Step 1: identifying varying regions.
Multi-chain and multi-model targets were checked for structural
consistency by superimposing their chains /models using LGA11.
If the distance between the corresponding residues in different chains
/models exceeded 3.5 Å, then the residue was marked as varying. Local
regions of three or more consecutive varying residues were removed from
the target. If varying regions were extensive, but superimposed well
when treated separately, then they were organized into separate domains.