Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:16:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoc_11840/04_2023/7aoc_11840.pdb" } resolution = 3.84 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= 0.020 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 570 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 165 5.16 5 C 18860 2.51 5 N 5136 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 647": "OD1" <-> "OD2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 819": "OD1" <-> "OD2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 882": "OD1" <-> "OD2" Residue "A TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 927": "OD1" <-> "OD2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1080": "OE1" <-> "OE2" Residue "A ASP 1103": "OD1" <-> "OD2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1122": "OD1" <-> "OD2" Residue "A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A GLU 1274": "OE1" <-> "OE2" Residue "A ARG 1280": "NH1" <-> "NH2" Residue "A ASP 1302": "OD1" <-> "OD2" Residue "A ASP 1311": "OD1" <-> "OD2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1481": "OD1" <-> "OD2" Residue "A GLU 1493": "OE1" <-> "OE2" Residue "A GLU 1501": "OE1" <-> "OE2" Residue "A GLU 1510": "OE1" <-> "OE2" Residue "A GLU 1554": "OE1" <-> "OE2" Residue "A ASP 1568": "OD1" <-> "OD2" Residue "A GLU 1588": "OE1" <-> "OE2" Residue "A PHE 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1615": "OE1" <-> "OE2" Residue "A PHE 1638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A ASP 1656": "OD1" <-> "OD2" Residue "A PHE 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 608": "OD1" <-> "OD2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 748": "OD1" <-> "OD2" Residue "B TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 770": "OD1" <-> "OD2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 858": "OE1" <-> "OE2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B GLU 870": "OE1" <-> "OE2" Residue "B ASP 877": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B ASP 900": "OD1" <-> "OD2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1027": "OD1" <-> "OD2" Residue "B PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1058": "OE1" <-> "OE2" Residue "B TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1112": "OE1" <-> "OE2" Residue "B ASP 1134": "OD1" <-> "OD2" Residue "B PHE 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 128": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G ASP 149": "OD1" <-> "OD2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "I PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "K ASP 96": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29724 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 11051 Classifications: {'peptide': 1394} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1327} Chain breaks: 12 Chain: "B" Number of atoms: 9148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9148 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 59, 'TRANS': 1099} Chain breaks: 3 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 483 SG CYS A 63 77.752 60.209 58.365 1.00 93.27 S ATOM 501 SG CYS A 66 74.149 61.180 57.450 1.00 95.46 S ATOM 565 SG CYS A 73 74.149 61.209 59.501 1.00 84.44 S ATOM 809 SG CYS A 103 81.341 18.476 87.647 1.00110.95 S ATOM 1540 SG CYS A 228 80.800 17.695 89.490 1.00102.85 S ATOM 1562 SG CYS A 231 82.126 13.918 87.382 1.00111.41 S ATOM 27663 SG CYS I 10 125.367 43.834 144.167 1.00100.65 S ATOM 27684 SG CYS I 13 126.037 44.283 140.827 1.00102.67 S ATOM 27789 SG CYS I 27 126.217 41.033 141.731 1.00128.76 S ATOM 27812 SG CYS I 30 127.155 42.411 141.870 1.00125.54 S ATOM 28111 SG CYS J 7 75.288 120.630 103.630 1.00 3.36 S ATOM 28134 SG CYS J 10 71.372 121.754 105.969 1.00 3.55 S ATOM 28406 SG CYS J 44 72.291 119.519 107.188 1.00 3.74 S ATOM 28412 SG CYS J 45 74.016 122.212 105.891 1.00 12.41 S ATOM 29399 SG CYS L 24 113.087 106.412 84.682 1.00 33.38 S ATOM 29418 SG CYS L 27 114.114 108.827 84.566 1.00 46.11 S ATOM 29525 SG CYS L 41 114.859 107.058 83.207 1.00 37.24 S ATOM 29551 SG CYS L 44 117.022 108.444 86.275 1.00 45.93 S Time building chain proxies: 14.78, per 1000 atoms: 0.50 Number of scatterers: 29724 At special positions: 0 Unit cell: (151.017, 155.271, 169.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 165 16.00 O 5557 8.00 N 5136 7.00 C 18860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B1089 " - pdb=" SG CYS B1092 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.52 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " Number of angles added : 21 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 43 sheets defined 36.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.551A pdb=" N VAL A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.793A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.840A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.706A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.795A pdb=" N PHE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.407A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 385 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 removed outlier: 3.622A pdb=" N GLN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.135A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.914A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.337A pdb=" N TRP A 775 " --> pdb=" O PRO A 771 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 776' Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.521A pdb=" N SER A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.545A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.727A pdb=" N VAL A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1022 removed outlier: 3.769A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 