Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:42:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aoe_11842/12_2022/7aoe_11842.pdb" } resolution = 3.9 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= 0.015 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 569 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 10": "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 GLU 135": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 688": "OD1" <-> "OD2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A ASP 927": "OD1" <-> "OD2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A ASP 1253": "OD1" <-> "OD2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A ARG 1280": "NH1" <-> "NH2" Residue "A ASP 1302": "OD1" <-> "OD2" Residue "A TYR 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1321": "OE1" <-> "OE2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1493": "OE1" <-> "OE2" Residue "A GLU 1510": "OE1" <-> "OE2" Residue "A GLU 1554": "OE1" <-> "OE2" Residue "A PHE 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1579": "OE1" <-> "OE2" Residue "A PHE 1593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1601": "OD1" <-> "OD2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A PHE 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 80": "OD1" <-> "OD2" 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 GLU 158": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" 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 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 581": "OD1" <-> "OD2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B ASP 900": "OD1" <-> "OD2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1006": "OE1" <-> "OE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 114": "OE1" <-> "OE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 130": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" 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 67": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 28": "OD1" <-> "OD2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "K ASP 31": "OD1" <-> "OD2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K ASP 96": "OD1" <-> "OD2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 30828 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1401, 11102 Classifications: {'peptide': 1401} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1334} Chain breaks: 11 Chain: "B" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9254 Classifications: {'peptide': 1174} Link IDs: {'PTRANS': 60, 'TRANS': 1113} 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': 5, 'PTRANS': 7, 'TRANS': 194} 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: "U" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} 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 63 105.178 56.173 89.829 1.00 73.94 S ATOM 501 SG CYS A 66 104.500 54.333 89.518 1.00 69.95 S ATOM 565 SG CYS A 73 102.390 56.260 89.059 1.00 69.42 S ATOM 809 SG CYS A 103 74.652 45.015 131.808 1.00 93.16 S ATOM 835 SG CYS A 106 75.286 41.093 132.530 1.00 94.91 S ATOM 1540 SG CYS A 228 72.874 44.805 132.585 1.00102.92 S ATOM 1562 SG CYS A 231 75.022 43.102 136.179 1.00105.69 S ATOM 19731 SG CYS B1089 95.549 39.542 95.331 1.00 47.27 S ATOM 19756 SG CYS B1092 94.762 41.006 97.061 1.00 52.44 S ATOM 19912 SG CYS B1115 97.730 42.128 96.500 1.00 57.89 S ATOM 19935 SG CYS B1118 96.363 38.955 98.731 1.00 67.35 S ATOM 27820 SG CYS I 10 36.598 102.678 138.458 1.00 85.76 S ATOM 27841 SG CYS I 13 40.186 102.456 138.365 1.00 84.93 S ATOM 27946 SG CYS I 27 38.860 101.194 140.972 1.00104.55 S ATOM 27969 SG CYS I 30 39.264 102.522 140.348 1.00 95.27 S ATOM 28268 SG CYS J 7 63.115 93.491 42.813 1.00 17.17 S ATOM 28563 SG CYS J 44 59.353 91.760 42.704 1.00 20.42 S ATOM 28569 SG CYS J 45 61.478 94.155 41.227 1.00 18.78 S ATOM 29556 SG CYS L 24 90.933 112.237 71.571 1.00 36.02 S ATOM 29575 SG CYS L 27 91.349 114.118 71.395 1.00 36.10 S ATOM 29682 SG CYS L 41 93.551 113.693 72.623 1.00 50.40 S ATOM 29708 SG CYS L 44 91.838 114.994 72.540 1.00 52.02 S Time building chain proxies: 17.46, per 1000 atoms: 0.57 Number of scatterers: 30828 At special positions: 0 Unit cell: (161.652, 137.192, 156.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 165 16.00 P 44 15.00 O 5862 8.00 N 5347 7.00 C 19404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 13.71 Conformation dependent library (CDL) restraints added in 4.7 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 106 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1118 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1089 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1115 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " Number of angles added : 27 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7062 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 37.6% alpha, 13.1% beta 11 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.789A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.694A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.885A pdb=" N LEU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.630A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.721A pdb=" N LEU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) 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 470 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: 3.593A 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 633 through 641 removed outlier: 3.923A pdb=" N CYS A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.570A pdb=" N ARG A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 686 through 698 removed outlier: 3.683A pdb=" N CYS A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.837A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.906A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 removed outlier: 3.615A pdb=" N GLU A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 936 through 944 removed outlier: 4.047A pdb=" N MET A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.748A 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 1026 removed outlier: 3.637A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.039A pdb=" N TYR A1031 " --> pdb=" O ARG