[phenixbb] refinement error with ligand

Christian Roth christian.roth at bbz.uni-leipzig.de
Wed Feb 17 08:58:47 PST 2010

Dear all,

I started a refinement of one of my structures using the GUI of phenix (Version 
1.6). I used the options of adding hydrogens and dis a suimulated annealing. I 
used the output file and corrected it manually using Coot. I incorporated a few 
Ethylenglycol Monomers which might have bound.  I merged everything wrote the 
file out  and loaded this pdb in the GUI. I got an error which might be du to 
the fact that I didnt specify a CIF file for the ligand. I started ready set 
from the GUI to check the pdb and used REEL to create a CIF File. I added the 
CIF-File to the  File list and tried to start again phenix.refine using the 
hydrogen option but no sim. annealing. However I got always the following 
error log:

# Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s)
#phil __OFF__

Command line arguments: 
"/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "--

HOST = bbzws339
HOSTTYPE = i486-linux
VENDOR = intel
USER = roth
PID = 29983

  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  Version: 1.6
  Release tag: 289
  Platform: intel-linux-2.6 linux
  User: roth

              phenix.refine: Macromolecular Structure Refinement

 Monomer Library directory:
  Total number of atoms: 16881
  Number of models: 1
  Model: ""
    Number of chains: 19
    Chain: "A"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1575
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 87} 
and so on for other chains
 Chain: "R"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'EDO': 1}
          Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1}
          Classifications: {'undetermined': 1}
  Number of atoms with unknown nonbonded energy type symbols: 16
    "HETATM16821  HO2 EDO K   1 .*.     H  "
    "HETATM16826  HO1 EDO K   1 .*.     H  "
    "HETATM16828  HO2 EDO L   1 .*.     H  "
    "HETATM16834  HO1 EDO L   1 .*.     H  "
    "HETATM16836  HO2 EDO M   1 .*.     H  "
    "HETATM16840  HO1 EDO M   1 .*.     H  "
    "HETATM16842  HO2 EDO N   1 .*.     H  "
    "HETATM16848  HO1 EDO N   1 .*.     H  "
    "HETATM16850  HO2 EDO O   1 .*.     H  "
    "HETATM16857  HO1 EDO O   1 .*.     H  "
    ... (remaining 6 not shown)

I looked in the pdb for this atoms, but I cannot find them.
When I use a cif file created directly by phenix elbow using command line and 
when I did not use the update hydrogen button the refinement works. But the new 
residues as well as the EDO molecules have no hydrogens in riding positions. 
Do I have to remove all hydrogens and attach them again for every cycle?
One Refinement runs for more then 5 hours regardless I use sim annealing or 
not. This seems to be very long for me. Maybe I want  too many optimization 

Could anyone explain me what goes wrong here. I am no so much experienced with 
phenix and now I run out of ideas. 

Thanks in advance 


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