removed outlier: 3.524A pdb=" N LYS A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.738A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.690A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.436A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.969A pdb=" N SER A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1138 through 1152 Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1171 through 1186 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 3.867A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1271 through 1274 Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 3.898A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 4.178A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1516 Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.506A pdb=" N ILE A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1593 Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.902A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1631 through 1639 removed outlier: 3.534A pdb=" N LYS A1635 " --> pdb=" O SER A1631 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A1636 " --> pdb=" O PRO A1632 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 3.581A pdb=" N PHE A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.503A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.205A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.032A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.825A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.843A pdb=" N ASN B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 205 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.153A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.540A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.668A pdb=" N GLY B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 4.022A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.768A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.595A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.772A pdb=" N ALA B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.856A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.736A pdb=" N MET B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.681A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.880A pdb=" N HIS B 749 " --> pdb=" O GLY B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.619A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1022 through 1026 removed outlier: 4.197A pdb=" N SER B1026 " --> pdb=" O HIS B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.682A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.669A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.731A pdb=" N LYS C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.534A pdb=" N ASN C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.935A pdb=" N ILE D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.525A pdb=" N ARG E 10 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.660A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'F' and resid 76 through 93 removed outlier: 4.033A pdb=" N ALA F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.763A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 24 through 37 removed outlier: 4.379A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.307A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.516A pdb=" N GLN I 38 " --> pdb=" O PRO I 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I 39 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 40 " --> pdb=" O GLU I 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 40' Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'J' and resid 21 through 26 removed outlier: 3.666A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 removed outlier: 3.871A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.565A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS K 56 " --> pdb=" O TYR K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.765A pdb=" N VAL K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1654 through 1655 removed outlier: 3.941A pdb=" N ASP A1655 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 14 " --> pdb=" O ASP A1655 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 87 removed outlier: 11.160A pdb=" N LEU A 82 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ALA A 366 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N ILE A 84 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ASN A 364 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 86 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 482 through 483 removed outlier: 3.595A pdb=" N PHE B1056 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 494 removed outlier: 3.764A pdb=" N ILE A 630 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE A 503 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 518 removed outlier: 6.668A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.158A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.905A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1044 through 1045 Processing sheet with id=AA9, first strand: chain 'A' and resid 1524 through 1529 removed outlier: 4.886A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1479 through 1482 removed outlier: 6.516A pdb=" N ALA A1298 " --> pdb=" O VAL A1281 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1281 " --> pdb=" O ALA A1298 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A1300 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A1279 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP A1302 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB3, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.733A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.607A pdb=" N VAL B 175 