A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1077 removed outlier: 4.068A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1072 through 1077' Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.709A pdb=" N SER A1082 " --> pdb=" O GLN A1078 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.768A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.188A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.865A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.582A pdb=" N LYS A1127 " --> pdb=" O PRO A1123 " (cutoff:3.500A) 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: 3.757A 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 1275 removed outlier: 3.785A pdb=" N VAL A1275 " --> pdb=" O VAL A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1275' Processing helix chain 'A' and resid 1305 through 1313 Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 3.533A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1515 Processing helix chain 'A' and resid 1548 through 1555 removed outlier: 3.622A pdb=" N GLU A1554 " --> pdb=" O LYS A1550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.741A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1595 removed outlier: 3.587A pdb=" N VAL A1595 " --> pdb=" O SER A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.826A 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 1633 through 1639 removed outlier: 4.442A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.682A 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 14 removed outlier: 3.556A pdb=" N ASN B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.237A 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: 3.851A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.577A 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: 3.858A pdb=" N ASN B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.796A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.750A pdb=" N GLU B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.689A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.849A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.531A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.687A 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 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.563A 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: 3.618A 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 795 through 800 removed outlier: 4.174A pdb=" N LYS B 799 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 795 through 800' 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: 3.896A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1059 through 1068 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 3.581A pdb=" N ASN B1156 " --> pdb=" O PRO B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.522A pdb=" N ALA C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.707A pdb=" N VAL C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.724A pdb=" N PHE C 119 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.605A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.613A pdb=" N VAL C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 4.053A 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 344 Processing helix chain 'D' and resid 18 through 33 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.692A pdb=" N VAL E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.739A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.520A pdb=" N LYS E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 122' Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.594A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.742A 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: 3.874A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 37 " --> pdb=" O MET G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.086A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.902A pdb=" N THR J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.658A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 50 removed outlier: 4.522A pdb=" N ILE J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.616A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.731A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 4.471A 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 81 removed outlier: 3.927A pdb=" N ILE A 365 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.623A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.986A pdb=" N SER A 493 " --> pdb=" O MET A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 6.852A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 736 removed outlier: 6.201A pdb=" N ILE H 75 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.609A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.753A pdb=" N GLY A 961 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1050 through 1052 removed outlier: 7.111A pdb=" N VAL A1051 " --> pdb=" O VAL A1059 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1524 through 1530 removed outlier: 4.751A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A1530 " --> pdb=" O LYS A1541 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS A1541 " --> pdb=" O LYS A1530 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1477 through 1482 removed outlier: 5.371A pdb=" N GLN A1278 " --> pdb=" O ASP A1302 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB5, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.548A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 180 through 182 Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.632A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 184 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.577A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 572 removed outlier: 4.022A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 561 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU B 625 " --> pdb=" O TRP B 558 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 628 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 646 through 649 Processing sheet with id=AC3, first strand: chain 'B' and resid 725 through 729 removed outlier: 3.917A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET L 49 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC5, first