[phenixbb] cis peptide question

Edward A. Berry BerryE at upstate.edu
Mon Jul 15 18:00:21 PDT 2013

I have a cis-peptide in my structure. Phenix recognizes it
and .geo file shows this is restrained to 0*:

dihedral pdb=" CA  ALA A 401 "
          pdb=" C   ALA A 401 "
          pdb=" N   SER A 402 "
          pdb=" CA  SER A 402 "
     ideal   model   delta  harmonic     sigma   weight residual
      0.00   -1.58    1.58     0      5.00e+00 4.00e-02 1.00e-01

However in statistics printed with the output pdb, I have
at least one dihedral that is flagged as off by about 180*:

REMARK   3                 RMSD     MAX  COUNT
REMARK   3   DIHEDRAL  : 12.902 168.987   3277

Could this be my cis peptide, or do I have a really bad dihedral somewhere else?

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