Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 02:09:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml1_23905/04_2023/7ml1_23905_updated.pdb" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 19 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 40326 2.51 5 N 11344 2.21 5 O 12371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 286": "NH1" <-> "NH2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 273": "NH1" <-> "NH2" Residue "0 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 251": "OD1" <-> "OD2" Residue "0 GLU 370": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 378": "NH1" <-> "NH2" Residue "2 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 503": "OD1" <-> "OD2" Residue "5 GLU 53": "OE1" <-> "OE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "7 ASP 311": "OD1" <-> "OD2" Residue "7 PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 37": "NH1" <-> "NH2" Residue "O PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1167": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 343": "NH1" <-> "NH2" Residue "Q TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 398": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 251": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "U TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 276": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 64538 Number of models: 1 Model: "" Number of chains: 43 Chain: "1" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2411 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'UNK:plan-1': 106, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2041 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'UNK:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "6" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2527 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 2, 'UNK:plan-1': 13, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 140 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'CIS': 3, 'PTRANS': 26, 'TRANS': 604} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "N" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1178 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "T" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1159 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9132 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 51, 'TRANS': 1095} Chain breaks: 6 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "V" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 984 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" 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: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" 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 4247 SG CYS 4 289 203.914 22.560 97.653 1.00 0.00 S ATOM 4266 SG CYS 4 292 206.052 23.878 100.475 1.00 0.00 S ATOM 4351 SG CYS 4 305 206.346 20.223 99.044 1.00 0.00 S ATOM 4367 SG CYS 4 308 203.623 21.387 101.429 1.00 0.00 S ATOM 5390 SG CYS 0 115 139.705 24.410 122.969 1.00117.61 S ATOM 5717 SG CYS 0 156 136.566 20.494 124.186 1.00 90.79 S ATOM 5532 SG CYS 0 133 136.955 22.844 127.098 1.00 46.59 S ATOM 5717 SG CYS 0 156 136.566 20.494 124.186 1.00 90.79 S ATOM 12773 SG CYS 6 403 218.660 48.410 117.176 1.00 0.00 S ATOM 12795 SG CYS 6 406 219.511 51.724 115.721 1.00 0.00 S ATOM 12963 SG CYS 6 437 215.876 50.959 116.774 1.00 0.00 S ATOM 12979 SG CYS 6 440 217.128 49.445 113.712 1.00 0.00 S ATOM 12921 SG CYS 6 429 213.099 37.214 116.773 1.00 0.00 S ATOM 12937 SG CYS 6 432 216.763 37.702 117.597 1.00 0.00 S ATOM 13057 SG CYS 6 451 215.474 38.843 114.307 1.00 0.00 S ATOM 13072 SG CYS 6 454 215.563 35.112 114.869 1.00 0.00 S ATOM 12418 SG CYS 6 349 202.700 31.849 77.560 1.00 0.00 S ATOM 12439 SG CYS 6 352 201.597 32.634 74.246 1.00 0.00 S ATOM 12508 SG CYS 6 363 198.927 32.568 77.077 1.00 0.00 S ATOM 12526 SG CYS 6 366 200.197 29.396 76.039 1.00 0.00 S ATOM 12335 SG CYS 6 336 200.122 44.164 72.433 1.00 30.00 S ATOM 12346 SG CYS 6 338 199.583 42.077 75.577 1.00 30.00 S ATOM 12473 SG CYS 6 357 202.238 44.926 75.601 1.00 30.00 S ATOM 21074 SG CYS 3 13 101.915 61.143 124.785 1.00 0.00 S ATOM 21268 SG CYS 3 39 102.005 62.574 125.879 1.00 0.00 S ATOM 21221 SG CYS 3 34 95.428 53.443 131.002 1.00 0.00 S ATOM 21417 SG CYS 3 59 94.875 50.891 126.832 1.00 0.00 S ATOM 26469 SG CYS A 107 117.277 105.265 120.803 1.00 0.00 S ATOM 26493 SG CYS A 110 116.761 102.957 123.731 1.00 0.00 S ATOM 26798 SG CYS A 148 119.107 105.858 124.067 1.00 0.00 S ATOM 26867 SG CYS A 167 120.027 102.815 121.914 1.00 0.00 S ATOM 26164 SG CYS A 67 69.735 98.271 119.173 1.00 0.00 S ATOM 26186 SG CYS A 70 69.608 99.443 122.722 1.00 0.00 S ATOM 26239 SG CYS A 77 69.268 101.924 120.003 1.00 0.00 S ATOM 45303 SG CYS B1163 81.304 100.442 133.481 1.00 0.00 S ATOM 45321 SG CYS B1166 83.152 101.642 130.101 1.00 0.00 S ATOM 45446 SG CYS B1182 80.874 98.665 130.298 1.00 0.00 S ATOM 45465 SG CYS B1185 