Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:58:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z10_14436/12_2022/7z10_14436.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "a PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 97": "NH1" <-> "NH2" Residue "a ARG 173": "NH1" <-> "NH2" Residue "a ARG 302": "NH1" <-> "NH2" Residue "a TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 154": "OE1" <-> "OE2" Residue "b ARG 159": "NH1" <-> "NH2" Residue "c ARG 6": "NH1" <-> "NH2" Residue "c ARG 67": "NH1" <-> "NH2" Residue "c GLU 72": "OE1" <-> "OE2" Residue "c PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 37": "NH1" <-> "NH2" Residue "e ARG 83": "NH1" <-> "NH2" Residue "f GLU 51": "OE1" <-> "OE2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 132": "NH1" <-> "NH2" Residue "g ARG 53": "NH1" <-> "NH2" Residue "h ARG 45": "NH1" <-> "NH2" Residue "i ARG 12": "NH1" <-> "NH2" Residue "i ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12574 Number of models: 1 Model: "" Number of chains: 13 Chain: "a" Number of atoms: 4162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4162 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 508} Chain: "b" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1889 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "c" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2146 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain: "d" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 913 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "e" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1049 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "f" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 851 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "g" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 484 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "h" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 383 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "i" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "a" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 202 Unusual residues: {' CU': 1, ' MG': 1, 'HEA': 2, 'PEF': 2} Unexpected atoms: {'HEA,NA': 2, 'HEA,NB': 2, 'HEA,NC': 2, 'HEA,ND': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 40 Unsupported chir.volume_sign: {'cros': 2} Unresolved non-hydrogen planarities: 8 Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Unknown residues: {'CUA': 1} Chain breaks: 1 Chain: "c" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PEF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5816 SG CYS b 221 41.626 44.743 98.383 1.00185.04 S ATOM 5845 SG CYS b 225 42.994 46.922 98.971 1.00187.71 S ATOM 5816 SG CYS b 221 41.626 44.743 98.383 1.00185.04 S ATOM 5845 SG CYS b 225 42.994 46.922 98.971 1.00187.71 S ATOM 8825 SG CYS d 111 31.726 68.541 41.463 1.00149.57 S ATOM 8995 SG CYS d 134 31.818 66.491 38.519 1.00145.04 S ATOM 9024 SG CYS d 137 28.762 67.906 37.385 1.00154.13 S Number of atoms with unknown nonbonded energy type symbols: 10 "HETATM12335 NB HEA a 602 .*. N " "HETATM12336 ND HEA a 602 .*. N " "HETATM12386 NA HEA a 602 .*. N " "HETATM12387 NC HEA a 602 .*. N " "HETATM12395 NB HEA a 603 .*. N " "HETATM12396 ND HEA a 603 .*. N " "HETATM12446 NA HEA a 603 .*. N " "HETATM12447 NC HEA a 603 .*. N " "HETATM12536 CU1 CUA b 301 .*. Cu " "HETATM12537 CU2 CUA b 301 .*. Cu " Time building chain proxies: 7.56, per 1000 atoms: 0.60 Number of scatterers: 12574 At special positions: 0 Unit cell: (83.945, 124.695, 136.105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Cu 3 28.99 Fe 2 26.01 S 61 16.00 P 3 15.00 Mg 1 11.99 O 2210 8.00 N 1986 7.00 C 8307 6.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 10 Please edit the model 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.