+
+target FGKIIVSKIPTQ-SQQRHVAYIKIPEN--AKYRIGFPKD---------------------
+pdb_id=5ltd, cha... ----------------RHFASLKVPASKETKTVVGVGSKIWDDLIP--------------
+
+target -------TTNTIHICGEDGNYLVYSIP-RNEVGPCTLVKSNTFD
+pdb_id=5ltd, cha... --DLVNKKLVHIMVITSEGFFYKFGLDPERG-GDCVLLHQQSL-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 15).
+Initialized default backbone scoring for modelling.
+Closed: A.THR159-()-A.ASP160 by relaxing A.SER158-(T)-A.ASP160
+Closed: A.PRO376-()-A.ARG377 by relaxing A.PRO376-(R)-A.ASN378
+Trying to merge 13 gap(s) with distance 0.
+Trying to fill 13 gap(s) by database.
+Resolved A.SER19-(S)-A.ASN21 by filling A.SER19-(SNKG)-A.VAL24 (40 candidates, BB_DB)
+Resolved A.LEU38-(EKSTSN)-A.ASP45 by filling A.LEU38-(EKSTSNDEE)-A.LEU48 (66 candidates, BB_DB)
+Resolved A.THR67-()-A.ILE68 by filling A.LYS66-(TIGASK)-A.ARG73 (41 candidates, BB_DB)
+Resolved A.LEU110-(K)-A.SER112 by filling A.VAL109-(LKSD)-A.GLN114 (51 candidates, BB_DB)
+Resolved A.ARG132-(GEKLKSTS)-A.LYS141 by filling A.VAL131-(RGEKLKSTSKF)-A.ARG143 (150 candidates, BB_DB)
+Resolved A.ASN144-(SEAVGDIG)-A.VAL153 by filling A.ARG143-(NSEAVGDIGV)-A.ARG154 (41 candidates, BB_DB)
+Resolved A.TYR170-(SKSDKENAP)-A.LEU180 by filling A.TYR170-(SKSDKENAPL)-A.ASN181 (52 candidates, BB_DB)
+Resolved A.ALA199-(V)-A.HIS201 by filling A.PRO198-(AVHQ)-A.SER203 (67 candidates, BB_DB)
+Resolved A.THR235-(ENDEP)-A.ILE241 by filling A.ILE233-(DTENDEP)-A.ILE241 (52 candidates, BB_DB)
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Resolved A.ASN346-()-A.ALA347 by filling A.PRO344-(ENAK)-A.TYR349 (86 candidates, BB_DB)
+Resolved A.ASP356-()-A.THR357 by filling A.ASP356-(TTN)-A.THR360 (82 candidates, BB_DB)
+Resolved A.GLU379-(V)-A.GLY381 by filling A.ILE375-(PRNEV)-A.GLY381 (60 candidates, BB_DB)
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Trying to fill 1 gap(s) by database.
+Failed at loop insertion (A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336), only 0 candidates
+Trying to fill 1 gap(s) by Monte Carlo.
+Resolved A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQ)-A.ARG336 by filling A.PRO282-(VTTTEADANEDDTLQQSSHSLSSSINGLQYISKGLANRFGKIIVSKIPTQSQQR)-A.HIS337 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.09317e+29)
+Perform energy minimization (iteration 2, energy: 35303.5)
+Perform energy minimization (iteration 3, energy: 25649.2)
+Perform energy minimization (iteration 4, energy: 22917.4)
+No more stereo-chemical problems -> final energy: 20987.1
+
+
+Build model with the following alignment:
+target SMSASLLEKQSTGGAIARVGFEYQDAFVLKNLPLWLSESAFSHIVSESIGDVEVCYFSLE
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target KDFQRVMYEAKNHSLTSTDFWKEIKRFKEAFDIPSSEFTRFGLVCPLYTSTLHPFLAQIE
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target RIRGVGSSYSADSVILQKSRQDITQWCSDKGFETSLAEFALDHVDFLSFNAEDSDSVFIG
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target EIEEKLSNIELTTRKAKQLRDQFKNLISRSSFGPIHRKDFENFICHALEEDRTQWLSDPI
+pdb_id=3ox5, cha... ------------VKELRDAFREF----DTNGDGEISTSELREAMRKLLGHQVGHR-----
+
+target KINLSASSSQHQDLNLDISDFNGPDRAQKTSSDWNSLIKKAVSIGDFIHNSGDRRTLLID