strand: chain 'B' and resid 932 through 934 removed outlier: 8.297A pdb=" N ILE B 932 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 757 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 934 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 759 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 754 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 Processing sheet with id=AC7, first strand: chain 'B' and resid 843 through 845 removed outlier: 7.307A pdb=" N GLU B 858 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC9, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AD1, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD2, first strand: chain 'B' and resid 1119 through 1121 removed outlier: 3.592A pdb=" N TRP B1132 " --> pdb=" O PHE B1140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 53 removed outlier: 6.722A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N ARG C 303 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N HIS C 241 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N ARG C 305 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N THR C 239 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS C 307 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 237 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.441A pdb=" N VAL C 140 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 112 through 113 removed outlier: 4.059A pdb=" N ARG C 192 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.738A pdb=" N GLU C 148 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.798A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AD9, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP G 77 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN G 53 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.541A pdb=" N LYS D 13 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 8 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.789A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AE4, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.894A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 109 through 114 removed outlier: 7.124A pdb=" N HIS G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 96 " --> pdb=" O HIS G 100 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY G 102 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 169 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.612A pdb=" N SER H 15 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE H 42 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 95 " --> pdb=" O MET H 102 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE8, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.518A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 34 through 35 1108 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 14.87 Time building geometry restraints manager: 14.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9098 1.33 - 1.46: 6431 1.46 - 1.58: 15657 1.58 - 1.70: 87 1.70 - 1.83: 266 Bond restraints: 31539 Sorted by residual: bond pdb=" CA ARG B1032 " pdb=" CB ARG B1032 " ideal model delta sigma weight residual 1.527 1.467 0.060 2.48e-02 1.63e+03 5.92e+00 bond pdb=" C ASP A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.336 1.313 0.023 9.80e-03 1.04e+04 5.44e+00 bond pdb=" CA ASP A 700 " pdb=" C ASP A 700 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.80e-02 3.09e+03 5.19e+00 bond pdb=" CB TRP A 695 " pdb=" CG TRP A 695 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 5.00e+00 bond pdb=" C LEU A 624 " pdb=" N PRO A 625 " ideal model delta sigma weight residual 1.333 1.308 0.025 1.20e-02 6.94e+03 4.30e+00 ... (remaining 31534 not shown) Histogram of bond angle deviations from ideal: 96.06 - 103.68: 588 103.68 - 111.29: 13349 111.29 - 118.90: 12084 118.90 - 126.52: 16273 126.52 - 134.13: 522 Bond angle restraints: 42816 Sorted by residual: angle pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta sigma weight residual 121.54 133.95 -12.41 1.91e+00 2.74e-01 4.22e+01 angle pdb=" C GLN K 112 " pdb=" N LEU K 113 " pdb=" CA LEU K 113 " ideal model delta sigma weight residual 123.15 108.87 14.28 2.23e+00 2.01e-01 4.10e+01 angle pdb=" C SER A1067 " pdb=" N LEU A1068 " pdb=" CA LEU A1068 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N ALA I 56 " pdb=" CA ALA I 56 " pdb=" C ALA I 56 " ideal model delta sigma weight residual 114.56 108.20 6.36 1.27e+00 6.20e-01 2.51e+01 angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 111.00 124.78 -13.78 2.80e+00 1.28e-01 2.42e+01 ... (remaining 42811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 16668 18.02 - 36.04: 1849 36.04 - 54.06: 383 54.06 - 72.08: 78 72.08 - 90.10: 31 Dihedral angle restraints: 19009 sinusoidal: 8057 harmonic: 10952 Sorted by residual: 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 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA LYS B 274 " pdb=" C LYS B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta harmonic sigma weight residual 180.00 133.59 46.41 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CA PRO B 498 " pdb=" C PRO B 498 " pdb=" N GLU B 499 " pdb=" CA GLU B 499 " ideal model delta harmonic sigma weight residual 180.00 137.28 42.72 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 19006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3759 0.058 - 0.115: 910 0.115 - 0.173: 115 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4788 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 2.08e+00 chirality pdb=" CA PHE B 939 " pdb=" N PHE B 939 " pdb=" C PHE B 939 " pdb=" CB PHE B 939 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU B 422 " pdb=" CB LEU B 422 " pdb=" CD1 LEU B 422 " pdb=" CD2 LEU B 422 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4785 not shown) Planarity restraints: 5346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 85 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 73 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 675 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 676 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.033 5.00e-02 4.00e+02 ... (remaining 5343 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 292 2.51 - 3.11: 24661 3.11 - 3.70: 47054 3.70 - 4.30: 65632 4.30 - 