[ccp4bb] antibody refinement in REFMAC with Kabat numbering

[John Pak]

Hi all.

I'm currently refining an Fab structure.  All was going reasonably  
well until I renumbered the PDB according to the Kabat numbering  
convention.  After which, REFMAC does not refine the inserted residues  
properly (ie. residues 82A, 82B, 100A, 100B, 100C, etc.).  It refines  
these residues into a steric jumble.  I think REFMAC can't recognize  
that the residues are connected or something.

So my question is, how do you refine this type of PDB in REFMAC?  Or  
do you just wait until the refinement is done, then change all the  
residue numbers and connect entries in the header afterwards?