before: Scoring was only affected by mapped chains. Penalties for additional
chains in reference/model could be added by enabling "penalize_extra_chains"
flag.
now: Non-mapped chains from the reference penalize the lDDT score. Penalties
for additional chains in model can be added by enabling "penalize_extra_chains"
flag.

If fault_tolerant is enabled, it might happily read a cif file as PDB file.
As a consequence, there are no residues in the returned entity.

Executed command: 2to3-2.7 -n -w actions/ost-compare-structures

fix: SCHWED-3121 Perform consistency checks by default - breaking change: consistency-checks to ignore-consistency-checks