4.90: 106496 Nonbonded interactions: 244135 Sorted by model distance: nonbonded pdb=" CB CYS J 10 " pdb="ZN ZN J 101 " model vdw 1.910 2.630 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 629 " model vdw 1.974 2.440 nonbonded pdb=" O LEU A1036 " pdb=" OG SER A1199 " model vdw 1.999 2.440 nonbonded pdb=" OE2 GLU A 893 " pdb=" OG SER B 617 " model vdw 2.064 2.440 nonbonded pdb=" O ALA E 61 " pdb=" OG1 THR E 71 " model vdw 2.065 2.440 ... (remaining 244130 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 S 165 5.16 5 C 19404 2.51 5 N 5347 2.21 5 O 5862 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 6.820 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.280 Process input model: 94.670 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 0.097 31539 Z= 0.492 Angle : 0.921 14.277 42816 Z= 0.522 Chirality : 0.048 0.289 4788 Planarity : 0.006 0.075 5346 Dihedral : 15.838 90.097 11947 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.38 % Favored : 88.30 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.39 % 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: -4.07 (0.11), residues: 3718 helix: -2.20 (0.12), residues: 1208 sheet: -2.67 (0.19), residues: 526 loop : -3.09 (0.12), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 669 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 683 average time/residue: 0.4790 time to fit residues: 511.9878 Evaluate side-chains 487 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 479 time to evaluate : 3.545 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3128 time to fit residues: 9.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 5.9990 chunk 283 optimal weight: 0.0270 chunk 157 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 113 optimal weight: 0.0980 chunk 178 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 255 ASN A 257 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 497 ASN A 543 HIS A 545 GLN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 655 GLN A 735 GLN A 860 GLN A 891 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1075 HIS ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1317 GLN A1345 GLN A1486 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 83 GLN B 98 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 203 ASN B 300 GLN B 305 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 HIS B 562 GLN B 619 ASN B 680 ASN ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 GLN B 752 ASN ** B 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1005 GLN ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS B1039 ASN ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN C 223 HIS C 292 HIS C 300 GLN D 27 ASN E 124 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN G 167 GLN H 45 GLN H 58 GLN H 118 HIS I 15 ASN J 63 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 31539 Z= 0.210 Angle : 0.726 17.821 42816 Z= 0.374 Chirality : 0.044 0.232 4788 Planarity : 0.005 0.081 5346 Dihedral : 11.288 88.774 4563 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.04 % Favored : 90.86 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.36 % 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: -2.67 (0.13), residues: 3718 helix: -0.64 (0.14), residues: 1219 sheet: -2.11 (0.20), residues: 533 loop : -2.46 (0.13), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 599 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 57 residues processed: 664 average time/residue: 0.4156 time to fit residues: 440.7683 Evaluate side-chains 546 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 489 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.2669 time to fit residues: 33.4491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 367 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 272 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 107 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN ** A1519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 374 HIS B 386 GLN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 HIS B 619 ASN B 621 GLN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 752 ASN ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS E 65 ASN E 138 ASN G 100 HIS ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.110 31539 Z= 0.542 Angle : 0.886 17.550 42816 Z= 0.453 Chirality : 0.050 0.241 4788 Planarity : 0.006 0.083 5346 Dihedral : 11.540 84.650 4563 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.38 % Favored : 88.46 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.71 (0.13), residues: 3718 helix: -0.70 (0.14), residues: 1219 sheet: -2.16 (0.21), residues: 516 loop : -2.46 (0.13), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 485 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 87 residues processed: 593 average time/residue: 0.4168 time to fit residues: 400.6500 Evaluate side-chains 537 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 450 time to evaluate : 3.700 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.2878 time to fit residues: 51.3673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 361 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 606 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1223 ASN A1519 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 687 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS E 65 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 31539 Z= 0.197 Angle : 0.704 17.991 42816 Z= 0.354 Chirality : 0.044 0.329 4788 Planarity : 0.005 0.084 5346 Dihedral : 11.138 85.497 4563 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.36 % Favored : 91.55 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.36 % 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: -2.16 (0.13), residues: 3718 helix: -0.07 (0.15), residues: 1228 sheet: -1.99 (0.21), residues: 535 loop : -2.21 (0.13), residues: 1955 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 568 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 46 residues processed: 628 average time/residue: 0.4218 time to fit residues: 430.9844 Evaluate side-chains 547 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 501 time to evaluate : 3.669 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2864 time to fit residues: 