[phenixbb] Problem with LLP ligand
James Naismith
naismith at st-andrews.ac.uk
Wed Aug 19 02:02:24 PDT 2009
Dear All,
I am trying to refine a structure which has a Lys linked to PLP. In
the PDB this is called LLP.
When I take it through refine it crashes complaining about the ligand.
"Sorry : Fatal problems interpreting PDB file:
Number of atoms with unknown nonbonded energy type symbols: 8
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.
Traceback:
None
"
I know I have to use REEL to fix this in some way. I have used REEL to
make ligands not bound to protein before. It is how to do this when
the ligand is covalently bound that I am stuck with.
Any help (particularly a cif restraints file!) gratefully received.
best
Jim
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-------------------------------------------------------------------------------
Processing inputs. This may take a minute or two.
Working crystal symmetry after inspecting all inputs:
Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90)
Space group: P 1 21 1 (No. 4)
Monomer Library directory:
"/usr/local/phenix-1.4-115/chem_data/mon_lib"
Total number of atoms: 13558
Number of models: 1
Model: ""
Number of chains: 3
Chain: "A"
Number of atoms: 6752
Number of conformers: 2
Conformer: "B"
Number of residues, atoms: 420, 6747
Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
1, 'LLP,HE3': 1}
Classifications: {'peptide': 420}
Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
Chain breaks: 3
Conformer: "A"
Number of residues, atoms: 420, 6747
Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
1, 'LLP,HE3': 1}
Classifications: {'peptide': 420}
Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4}
Chain breaks: 3
bond proxies already assigned to first conformer: 6820
Chain: "B"
Number of atoms: 6800
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 423, 6800
Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3':
1, 'LLP,HE3': 1}
Classifications: {'peptide': 423}
Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4}
Chain breaks: 3
Chain: "M"
Number of atoms: 6
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 6
Unusual residues: {' SM': 6}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Number of atoms with unknown nonbonded energy type symbols: 8
"ATOM 3149 HG3 LLP A 211 .*. H "
"ATOM 3151 HE3 LLP A 211 .*. H "
"ATOM 3153 HD3 LLP A 211 .*. H "
"ATOM 3155 HB3 LLP A 211 .*. H "
"ATOM 9896 HG3 LLP B 211 .*. H "
"ATOM 9898 HE3 LLP B 211 .*. H "
"ATOM 9900 HD3 LLP B 211 .*. H "
"ATOM 9902 HB3 LLP B 211 .*. H "
Time building chain proxies: 9.24, per 1000 atoms: 0.68
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