diff --git a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
index 2569e8ab09d9221844738f6988598e2ab02fd7e4..75488947b84906db6443b9a7e0f30630b4de8175 100644
--- a/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
+++ b/modules/mol/alg/pymod/ligand_scoring_scrmsd.py
@@ -274,10 +274,6 @@ class SCRMSDScorer(ligand_scoring_base.LigandScorer):
                 if len(ref_bs.residues) == 0:
                     raise RuntimeError("Failed to add proximity residues to "
                                        "the reference binding site entity")
-            else:
-                # Flag missing binding site
-                self._unassigned_target_ligands_reason[target_ligand] = ("binding_site",
-                    "No residue in proximity of the target ligand")
 
             self._binding_sites[target_ligand.handle.hash_code] = ref_bs