[phenixbb] log file

Young-Jin Cho yjcho at brandeis.edu
Tue Oct 6 12:49:59 PDT 2009

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, 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

Thanks in advance,


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