84.263 98.610 131.955 1.00 0.00 S ATOM 46432 SG CYS C 86 14.977 138.418 109.162 1.00 0.00 S ATOM 46449 SG CYS C 88 16.354 135.086 107.664 1.00 0.00 S ATOM 46482 SG CYS C 92 13.439 136.878 106.162 1.00 0.00 S ATOM 46505 SG CYS C 95 17.085 138.266 105.924 1.00 0.00 S ATOM 53995 SG CYS I 7 134.144 153.045 74.636 1.00 0.00 S ATOM 54020 SG CYS I 10 133.195 149.129 74.468 1.00 0.00 S ATOM 54186 SG CYS I 29 134.112 150.784 77.758 1.00 0.00 S ATOM 54210 SG CYS I 32 136.574 150.526 74.685 1.00 0.00 S ATOM 54537 SG CYS I 75 105.791 186.129 82.266 1.00 0.00 S ATOM 54559 SG CYS I 78 104.551 188.807 79.835 1.00 0.00 S ATOM 54775 SG CYS I 103 104.341 185.193 78.884 1.00 0.00 S ATOM 54795 SG CYS I 106 107.731 186.813 79.068 1.00 0.00 S ATOM 54940 SG CYS J 7 37.005 160.225 99.257 1.00 0.00 S ATOM 54963 SG CYS J 10 33.648 161.980 100.169 1.00 0.00 S ATOM 55243 SG CYS J 45 36.780 164.023 100.356 1.00 0.00 S ATOM 55249 SG CYS J 46 35.287 162.891 97.131 1.00 0.00 S ATOM 56372 SG CYS L 31 43.151 125.472 72.632 1.00 0.00 S ATOM 56392 SG CYS L 34 39.762 125.914 70.097 1.00 0.00 S ATOM 56496 SG CYS L 48 41.145 122.742 71.359 1.00 0.00 S ATOM 56519 SG CYS L 51 43.092 124.829 68.920 1.00 0.00 S ATOM 56747 SG CYS M 24 44.409 102.570 122.965 1.00 0.00 S ATOM 56769 SG CYS M 27 40.773 102.281 122.884 1.00 0.00 S ATOM 56913 SG CYS M 45 42.397 104.793 120.535 1.00 0.00 S ATOM 56932 SG CYS M 48 42.672 105.599 124.160 1.00 0.00 S ATOM 62958 SG CYS W 124 66.174 80.590 118.931 1.00 0.00 S ATOM 62979 SG CYS W 127 69.097 82.856 118.694 1.00 0.00 S ATOM 63164 SG CYS W 149 66.893 83.212 121.642 1.00 0.00 S ATOM 63184 SG CYS W 152 65.509 84.365 118.360 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" P DA N 52 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 52 " occ=0.00 residue: pdb=" P DA N 54 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 54 " occ=0.00 residue: pdb=" P DA N 56 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 56 " occ=0.00 residue: pdb=" P DA N 58 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 58 " occ=0.00 residue: pdb=" P DT T 108 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 108 " occ=0.00 residue: pdb=" P DT T 110 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 110 " occ=0.00 residue: pdb=" P DT T 112 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 112 " occ=0.00 residue: pdb=" P DT T 114 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 114 " occ=0.00 Time building chain proxies: 24.64, per 1000 atoms: 0.38 Number of scatterers: 64538 At special positions: 0 Unit cell: (259.7, 209.88, 188.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 19 29.99 Fe 4 26.01 S 359 16.00 P 114 15.00 Mg 1 11.99 O 12371 8.00 N 11344 7.00 C 40326 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: 23.34 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" NE2 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 84 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 62 sheets defined 39.2% alpha, 9.1% beta 38 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 18.39 Creating SS restraints... Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 189 through 198 Processing helix chain '1' and resid 206 through 224 removed outlier: 3.702A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Proline residue: 1 215 - end of helix Processing helix chain '1' and resid 232 through 235 No H-bonds generated for 'chain '1' and resid 232 through 235' Processing helix chain '1' and resid 252 through 262 Processing helix chain '1' and resid 264 through 272 Processing helix chain '1' and resid 280 through 294 removed outlier: 3.789A pdb=" N ALA 1 285 " --> pdb=" O PRO 1 281 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 328 removed outlier: 3.746A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 342 No H-bonds generated for 'chain '1' and resid 339 through 342' Processing helix chain '1' and resid 372 through 389 removed outlier: 4.024A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 468 through 482 Processing helix chain '1' and resid 497 through 515 removed outlier: 3.804A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA 1 514 " --> pdb=" O ASN 1 510 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 566 removed outlier: 3.621A pdb=" N THR 1 556 " --> pdb=" O MET 1 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 1 561 " --> pdb=" O CYS 1 557 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 603 Processing helix chain '1' and resid 607 through 638 removed outlier: 3.559A pdb=" N TYR 1 615 " --> pdb=" O THR 1 611 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 616 " --> pdb=" O CYS 1 612 " (cutoff:3.500A) Proline residue: 1 618 - end of helix Processing helix chain '4' and resid 34 through 42 Processing helix chain '4' and resid 50 through 67 removed outlier: 4.021A pdb=" N VAL 4 59 " --> pdb=" O GLU 4 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS 4 64 " --> pdb=" O PHE 4 60 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU 4 65 " --> pdb=" O LEU 4 61 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 134 Processing helix chain '4' and resid 149 through 168 removed outlier: 3.646A pdb=" N SER 4 154 " --> pdb=" O ALA 4 150 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU 4 157 " --> pdb=" O MET 4 153 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 4 158 " --> pdb=" O SER 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 193 through 206 removed outlier: 3.537A pdb=" N ASN 4 198 " --> pdb=" O ILE 4 194 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 245 through 251 Processing helix chain '4' and resid 314 through 322 Processing helix chain '0' and resid 19 through 33 Processing helix chain '0' and resid 48 through 62 removed outlier: 3.998A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 118 through 122 Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 139 through 146 removed outlier: 3.783A pdb=" N ARG 0 143 " --> pdb=" O GLY 0 139 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 164 Processing helix chain '0' and resid 166 through 168 No H-bonds generated for 'chain '0' and resid 166 through 168' Processing helix chain '0' and resid 178 through 187 Processing helix chain '0' and resid 192 through 201 removed outlier: 5.723A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 214 Processing helix chain '0' and resid 224 through 227 No H-bonds generated for 'chain '0' and resid 224 through 227' Processing helix chain '0' and resid 237 through 247 removed outlier: 3.923A pdb=" N ASP 0 241 " --> pdb=" O HIS 0 238 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN 0 242 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 278 Processing helix chain '0' and resid 280 through 291 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 328 through 346 removed outlier: 3.507A pdb=" N GLU 0 340 " --> pdb=" O LYS 0 336 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 4.147A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG 0 386 " --> pdb=" O SER 0 382 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 411 removed outlier: 4.450A pdb=" N ALA 0 398 " --> pdb=" O GLU 0 394 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU 0 399 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) Processing helix chain '0' and resid 425 through 427 No H-bonds generated for 'chain '0' and resid 425 through 427' Processing helix chain '0' and resid 442 through 452 Proline residue: 0 448 - end of helix removed outlier: 3.615A pdb=" N ARG 0 452 " --> pdb=" O VAL 0 449 " (cutoff:3.500A) Processing helix chain '0' and resid 468 through 473 Processing helix chain '0' and resid 516 through 532 removed outlier: 3.970A pdb=" N ASN 0 521 " --> pdb=" O SER 0 517 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU 0 528 " --> pdb=" O SER 0 524 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE 0 529 " --> pdb=" O MET 0 525 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA 0 530 " --> pdb=" O LEU 0 526 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 556 removed outlier: 4.264A pdb=" N MET 0 553 " --> pdb=" O SER 0 549 " (cutoff:3.500A) Processing helix chain '0' and resid 558 through 566 removed outlier: 3.697A pdb=" N ASP 0 561 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU 0 562 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 0 563 " --> pdb=" O LEU 0 560 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 606 through 609 No H-bonds generated for 'chain '0' and resid 606 through 609' Processing helix chain '0' and resid 634 through 645 Processing helix chain '0' and resid 650 through 669 removed outlier: 4.621A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 690 removed outlier: 3.533A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 removed outlier: 3.795A pdb=" N ARG 0 722 " --> pdb=" O LYS 0 718 " (cutoff:3.500A) Processing helix chain '0' and resid 734 through 738 Processing helix chain '0' and resid 744 through 753 removed outlier: 3.504A pdb=" N SER 0 750 " --> pdb=" O LYS 0 746 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '6' and resid 145 through 163 removed outlier: 3.716A pdb=" N ASP 6 155 " --> pdb=" O GLN 6 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE 6 156 " --> pdb=" O TYR 6 152 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU 6 159 " --> pdb=" O ASP 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 189 through 201 removed outlier: 3.512A pdb=" N LYS 6 197 " --> pdb=" O ILE 6 193 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER 6 198 " --> pdb=" O ASP 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 304 removed outlier: 3.815A pdb=" N LEU 6 300 " --> pdb=" O HIS 6 296 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE 6 301 " --> pdb=" O LEU 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 374 through 383 removed outlier: 