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target GKQRMSTACMLGYVFSATRNFLLEIEHNGLAYRTDDHKQKEGQFFNKTNSIELHGKTEAI
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target VTIGFPTAIGKDIDSTINEIKNLPRLNLESSNVIDNMETLNLAVKEAKSALVSFKAENKL
+pdb_id=3ox5, cha... ------------------------------------------------------------
+
+target SKLHLFIKAPSVFAMVLGHRLNGVCNIQLYDWVNGEYMPTAELNI
+pdb_id=3ox5, cha... ---------------------------------------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.PHE203-(KNLI)-A.SER208 by filling A.PHE203-(KNLISRSS)-A.PHE212 (71 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.96286e+07)
+No more stereo-chemical problems -> final energy: -817.898
+
+
+Build model with the following alignment:
+target MSELIRVERETGLLTLRLDRQDKKNALTRAMYSRMAEALLEAQADTAVRVVLITGGD-AC
+pdb_id=4jwv, cha... ----IDFRIEGHVAHVRLNRPQGLNAITQEMDDLLLDAWTEVNANSDIWAVVLSAEGEKA
+
+target FTSGNDILDFLEQPPSLR-DSPVGRFMSALLEFPKPVIAAVNGPAVGIGTTLLLHCDLVF
+pdb_id=4jwv, cha... FCIGADV-----RKTRMALGGGLTGIGGPLVTCKKPMVAAVQGFCVGGGFELAMCADIIV
+
+target VGRNARLKMPFVNLGLTPEFGSSLILPRMLGHAKAAELLMLGQDFSGEQAAAWGLANAAL
+pdb_id=4jwv, cha... AADTAQFGLPETKVGIIGECGVVHRAMRQLPYHIALQLILTGERIKADEARHYGLVNEVV
+
+target EDGATVLEHARDAARRFLHLAPSAVVESKRLMKAPFIEELRRVIAEEGDIFSTRLRSPEA
+pdb_id=4jwv, cha... P-FAELEEAALRWASKLNAASPLAVQAAKAAALGRLGHPLEVALMTRFEPIEEYAATEDK
+
+target IEALSAFMHRRQPDFSRFA
+pdb_id=4jwv, cha... KEGERAAGERRKPVWTGK-
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 4).
+Initialized default backbone scoring for modelling.
+Closed: A.ASP57-()-A.ALA58 by relaxing A.GLY56-(DA)-A.CYS59
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.ILE66-(LDFLE)-A.GLN72 by filling A.ILE66-(LDFLE)-A.GLN72 (274 candidates, BB_DB)
+Resolved A.ARG77-()-A.ASP78 by filling A.SER75-(LRDS)-A.PRO80 (45 candidates, BB_DB)
+Resolved A.GLU179-(D)-A.GLY181 by filling A.ALA177-(LED)-A.GLY181 (55 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 7.60042e+10)
+No more stereo-chemical problems -> final energy: 403.418
+
+
+Build model with the following alignment:
+target MGSHHHHHHSVPRGSHMHQCYNGSGMDYRGTASTTKSGHQCQPWALQHPHSHHLSSTDFP
+pdb_id=1pkr, cha... ------------------ECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHP
+
+target ELGGGHAYCRNPGGQMEGPWCFTQNKNVRMELCDVPSC
+pdb_id=1pkr, cha... SEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILEC
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 1.10965e+06)
+No more stereo-chemical problems -> final energy: 5395.46
+
+
+Build model with the following alignment:
+target QLVETGGGLVQPGGSLRLSCAASGSIFSINAMGWYRQAPGKERELVADISSSGRINEADS
+pdb_id=5f7l, cha... QLQESGGGLVQPGGSLRLSCAASGSIYSLIAMGWYRQAPGKEHELVATISSGSTTYYADS
+
+target VKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVLA---GSHYYDEYEYWGQGTQVTVS
+pdb_id=5f7l, cha... VKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAYSDRLTDCSNCEADYWGQGTQVTV-
+
+Starting modelling based on a raw model.
+Removed 1 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 1).
+Initialized default backbone scoring for modelling.
+Trying to fill 1 gap(s) by database.
