Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:18:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ymy_10848/12_2022/6ymy_10848.pdb" } resolution = 3.41 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= 0.005 sd= 0.058 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 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 97": "NH1" <-> "NH2" Residue "a ASP 145": "OD1" <-> "OD2" Residue "a GLU 222": "OE1" <-> "OE2" Residue "a ASP 228": "OD1" <-> "OD2" Residue "a TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 369": "OD1" <-> "OD2" Residue "a TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 438": "NH1" <-> "NH2" Residue "a TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 515": "OE1" <-> "OE2" Residue "b ASP 41": "OD1" <-> "OD2" Residue "b TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 162": "OD1" <-> "OD2" Residue "b ASP 183": "OD1" <-> "OD2" Residue "b PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 98": "OE1" <-> "OE2" Residue "c ARG 164": "NH1" <-> "NH2" Residue "c PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 229": "NH1" <-> "NH2" Residue "c TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "d ASP 79": "OD1" <-> "OD2" Residue "d ASP 82": "OD1" <-> "OD2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 107": "NH1" <-> "NH2" Residue "d GLU 136": "OE1" <-> "OE2" Residue "e ARG 37": "NH1" <-> "NH2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 79": "OE1" <-> "OE2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 50": "OE1" <-> "OE2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 65": "OD1" <-> "OD2" Residue "f PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 97": "NH1" <-> "NH2" Residue "f ASP 100": "OD1" <-> "OD2" Residue "f ARG 106": "NH1" <-> "NH2" Residue "f GLU 109": "OE1" <-> "OE2" Residue "g PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 25": "NH1" <-> "NH2" Residue "g TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 32": "OD1" <-> "OD2" Residue "h TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 17": "OD1" <-> "OD2" Residue "i ASP 39": "OD1" <-> "OD2" Residue "i TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 50": "OE1" <-> "OE2" Residue "i GLU 53": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 44": "OD1" <-> "OD2" Residue "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "k PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 79": "OE1" <-> "OE2" Residue "k GLU 82": "OE1" <-> "OE2" Residue "k ASP 95": "OD1" <-> "OD2" Residue "k PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 102": "NH1" <-> "NH2" Residue "k PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "m ARG 35": "NH1" <-> "NH2" Residue "m PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14612 Number of models: 1 Model: "" Number of chains: 19 Chain: "a" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4126 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 504} Chain: "b" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1888 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain: "c" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2138 Classifications: {'peptide': 268} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 258} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "e" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 828 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "g" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 5, 'TRANS': 49} Chain: "h" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "i" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "j" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 649 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "k" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 941 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "m" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 308 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "a" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 245 Unusual residues: {' CU': 1, 'CN3': 1, 'HEA': 2, 'PTY': 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: 57 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 59 Unsupported chir.volume_sign: {'cros': 2} Unresolved non-hydrogen planarities: 8 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unknown residues: {'CUA': 1} Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unknown residues: {'PCF': 1} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unknown residues: {'PCF': 1} Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "i" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Unknown residues: {'PCF': 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5780 SG CYS b 221 56.980 92.237 58.205 1.00 99.91 S ATOM 8943 SG CYS d 134 47.478 28.699 70.624 1.00102.47 S Number of atoms with unknown nonbonded energy type symbols: 127 "HETATM14066 NB HEA a 602 .*. N " "HETATM14067 ND HEA a 602 .*. N " "HETATM14117 NA HEA a 602 .*. N " "HETATM14118 NC HEA a 602 .*. N " "HETATM14126 NB HEA a 603 .*. N " "HETATM14127 ND HEA a 603 .*. N " "HETATM14177 NA HEA a 603 .*. N " "HETATM14178 NC HEA a 603 .*. N " "HETATM14310 CU1 CUA b 301 .*. Cu " "HETATM14311 CU2 CUA b 301 .*. Cu " ... (remaining 117 not shown) Time building chain proxies: 8.58, per 1000 atoms: 0.59 Number of scatterers: 14612 At special positions: 0 Unit cell: (108.12, 128.26, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Cu 3 28.99 Fe 2 26.01 S 68 16.00 P 12 15.00 O 2588 8.00 N 2281 7.00 C 9657 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: 127 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.