3.891A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 419 through 422 No H-bonds generated for 'chain '6' and resid 419 through 422' Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 455 No H-bonds generated for 'chain '6' and resid 452 through 455' Processing helix chain '2' and resid 10 through 16 Processing helix chain '2' and resid 19 through 26 Processing helix chain '2' and resid 29 through 38 removed outlier: 3.690A pdb=" N TYR 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 52 removed outlier: 3.612A pdb=" N MET 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 71 through 84 Processing helix chain '2' and resid 102 through 113 removed outlier: 3.978A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR 2 113 " --> pdb=" O ARG 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 122 Processing helix chain '2' and resid 137 through 151 Processing helix chain '2' and resid 161 through 170 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 197 through 210 Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 244 through 255 Processing helix chain '2' and resid 263 through 265 No H-bonds generated for 'chain '2' and resid 263 through 265' Processing helix chain '2' and resid 273 through 280 removed outlier: 3.673A pdb=" N LEU 2 278 " --> pdb=" O LEU 2 274 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 363 removed outlier: 3.623A pdb=" N VAL 2 359 " --> pdb=" O LEU 2 355 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU 2 360 " --> pdb=" O GLN 2 356 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 388 Processing helix chain '2' and resid 395 through 402 Processing helix chain '2' and resid 405 through 407 No H-bonds generated for 'chain '2' and resid 405 through 407' Processing helix chain '2' and resid 409 through 416 Processing helix chain '2' and resid 435 through 447 removed outlier: 3.528A pdb=" N TRP 2 444 " --> pdb=" O GLN 2 440 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU 2 446 " --> pdb=" O ARG 2 442 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU 2 447 " --> pdb=" O LEU 2 443 " (cutoff:3.500A) Processing helix chain '2' and resid 465 through 478 Processing helix chain '2' and resid 496 through 502 Processing helix chain '5' and resid 14 through 26 removed outlier: 4.266A pdb=" N GLN 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 46 No H-bonds generated for 'chain '5' and resid 44 through 46' Processing helix chain '5' and resid 48 through 59 removed outlier: 3.760A pdb=" N GLU 5 53 " --> pdb=" O PHE 5 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 5 58 " --> pdb=" O LEU 5 54 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 127 No H-bonds generated for 'chain '7' and resid 125 through 127' Processing helix chain '7' and resid 150 through 160 removed outlier: 3.637A pdb=" N THR 7 159 " --> pdb=" O ASP 7 155 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 186 Processing helix chain '7' and resid 190 through 200 removed outlier: 3.923A pdb=" N LEU 7 197 " --> pdb=" O ILE 7 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP 7 198 " --> pdb=" O ILE 7 194 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU 7 200 " --> pdb=" O VAL 7 196 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 217 Processing helix chain '7' and resid 239 through 246 Processing helix chain '7' and resid 252 through 254 No H-bonds generated for 'chain '7' and resid 252 through 254' Processing helix chain '7' and resid 263 through 267 Processing helix chain '7' and resid 323 through 333 removed outlier: 3.594A pdb=" N ARG 7 329 " --> pdb=" O VAL 7 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS 7 330 " --> pdb=" O VAL 7 326 " (cutoff:3.500A) Processing helix chain '7' and resid 343 through 345 No H-bonds generated for 'chain '7' and resid 343 through 345' Processing helix chain '7' and resid 364 through 374 removed outlier: 3.786A pdb=" N SER 7 371 " --> pdb=" O GLU 7 367 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 425 removed outlier: 4.025A pdb=" N GLN 7 419 " --> pdb=" O VAL 7 415 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN 7 423 " --> pdb=" O GLN 7 419 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE 7 424 " --> pdb=" O TRP 7 420 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU 7 425 " --> pdb=" O ARG 7 421 " (cutoff:3.500A) Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 471 through 479 Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 495 through 501 removed outlier: 3.600A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) Processing helix chain '7' and resid 527 through 529 No H-bonds generated for 'chain '7' and resid 527 through 529' Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 575 through 581 removed outlier: 3.875A pdb=" N TYR 7 581 " --> pdb=" O MET 7 578 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 613 through 622 removed outlier: 4.088A pdb=" N LYS 7 621 " --> pdb=" O GLU 7 617 " (cutoff:3.500A) Processing helix chain '7' and resid 633 through 641 Processing helix chain '7' and resid 680 through 690 removed outlier: 4.466A pdb=" N GLY 7 688 " --> pdb=" O ALA 7 684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 728 removed outlier: 3.752A pdb=" N TYR 7 718 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 758 Processing helix chain '7' and resid 760 through 765 removed outlier: 3.808A pdb=" N LEU 7 764 " --> pdb=" O LEU 7 760 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 760 through 765' Processing helix chain '3' and resid 40 through 47 removed outlier: 4.493A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 76 through 91 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 128 through 144 Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.668A pdb=" N ILE O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 236 Proline residue: O 232 - end of helix Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 105 removed outlier: 4.155A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.713A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.805A pdb=" N ALA A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.604A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.589A pdb=" N LEU A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.595A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.186A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.128A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 660 Proline residue: A 639 - end of helix removed outlier: 3.754A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.806A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 914 through 919 removed outlier: 4.064A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.716A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 983 through 995 removed outlier: 3.862A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.817A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.550A pdb=" N LEU A1101 " --> pdb=" O GLY A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1138 removed outlier: 3.512A pdb=" N ILE A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 4.145A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1220 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1333 through 1338 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 3.772A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 3.580A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1414 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.800A pdb=" N ILE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 309 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.246A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 389 removed outlier: 3.602A pdb=" N ILE B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 386 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.899A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 605 removed outlier: 3.648A pdb=" N GLU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.586A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 4.226A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.922A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.623A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.668A pdb=" N TYR B 931 " --> pdb=" O ARG B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 removed outlier: 3.546A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.507A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 240 through 264 removed outlier: 4.144A pdb=" N GLN C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 54 through 74 removed outlier: 3.818A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.559A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.528A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 4 through 26 removed outlier: 4.370A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.286A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 30 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU G 32 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.616A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 removed outlier: 3.725A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 removed outlier: 3.734A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.885A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 10 No H-bonds generated for 'chain 'K' and resid 7 through 10' Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.350A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.690A pdb=" N ALA K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.754A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU M 110 " --> pdb=" O PHE M 106 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 120 No H-bonds generated for 'chain 'M' and resid 118 through 120' Processing helix chain 'M' and resid 123 through 139 removed outlier: 3.658A pdb=" N ALA M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 