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.