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.580A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 226 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 242 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 571 removed outlier: 5.553A pdb=" N ILE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 563 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.029A pdb=" N GLN B 885 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC4, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 932 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 removed outlier: 3.615A pdb=" N VAL B 845 " --> pdb=" O GLU B 858 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC8, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.742A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 300 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 241 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 237 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASP C 306 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 235 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N TYR C 308 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N SER C 233 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N PHE C 310 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR C 231 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N VAL C 312 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 229 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 175 through 176 removed outlier: 6.894A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.664A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.714A pdb=" N GLN C 274 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.905A pdb=" N TYR E 73 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 149 removed outlier: 4.231A pdb=" N LYS E 147 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 17 removed outlier: 3.954A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 17 Processing sheet with id=AD9, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.781A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 109 through 114 removed outlier: 6.179A pdb=" N LEU G 104 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE G 93 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 123 through 124 Processing sheet with id=AE3, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.021A pdb=" N LEU H 101 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU H 100 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL H 80 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.682A pdb=" N THR I 25 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR I 34 " --> pdb=" O THR I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.595A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.666A pdb=" N GLN K 80 " --> pdb=" O GLU K 61 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.19 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9716 1.34 - 1.46: 5308 1.46 - 1.58: 15026 1.58 - 1.70: 0 1.70 - 1.81: 266 Bond restraints: 30316 Sorted by residual: bond pdb=" CA ASN B 147 " pdb=" C ASN B 147 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.37e-02 5.33e+03 1.40e+01 bond pdb=" CA ASN B 680 " pdb=" C ASN B 680 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.69e+00 bond pdb=" C GLN A 735 " pdb=" N ARG A 736 " ideal model delta sigma weight residual 1.325 1.289 0.036 1.25e-02 6.40e+03 8.22e+00 bond pdb=" C GLN E 169 " pdb=" N LEU E 170 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.45e-02 4.76e+03 7.09e+00 bond pdb=" N SER A1067 " pdb=" CA SER A1067 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 ... (remaining 30311 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.76: 568 104.76 - 112.10: 15016 112.10 - 119.43: 10040 119.43 - 126.77: 14974 126.77 - 134.10: 362 Bond angle restraints: 40960 Sorted by residual: angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 110.80 126.20 -15.40 2.13e+00 2.20e-01 5.23e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 132.26 -10.56 1.80e+00 3.09e-01 3.44e+01 angle pdb=" N ASP A1066 " pdb=" CA ASP A1066 " pdb=" C ASP A1066 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.85e+01 angle pdb=" C ASP H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta sigma weight residual 121.70 130.90 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" N SER G 99 " pdb=" CA SER G 99 " pdb=" C SER G 99 " ideal model delta sigma weight residual 114.62 108.94 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 40955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.39: 17425 26.39 - 52.79: 944 52.79 - 79.18: 61 79.18 - 105.57: 13 105.57 - 131.96: 1 Dihedral angle restraints: 18444 sinusoidal: 7554 harmonic: 10890 Sorted by residual: dihedral pdb=" CA HIS E 23 " pdb=" C HIS E 23 " pdb=" N ASP E 24 " pdb=" CA ASP E 24 " ideal model delta harmonic sigma weight residual -180.00 -48.04 -131.96 0 5.00e+00 4.00e-02 6.97e+02 dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 -122.13 -57.87 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLU A1065 " pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta harmonic sigma weight residual -180.00 -138.67 -41.33 0 5.00e+00 4.00e-02 6.83e+01 ... (remaining 18441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3620 0.059 - 0.117: 861 0.117 - 0.176: 86 0.176 - 0.234: 6 0.234 - 0.292: 4 Chirality restraints: 4577 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE I 8 " pdb=" CA ILE I 8 " pdb=" CG1 ILE I 8 " pdb=" CG2 ILE I 8 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB VAL E 137 " pdb=" CA VAL E 137 " pdb=" CG1 VAL E 137 " pdb=" CG2 VAL E 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4574 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO A 85 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 786 " 0.025 2.00e-02 