+Resolved A.ALA97-()-A.GLY98 by filling A.ALA97-(GSHY)-A.TYR102 (60 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 6.88931e+15)
+Perform energy minimization (iteration 2, energy: 4795.61)
+Perform energy minimization (iteration 3, energy: 4161.9)
+Perform energy minimization (iteration 4, energy: 3843.13)
+Perform energy minimization (iteration 5, energy: 3630.53)
+Perform energy minimization (iteration 6, energy: 3460.85)
+Perform energy minimization (iteration 7, energy: 3329.81)
+No more stereo-chemical problems -> final energy: 3215.15
+
+
+Build model with the following alignment:
+target MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSALQVSDVDKLVCRDKLSST
+pdb_id=5fhc, cha... --------------------------------IPLGVIHNSTLQVSDVDKLVCRDKLSST
+
+target NQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSE
+pdb_id=5fhc, cha... NQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSE
+
+target CLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGV
+pdb_id=5fhc, cha... CLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGV
+
+target VAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLT
+pdb_id=5fhc, cha... VAFLILPQA------------------------YSTTIRYQATGFGTNETEYLFEVDNLT
+
+target YVQLESRFTPQFLLQLNETIYASGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRK
+pdb_id=5fhc, cha... YVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVN----------------------
+
+target IRSEELSFTAVSNSASSGKLGLITNTIAGVAGLITGGRRTRREVIVNAQPKCNPNLHYWT
+pdb_id=5fhc, cha... -RSEELSFS---------------------------------------------------
+
+target TQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATPEL
+pdb_id=5fhc, cha... ------------------------------------------------------------
+
+target RTFSILNRFAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKTLPDQG
+pdb_id=5fhc, cha... ------------------------------------------------------------
+
+target DNDNWWTGHHHHHH
+pdb_id=5fhc, cha... --------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 2).
+Initialized default backbone scoring for modelling.
+Trying to merge 2 gap(s) with distance 0.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to merge 2 gap(s) with distance 1.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to merge 2 gap(s) with distance 2.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to merge 2 gap(s) with distance 3.
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to fill 2 gap(s) by database.
+Failed at loop insertion (A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214), only 0 candidates
+Failed at loop insertion (A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302), only 0 candidates
+Trying to fill 2 gap(s) by Monte Carlo.
+Resolved A.ALA189-(KKDFFSSHPLREPVNATEDPSSGY)-A.TYR214 by filling A.GLN188-(AKKDFFSSHPLREPVNATEDPSSGY)-A.TYR214 (6 candidates, BB)
+Resolved A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302 by filling A.ASN278-(PEIDTTIGEWAFWETKKNLTRKI)-A.ARG302 (6 candidates, BB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 5.48423e+14)
+Perform energy minimization (iteration 2, energy: 16118.5)
+No more stereo-chemical problems -> final energy: 13645.3
+
+
+Build model with the following alignment:
+target GSHMRQPIALISVHGDPAADVGHESAGGQNIYVRQLGEALAAAGWHVDMFTRKTDPNDPD
+pdb_id=3c48, cha... -----MRVAMISMHTSPLQQ-------GMNVYILSTATELAKQGIEVDIYTRATRPSQGE
+
+target VIEHSPHCRTIRLQAGPLTYIPREKLFETLPKFVEAFKAYH--AKYGYPLIHTNYWLSGW
+pdb_id=3c48, cha... IVRVAENLRVINIAAGPYEGLSKEELPTQLAAFTGGMLSFTRREKVTYDLIHSHYWLSGQ
+
+target VGWQLRQQFNFQWLHTYHSLGVVKYQVASEQAQR-DETRLMVEKAILENADCVIVTSPQE
+pdb_id=3c48, cha... VGWLLRDLWRIPLIHTAHTLAAVKNSY----DTPESEARRICEQQLVDNADVLAVNTQEE
+
+target EAYL-RRWVSKAGQTRLIPCGTNWEAIALQMGQLYRQLFAASL
+pdb_id=3c48, cha... MQDLMHHYDADPDRISVVSPGADVELYSP--------------
+
+Starting modelling based on a raw model.
+Removed 2 terminal gap(s).
+Trying to close small deletions (no. of gap(s): 5).
+Initialized default backbone scoring for modelling.
