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> refmac5 must be assuming that you number your protein according to your
protein sequence, which is continuous. In my opinion, this is reasonable.

Uhhh... this assumption turns perilious quickly, because there
are post-translational mods and splicing (see Concanavalin), 
and biologists sometimes prefer keeping the
key residues in related structures (trypsin, fabs, etc) at 
a certain residue number. This causes 
sequence insertions (addressed correctly, as you say) 
and gaps (not addressed correctly, my situation.) 

>to solve your problem

As I sent before, it can be fixed by replacing 
'gap' with 'TRANS', left-adjusted. 

Thx!

br


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