2.50e+03 2.17e-02 8.25e+00 pdb=" CG PHE A 786 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 786 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 786 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 786 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 786 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 786 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 895 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 896 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 896 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 896 " 0.037 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 23683 3.12 - 3.71: 44440 3.71 - 4.31: 61939 4.31 - 4.90: 104375 Nonbonded interactions: 234670 Sorted by model distance: nonbonded pdb=" OG SER B1097 " pdb=" OG SER B1117 " model vdw 1.929 2.440 nonbonded pdb=" OH TYR A 19 " pdb="ZN ZN B1301 " model vdw 1.993 2.230 nonbonded pdb=" OG SER B1117 " pdb="ZN ZN B1301 " model vdw 2.032 2.230 nonbonded pdb=" SG CYS A 103 " pdb=" CB CYS A 106 " model vdw 2.039 3.800 nonbonded pdb=" CB CYS A 106 " pdb="ZN ZN A1702 " model vdw 2.074 2.630 ... (remaining 234665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 5.380 Check model and map are aligned: 0.470 Set scattering table: 0.250 Process input model: 79.490 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 30316 Z= 0.492 Angle : 0.878 15.399 40960 Z= 0.502 Chirality : 0.049 0.292 4577 Planarity : 0.005 0.085 5268 Dihedral : 15.048 131.965 11415 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.20 % Favored : 88.53 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.12), residues: 3688 helix: -2.06 (0.12), residues: 1205 sheet: -2.88 (0.19), residues: 536 loop : -3.14 (0.12), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 636 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 643 average time/residue: 0.4666 time to fit residues: 454.2888 Evaluate side-chains 437 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2080 time to fit residues: 4.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.9990 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS A 60 ASN A 67 HIS A 79 HIS A 94 GLN A 108 HIS A 232 GLN A 257 GLN A 501 ASN A 533 ASN A 543 HIS A 599 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 655 GLN A 735 GLN A 952 ASN A 963 GLN A1075 HIS A1476 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 32 HIS ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 300 GLN B 374 HIS B 386 GLN B 530 HIS ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 887 HIS B1038 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 HIS B1145 ASN C 182 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS C 300 GLN C 307 HIS D 51 ASN E 19 HIS E 20 GLN E 65 ASN E 98 ASN E 99 HIS ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN G 167 GLN H 37 ASN H 118 HIS I 41 ASN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 30316 Z= 0.244 Angle : 0.695 11.454 40960 Z= 0.360 Chirality : 0.045 0.270 4577 Planarity : 0.005 0.085 5268 Dihedral : 6.181 62.011 4071 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.35 % Favored : 90.59 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3688 helix: -0.76 (0.14), residues: 1238 sheet: -2.53 (0.20), residues: 553 loop : -2.67 (0.13), residues: 1897 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 502 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 68 residues processed: 579 average time/residue: 0.3826 time to fit residues: 351.9208 Evaluate side-chains 491 residues out of total 3301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 423 time to evaluate : 2.574 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.2186 time to fit residues: 32.9297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2346 > 50: distance: 19 - 78: 28.664 distance: 22 - 75: 11.301 distance: 45 - 51: 35.117 distance: 52 - 55: 31.047 distance: 53 - 54: 39.904 distance: 55 - 56: 30.527 distance: 56 - 57: 34.097 distance: 56 - 58: 47.832 distance: 57 - 59: 3.316 distance: 58 - 60: 33.980 distance: 59 - 60: 3.203 distance: 61 - 62: 12.609 distance: 62 - 63: 27.215 distance: 62 - 65: 37.890 distance: 63 - 64: 21.165 distance: 63 - 68: 39.349 distance: 65 - 66: 11.243 distance: 65 - 67: 37.738 distance: 68 - 69: 16.209 distance: 69 - 70: 17.439 distance: 69 - 72: 11.649 distance: 70 - 71: 20.444 distance: 70 - 75: 12.983 distance: 72 - 73: 22.005 distance: 72 - 74: 22.785 distance: 75 - 76: 12.258 distance: 76 - 77: 28.795 distance: 76 - 79: 12.804 distance: 77 - 78: 10.123 distance: 77 - 86: 43.505 distance: 79 - 80: 20.620 distance: 80 - 81: 39.283 distance: 81 - 82: 18.134 distance: 82 - 83: 7.706 distance: 83 - 84: 8.164 distance: 83 - 85: 13.879 distance: 86 - 87: 20.123 distance: 87 - 88: 16.620 distance: 87 - 90: 18.751 distance: 88 - 89: 43.189 distance: 88 - 94: 12.677 distance: 90 - 91: 33.766 distance: 91 - 92: 14.011 distance: 91 - 93: 26.709 distance: 94 - 95: 21.985 distance: 95 - 96: 27.488 distance: 95 - 98: 10.976 distance: 96 - 97: 9.575 distance: 96 - 100: 5.418 distance: 98 - 99: 18.874 distance: 100 - 101: 23.598 distance: 101 - 102: 33.404 distance: 101 - 104: 21.951 distance: 102 - 103: 10.691 distance: 102 - 108: 19.482 distance: 104 - 105: 39.460 distance: 105 - 106: 39.459 distance: 105 - 107: 16.124 distance: 108 - 109: 11.192 distance: 109 - 110: 16.745 distance: 110 - 111: 30.332 distance: 110 - 112: 13.069 distance: 112 - 113: 31.564 distance: 113 - 114: 31.523 distance: 113 - 116: 9.894 distance: 114 - 115: 26.768 distance: 114 - 118: 13.425 distance: 116 - 117: 39.204 distance: 118 - 119: 8.733 distance: 119 - 120: 23.332 distance: 119 - 122: 21.472 distance: 120 - 121: 17.806 distance: 120 - 126: 10.822 distance: 122 - 123: 8.884 distance: 122 - 124: 12.563 distance: 123 - 125: 14.368