29.5909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 269 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 249 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1499 ASN A1548 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 31539 Z= 0.291 Angle : 0.733 17.660 42816 Z= 0.369 Chirality : 0.045 0.225 4788 Planarity : 0.005 0.084 5346 Dihedral : 11.101 84.550 4563 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.92 % Favored : 89.97 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.31 % 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: -2.07 (0.13), residues: 3718 helix: 0.01 (0.15), residues: 1236 sheet: -2.00 (0.21), residues: 529 loop : -2.15 (0.13), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 513 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 57 residues processed: 570 average time/residue: 0.4024 time to fit residues: 374.9420 Evaluate side-chains 536 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 479 time to evaluate : 3.611 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.2733 time to fit residues: 34.3148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 189 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 150 HIS B 192 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 45 ASN L 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 31539 Z= 0.180 Angle : 0.697 17.831 42816 Z= 0.346 Chirality : 0.043 0.218 4788 Planarity : 0.005 0.085 5346 Dihedral : 10.931 85.878 4563 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.20 % Favored : 91.69 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % 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: -1.73 (0.13), residues: 3718 helix: 0.34 (0.15), residues: 1226 sheet: -1.69 (0.21), residues: 564 loop : -2.02 (0.14), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 565 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 29 residues processed: 612 average time/residue: 0.4182 time to fit residues: 416.1488 Evaluate side-chains 521 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 492 time to evaluate : 3.756 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2923 time to fit residues: 21.0886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS J 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 31539 Z= 0.371 Angle : 0.771 17.464 42816 Z= 0.390 Chirality : 0.046 0.257 4788 Planarity : 0.005 0.084 5346 Dihedral : 11.085 84.604 4563 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.22 % Favored : 89.67 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.22 % 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: -1.94 (0.13), residues: 3718 helix: 0.08 (0.15), residues: 1246 sheet: -1.88 (0.21), residues: 541 loop : -2.07 (0.14), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 487 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 60 residues processed: 533 average time/residue: 0.4222 time to fit residues: 369.0956 Evaluate side-chains 519 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 459 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3061 time to fit residues: 39.7473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS A1317 GLN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 32 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31539 Z= 0.191 Angle : 0.711 17.690 42816 Z= 0.354 Chirality : 0.043 0.231 4788 Planarity : 0.005 0.085 5346 Dihedral : 10.928 85.884 4563 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.26 % Favored : 91.66 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.29 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.66 (0.14), residues: 3718 helix: 0.39 (0.15), residues: 1217 sheet: -1.69 (0.21), residues: 549 loop : -1.94 (0.14), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 545 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 561 average time/residue: 0.4411 time to fit residues: 402.6463 Evaluate side-chains 519 residues out of total 3316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 496 time to evaluate : 3.555 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2928 time to fit residues: 17.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/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-dev-4807/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-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/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-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/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-dev-4807/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-dev-4807/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-dev-4807/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: 72.8412 > 50: distance: 19 - 133: 35.778 distance: 22 - 130: 34.862 distance: 34 - 120: 34.491 distance: 37 - 117: 33.626 distance: 63 - 142: 32.751 distance: 66 - 139: 35.694 distance: 76 - 125: 37.836 distance: 79 - 122: 33.625 distance: 94 - 109: 35.263 distance: 104 - 109: 35.899 distance: 110 - 111: 39.212 distance: 110 - 113: 39.547 distance: 111 - 112: 31.056 distance: 111 - 117: 57.405 distance: 113 - 114: 40.284 distance: 114 - 115: 39.305 distance: 115 - 116: 40.309 distance: 117 - 118: 39.747 distance: 118 - 119: 40.037 distance: 119 - 122: 40.077 distance: 122 - 123: 39.198 distance: 123 - 124: 40.794 distance: 123 - 126: 39.500 distance: 124 - 130: 41.106 distance: 126 - 127: 56.007 distance: 126 - 128: 38.879 distance: 127 - 129: 40.925 distance: 130 - 131: 40.473 distance: 131 - 132: 40.958 distance: 132 - 133: 39.036 distance: 136 - 137: 27.684 distance: 136 - 138: 62.177 distance: 140 - 141: 55.396 distance: 141 - 142: 40.524 distance: 141 - 143: 40.710 distance: 144 - 145: 56.679 distance: 145 - 149: 39.545 distance: 151 - 159: 40.471 distance: 153 - 154: 34.318 distance: 154 - 155: 13.078 distance: 154 - 156: 41.088 distance: 155 - 157: 26.706 distance: 161 - 170: 39.728 distance: 164 - 165: 39.793 distance: 165 - 166: 18.406 distance: 166 - 167: 24.030 distance: 167 - 168: 25.556 distance: 167 - 169: 25.491 distance: 170 - 171: 10.029 distance: 171 - 172: 32.103 distance: 171 - 174: 29.682 distance: 172 - 179: 56.348 distance: 177 - 178: 57.486 distance: 181 - 187: 34.139 distance: 184 - 185: 20.173 distance: 184 - 186: 39.899