[phenixbb] conflicting bond_simple restraints

22 May 2013

      Hi,

I had a phosphoserine (SEP) in my structure that is attached in this message.  The data_link file for SEP already exists in the mon_lib (data_link_SEPC-N) and the corresponding cif_link I used is as follow:

refinement.pdb_interpretation {
  apply_cif_link {
    data_link = "SEPC-N"
    residue_selection_1 = "chain C and resname PHE and resid 3"
    residue_selection_2 = "chain C and resname SEP and resid 4"
  }
  apply_cif_link {
    data_link = "SEPC-N"
    residue_selection_1 = "chain C and resname SEP and resid 4"
    residue_selection_2 = "chain C and resname ARG and resid 5"
  }
}

When I run the phenix.refine (my version is phenix-1.8-1069), it said conflicting bond_simple restraints:

Sorry: Conflicting bond_simple restraints:
  1. definition from: residues: PHE + SEP
  2. definition from: residues: PHE + SEP
  atoms:
    "ATOM   3121  C   PHE C   3 .*.     C  "
    "ATOM   3192  N   SEP C   4 .*.     N  "

Has anyone ever experienced this case before? Any hints are welcome.

Regards

Jianxun Qi
May 22,2013