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 ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- 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 The University of St Andrews is a charity registered in Scotland : No SC013532