[phenixbb] NAG-ASN link

[Jianghai Zhu]

Hi,

I got the following error when I added a NAG-ASN link in the def file.

/nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb
   Monomer Library directory:
     "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib"
   Total number of atoms: 46651
   apply_cif_link:
     data_link: NAG-ASN
       mod_id_1: DEL-O1
       mod_id_2: DEL-HD22
     residue_selection_1: chain S and resname NAG and resid 1001
     residue_selection_2: chain A and resname ASN and resid 15
   Number of models: 1
   Model: 0
     Number of conformers: 1
     Conformer: " "
       Number of atoms: 46651
       Number of chains: 8
         Number of residues, atoms: 909, 13713
           Unexpected atoms: {'ASN%DEL-HD22,HD22': 1}
           Classifications: {'peptide': 909}
           Modifications used: {'DEL-HD22': 1, 'NH3': 1}
           Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2}
           Chain breaks: 3
         Number of residues, atoms: 601, 8947
           Classifications: {'peptide': 601}
           Modifications used: {'NH3': 1}
           Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3}
           Chain breaks: 2
         Number of residues, atoms: 898, 13559
           Classifications: {'peptide': 898}
           Modifications used: {'NH3': 1}
           Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2}
           Chain breaks: 3
         Number of residues, atoms: 602, 8954
           Classifications: {'peptide': 602}
           Modifications used: {'NH3': 1}
           Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3}
           Chain breaks: 2
         Number of residues, atoms: 642, 642
           Classifications: {'water': 642}
           Link IDs: {None: 641}
         Number of residues, atoms: 31, 780
           Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23}
           Classifications: {'undetermined': 31}
           Modifications used: {'DEL-O1': 1}
           Link IDs: {None: 30, 'NAG-ASN': 1}
           Unresolved non-hydrogen bonds: 30
           Unresolved non-hydrogen angles: 60
           Unresolved non-hydrogen chiralities: 30
         Number of residues, atoms: 16, 16
           Unusual residues: {' MG': 2, ' CA': 14}
           Classifications: {'undetermined': 16}
           Link IDs: {None: 15}
         Number of residues, atoms: 4, 40
           Unusual residues: {'IMD': 4}
           Classifications: {'undetermined': 4}
           Link IDs: {None: 3}
   Number of atoms with unknown nonbonded energy type symbols: 1
     "HD22 ASN A  15 "
   Time building chain proxies: 32.54, per 1000 atoms: 0.70

Sorry: Fatal problems interpreting PDB file:
   Number of atoms with unknown nonbonded energy type symbols: 1
   Please edit the PDB file to resolve the problems and/or supply a
   CIF file with matching restraint definitions, along with
   apply_cif_modification and apply_cif_link parameter definitions
   if necessary (see phenix.refine documentation).
   Also note that phenix.elbow is available to create restraint
   definitions for unknown ligands.

Couldn't figure out what went wrong.  Can somebody help me?  Thanks.

Jianghai

+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++++++++++++++++++++++++++++++



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