Starting phenix.real_space_refine (version: dev) on Tue Dec 20 13:26:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yez_10798/12_2022/6yez_10798.pdb" } resolution = 2.7 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 504 atoms to isotropic. 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 GLU 17": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 549": "OD1" <-> "OD2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 622": "OD1" <-> "OD2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "E PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 127": "OD1" <-> "OD2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K ASP 103": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ARG 98": "NH1" <-> "NH2" Residue "L PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ASP 174": "OD1" <-> "OD2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "L PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 40": "OD1" <-> "OD2" Residue "1 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 62": "OD1" <-> "OD2" Residue "1 GLU 74": "OE1" <-> "OE2" Residue "1 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 110": "OE1" <-> "OE2" Residue "1 GLU 156": "OE1" <-> "OE2" Residue "1 ASP 173": "OD1" <-> "OD2" Residue "1 GLU 179": "OE1" <-> "OE2" Residue "1 TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 220": "OD1" <-> "OD2" Residue "2 ASP 84": "OD1" <-> "OD2" Residue "2 PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 95": "OD1" <-> "OD2" Residue "2 GLU 97": "OE1" <-> "OE2" Residue "2 GLU 106": "OE1" <-> "OE2" Residue "2 TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 192": "OD1" <-> "OD2" Residue "2 TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 256": "OD1" <-> "OD2" Residue "2 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 69": "OD1" <-> "OD2" Residue "3 ASP 75": "OD1" <-> "OD2" Residue "3 ASP 85": "OD1" <-> "OD2" Residue "3 GLU 94": "OE1" <-> "OE2" Residue "3 GLU 120": "OE1" <-> "OE2" Residue "3 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 153": "OD1" <-> "OD2" Residue "3 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 216": "OD1" <-> "OD2" Residue "3 GLU 217": "OE1" <-> "OE2" Residue "3 GLU 227": "OE1" <-> "OE2" Residue "3 ARG 232": "NH1" <-> "NH2" Residue "4 GLU 132": "OE1" <-> "OE2" Residue "4 GLU 133": "OE1" <-> "OE2" Residue "4 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 153": "OE1" <-> "OE2" Residue "4 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 181": "OE1" <-> "OE2" Residue "4 TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 199": "OE1" <-> "OE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 26": "OD1" <-> "OD2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N GLU 55": "OE1" <-> "OE2" Residue "N ASP 65": "OD1" <-> "OD2" Residue "N ASP 66": "OD1" <-> "OD2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "P GLU 2": "OE1" <-> "OE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ASP 51": "OD1" <-> "OD2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 39217 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5858 Classifications: {'peptide': 743} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 712} Chain: "B" Number of atoms: 5857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5857 Classifications: {'peptide': 733} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 702} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 612 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 74} Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1132 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 128} Chain: "E" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 528 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "F" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1206 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 757 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 712 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 8, 'TRANS': 84} Chain: "I" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 240 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain: "J" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 338 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "K" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 569 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "L" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1197 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 146} Chain: "1" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1508 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 172} Chain: "2" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1620 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 19, 'TRANS': 