[phenixbb] log file

[Ralf W. Grosse-Kunstleve]

> While I refining I found the following is included in the .log
> file. I am using different pdb files.  When I looked up residue
> number 175,

That's just a count, the "number of residues", not the "residue number".

> it looked ok to me. Do you guys have any idea how to deal
> with this?
>
> Conformer: "C"
>         Number of residues, atoms: 175, 1321
>           Classifications: {'peptide': 175}
>           Link IDs: {'PTRANS': 14, 'TRANS': 159, 'PCIS': 1}
>           Chain breaks: 24
>           Unresolved chain link angles: 14
>           Unresolved chain link dihedrals: 28
>           Unresolved chain link planarities: 14
>           Unresolved non-hydrogen bonds: 50
>           Unresolved non-hydrogen angles: 60
>           Unresolved non-hydrogen dihedrals: 26
>           Unresolved non-hydrogen chiralities: 8
>           Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
>           Unresolved non-hydrogen planarities: 9
>           bond proxies already assigned to first conformer: 1313

I'm guessing there are stretches of residues with only "A" and "B"
altloc (pdb column 17) but no " " (blank).
phenix.refine builds the conformers by combining all atoms with altloc
"A" or " " for conformer A, all "B" or " " for B, and so on.
The assignment to conformers determines the nonbonded interactions:
they are only between atoms in the same conformer.
Your refinement may be OK, it depends on what you want.

Ralf