+Closed: A.ARG152-()-A.ASP153 by relaxing A.GLN151-(RDE)-A.THR155
+Closed: A.LEU181-()-A.ARG182 by relaxing A.TYR180-(LR)-A.ARG183
+Trying to merge 3 gap(s) with distance 0.
+Trying to fill 3 gap(s) by database.
+Resolved A.ASP20-(VGHESAG)-A.GLY28 by filling A.ASP20-(VGHESAG)-A.GLY28 (72 candidates, BB_DB)
+Resolved A.HIS101-()-A.ALA102 by filling A.HIS101-(AKYGY)-A.PRO107 (79 candidates, BB_DB)
+Resolved A.VAL145-(ASEQ)-A.ALA150 by filling A.VAL145-(ASEQA)-A.GLN151 (51 candidates, BB_DB)
+Rebuilding sidechains.
+Minimize energy.
+Perform energy minimization (iteration 1, energy: 9.2768e+11)
+No more stereo-chemical problems -> final energy: 9213.75
+
+full modelling time: 1595.06853890419
diff --git a/other/structural_coverage_in_StructureDB.py b/other/structural_coverage_in_StructureDB.py
new file mode 100644
index 0000000000000000000000000000000000000000..b1b8719118882273036fc0590939d574cd73d382
--- /dev/null
+++ b/other/structural_coverage_in_StructureDB.py
@@ -0,0 +1,67 @@
+from promod3 import loop
+import random
+
+def GetCoveredFraction(db, length, N, rmsd_thresh, coil_thresh):
+
+ # get all possible fragments
+ frag_infos = list()
+ for coord_idx in range(db.GetNumCoords()):
+ coord_info = db.GetCoordInfo(coord_idx)
+ for frag_start_idx in range(coord_info.size - length):
+ frag_info = loop.FragmentInfo(coord_idx, frag_start_idx, length)
+ frag_infos.append((frag_info, coord_info.id))
+
+ # randomize
+ random.shuffle(frag_infos)
+
+ N_processed = 0
+ N_covered = 0
+ dummy_seq = 'A' * length
+
+ for frag_idx in range(len(frag_infos)):
+ if N_processed >= N:
+ break # its enough!
+
+ frag_info = frag_infos[frag_idx][0]
+ pdb_id = frag_infos[frag_idx][1]
+
+ # check whether coil threshold is fulfilled
+ ss = db.GetDSSPStates(frag_info)
+ n_coil = ss.count('C')
+ if float(n_coil) / length < coil_thresh:
+ continue
+
+ # search for similar fragment in other entry
+ frag = db.GetBackboneList(frag_info, dummy_seq)
+ is_covered = False
+ for coord_idx in range(db.GetNumCoords()):
+ if is_covered:
+ break
+ coord_info = db.GetCoordInfo(coord_idx)
+ if pdb_id == coord_info.id:
+ # same entry with respect to pdb id
+ continue
+ for frag_start_idx in range(coord_info.size - length):
+ current_frag_info = loop.FragmentInfo(coord_idx, frag_start_idx,
+ length)
+ current_frag = db.GetBackboneList(current_frag_info, dummy_seq)
+ rmsd = frag.CARMSD(current_frag, superposed_rmsd=True)
+ if rmsd < rmsd_thresh:
+ is_covered = True
+ break
+ # add up results
+ N_processed += 1
+ if is_covered:
+ N_covered += 1
+ return float(N_covered) / N_processed
+
+db = loop.LoadStructureDB()
+
+print('No Thresh:')
+for i in range(3,16):
+ print('Fraction Covered', i, GetCoveredFraction(db, i, 1000, 1.0, 0.0))
+
+print('50 percent coils:')
+for i in range(3,16):
+ print('Fraction Covered', i, GetCoveredFraction(db, i, 1000, 1.0, 0.5))
+
diff --git a/sidechain/.~lock.eval_promod_frm_no_subrotamer_optimization.csv# b/sidechain/.~lock.eval_promod_frm_no_subrotamer_optimization.csv#
deleted file mode 100644
index e5924452bbd193f2f3d83260ba1210f159766da4..0000000000000000000000000000000000000000
--- a/sidechain/.~lock.eval_promod_frm_no_subrotamer_optimization.csv#
+++ /dev/null
@@ -1 +0,0 @@
-,schdaude,schdaudoputer,29.06.2020 09:45,file:///home/schdaude/.config/libreoffice/4;
\ No newline at end of file