OK, although the issue of non correspondence of SEQRES and ATOM list
remains, five models were built. I'll check the quality. On Chimera
the structures are, at first sight, as expected.
Modeller does not read the SEQRES records. It only reads the structure
(ATOM and HETATM records). It says this in the log file you posted
A question: of the homomer in the pdb I have modeled a subunit only.
Should I had best modeled all chains for the homomer? On using
Chimera to get the homomer from the homology model, can the BIOMT
transformation matrix given in the pdb file (for both crystallographic
and non-crystallographic operation) be used with the model?
Modeller certainly has no methods for applying such matrices. I think
Chimera does, but you'd be better off asking that on the Chimera mailing