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