188} Chain: "3" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1706 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1559 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 15, 'TRANS': 182} Chain: "N" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 724 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "P" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 728 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 3099 Unknown residues: {'CL0': 1} Unusual residues: {' CA': 1, 'BCR': 6, 'CLA': 43, 'LHG': 2, 'LMG': 1, 'LMT': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 56} Link IDs: {None: 55} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 3140 Unusual residues: {' CA': 1, 'BCR': 5, 'CLA': 42, 'DGD': 1, 'LHG': 2, 'LMG': 3, 'LMT': 2, 'PQN': 1} Classifications: {'undetermined': 57} Link IDs: {None: 56} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 427 Unusual residues: {'BCR': 2, 'CLA': 2, 'DGD': 1, 'LMG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LMG:plan-2': 1, 'LMG:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 443 Unusual residues: {'BCR': 1, 'CLA': 3, 'DGD': 1, 'LMG': 3, 'LMT': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unknown residues: {'LUT': 1} Unusual residues: {'BCR': 1, 'CLA': 1, 'DGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 279 Unusual residues: {'BCR': 2, 'CLA': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "1" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 824 Unknown residues: {'CHL': 3, 'LUT': 2} Unusual residues: {'BCR': 2, 'CLA': 11, 'DGD': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 16} Link IDs: {None: 11} Chain breaks: 5 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'CLA:plan-5': 4} Unresolved non-hydrogen planarities: 17 Chain: "2" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 843 Unknown residues: {'CHL': 5, 'LUT': 1} Unusual residues: {'3PH': 1, 'BCR': 1, 'CLA': 9, 'LHG': 1, 'LMG': 5, 'LMT': 1, 'XAT': 1} Classifications: {'undetermined': 19} Link IDs: {None: 15} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'LMG:plan-2': 1, 'LMG:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "3" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 756 Unknown residues: {'CHL': 3, 'LUT': 2} Unusual residues: {'BCR': 2, 'CLA': 11, 'DGD': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 16} Link IDs: {None: 12} Chain breaks: 5 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'LHG:plan-2': 1, 'LHG:plan-1': 1, 'CLA:plan-4': 1, 'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 18 Chain: "4" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 761 Unknown residues: {'C7Z': 1, 'CHL': 4, 'LUT': 1} Unusual residues: {'CLA': 11, 'DGD': 1, 'LHG': 1, 'XAT': 1} Classifications: {'undetermined': 14} Link IDs: {None: 10} Chain breaks: 6 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4465 SG CYS A 581 89.693 94.607 58.846 1.00 66.30 S ATOM 10265 SG CYS B 559 95.416 94.783 59.794 1.00 63.72 S ATOM 10320 SG CYS B 568 92.989 89.131 60.717 1.00 59.56 S ATOM 4520 SG CYS A 590 91.183 94.576 65.176 1.00 62.38 S ATOM 11863 SG CYS C 21 90.117 108.087 51.172 1.00 71.31 S ATOM 12107 SG CYS C 54 94.601 103.010 50.356 1.00 69.29 S ATOM 12081 SG CYS C 51 89.922 103.119 54.648 1.00 64.46 S ATOM 12064 SG CYS C 48 95.049 107.410 55.728 1.00 71.37 S ATOM 11812 SG CYS C 14 92.504 100.917 39.748 1.00 87.76 S ATOM 11794 SG CYS C 11 98.309 104.739 39.445 1.00 81.62 S ATOM 12133 SG CYS C 58 97.193 99.143 43.588 1.00 74.24 S ATOM 11834 SG CYS C 17 93.578 104.482 44.461 1.00 77.31 S ATOM 25702 SG CYS N 39 91.074 95.666 35.426 1.00170.10 S ATOM 25734 SG CYS N 44 89.201 98.810 34.889 1.00181.76 S ATOM 25752 SG CYS N 47 87.053 96.099 30.199 1.00199.09 S ATOM 25967 SG CYS N 77 88.943 92.975 31.135 1.00203.72 S ATOM 26748 SG CYS P 84 88.851 55.916 98.632 1.00165.20 S Number of atoms with unknown nonbonded energy type symbols: 1203 "HETATM26852 NB CL0 A1011 .*. N " "HETATM26853 ND CL0 A1011 .*. N " "HETATM26854 C1 CL0 A1011 .*. C " "HETATM26855 C10 CL0 A1011 .*. C " "HETATM26856 C11 CL0 A1011 .*. C " "HETATM26857 C12 CL0 A1011 .*. C " "HETATM26858 C13 CL0 A1011 .*. C " "HETATM26859 C14 CL0 A1011 .*. C " "HETATM26860 C15 CL0 A1011 .*. C " "HETATM26861 C16 CL0 A1011 .*. C " ... (remaining 1193 not shown) Time building chain proxies: 21.41, per 1000 atoms: 0.55 Number of scatterers: 39217 At special positions: 0 Unit cell: (181.662, 145.494, 132.342, 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) Cu 1 28.99 Fe 14 26.01 Ca 2 19.99 S 93 16.00 P 9 15.00 Mg 157 11.99 O 6042 8.00 N 5115 7.00 C 27784 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: 1203 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.