removed outlier: 3.716A pdb=" N ASP M 148 " --> pdb=" O LYS M 144 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 182 removed outlier: 4.108A pdb=" N SER M 175 " --> pdb=" O ILE M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'M' and resid 201 through 217 removed outlier: 3.727A pdb=" N ILE M 209 " --> pdb=" O LYS M 205 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS M 211 " --> pdb=" O LEU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 244 removed outlier: 4.079A pdb=" N ILE M 239 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 266 removed outlier: 3.784A pdb=" N THR M 253 " --> pdb=" O MET M 250 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR M 254 " --> pdb=" O GLN M 251 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR M 258 " --> pdb=" O SER M 255 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS M 264 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU M 265 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE M 266 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 286 removed outlier: 3.706A pdb=" N TYR M 283 " --> pdb=" O VAL M 280 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU M 284 " --> pdb=" O SER M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 306 through 318 Processing helix chain 'M' and resid 320 through 322 No H-bonds generated for 'chain 'M' and resid 320 through 322' Processing helix chain 'Q' and resid 28 through 34 removed outlier: 3.816A pdb=" N LEU Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 113 Processing helix chain 'Q' and resid 130 through 133 No H-bonds generated for 'chain 'Q' and resid 130 through 133' Processing helix chain 'Q' and resid 338 through 345 Processing helix chain 'Q' and resid 409 through 414 removed outlier: 4.539A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 81 removed outlier: 3.555A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 244 Processing helix chain 'R' and resid 259 through 264 Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 321 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.677A pdb=" N ASP R 334 " --> pdb=" O LYS R 330 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 Processing helix chain 'W' and resid 23 through 34 removed outlier: 3.589A pdb=" N LEU W 27 " --> pdb=" O SER W 24 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL W 28 " --> pdb=" O PHE W 25 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE W 32 " --> pdb=" O LEU W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 removed outlier: 3.630A pdb=" N LEU W 47 " --> pdb=" O LEU W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 53 No H-bonds generated for 'chain 'W' and resid 51 through 53' Processing helix chain 'W' and resid 55 through 63 Processing helix chain 'W' and resid 91 through 115 removed outlier: 3.596A pdb=" N ILE W 95 " --> pdb=" O TYR W 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP W 96 " --> pdb=" O PRO W 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS W 99 " --> pdb=" O ILE W 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP W 100 " --> pdb=" O ASP W 96 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 139 removed outlier: 3.511A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 187 removed outlier: 3.805A pdb=" N LYS W 166 " --> pdb=" O GLY W 162 " (cutoff:3.500A) Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 138 Processing helix chain 'X' and resid 144 through 151 removed outlier: 3.606A pdb=" N ASP X 149 " --> pdb=" O ASN X 145 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 165 Processing helix chain 'X' and resid 189 through 199 Processing helix chain 'X' and resid 208 through 213 Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 257 through 265 Processing helix chain 'X' and resid 273 through 280 Processing sheet with id= A, first strand: chain '4' and resid 234 through 238 removed outlier: 6.624A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 4 179 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 2 through 4 Processing sheet with id= C, first strand: chain '0' and resid 456 through 459 removed outlier: 6.092A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP 0 235 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER 0 209 " --> pdb=" O LEU 0 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '0' and resid 352 through 354 Processing sheet with id= E, first strand: chain '0' and resid 494 through 496 removed outlier: 6.774A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 0 620 " --> pdb=" O VAL 0 678 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET 0 622 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '0' and resid 568 through 570 Processing sheet with id= G, first strand: chain '6' and resid 229 through 231 removed outlier: 3.604A pdb=" N ILE 6 127 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN 6 168 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU 6 128 " --> pdb=" O GLN 6 168 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY 6 170 " --> pdb=" O LEU 6 128 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE 6 173 " --> pdb=" O LEU 6 181 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU 6 181 " --> pdb=" O ILE 6 173 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG 6 175 " --> pdb=" O ALA 6 179 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA 6 179 " --> pdb=" O ARG 6 175 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '7' and resid 133 through 135 Processing sheet with id= I, first strand: chain '7' and resid 408 through 411 removed outlier: 5.908A pdb=" N VAL 7 453 " --> pdb=" O VAL 7 409 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N CYS 7 411 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER 7 455 " --> pdb=" O CYS 7 411 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '7' and resid 486 through 488 removed outlier: 6.999A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '7' and resid 605 through 608 removed outlier: 6.392A pdb=" N CYS 7 669 " --> pdb=" O ILE 7 606 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE 7 608 " --> pdb=" O CYS 7 669 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE 7 671 " --> pdb=" O PHE 7 608 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE 7 704 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN 7 672 " --> pdb=" O PHE 7 704 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR 7 706 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'O' and resid 112 through 115 Processing sheet with id= M, first strand: chain 'O' and resid 183 through 186 removed outlier: 4.830A pdb=" N GLU O 186 " --> pdb=" O GLY O 192 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLY O 192 " --> pdb=" O GLU O 186 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= O, first strand: chain 'A' and resid 182 through 184 Processing sheet with id= P, first strand: chain 'A' and resid 249 through 252 Processing sheet with id= Q, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.786A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.134A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.590A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 587 through 590 removed outlier: 3.556A pdb=" N LEU A 588 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 606 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.856A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 851 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= W, first strand: chain 'A' and resid 1115 through 1118 Processing sheet with id= X, first strand: chain 'A' and resid 1225 through 1228 removed outlier: 3.564A pdb=" N ILE A1238 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id= Z, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= AA, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.735A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= AC, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= AD, first strand: chain 'B' and resid 215 through 218 Processing sheet with id= AE, first strand: chain 'B' and resid 255 through 258 removed outlier: 4.288A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= AG, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.180A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.723A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 1010 through 1012 removed outlier: 4.288A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= AK, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id= AL, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.680A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.544A pdb=" N GLU C 12 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 96 through 104 removed outlier: 3.560A pdb=" N THR C 156 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AP, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.516A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 176 through 178 Processing sheet with id= AR, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AS, first strand: chain 'G' and resid 2 through 12 removed outlier: 4.685A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 169 through 171 removed outlier: 4.113A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG G 142 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.916A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 146 through 153 removed outlier: 6.498A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER G 152 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 54 through 57 removed outlier: 6.519A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= AY, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= AZ, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BA, first strand: chain 'Q' and resid 117 through 121 removed outlier: 6.995A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'Q' and resid 138 through 141 Processing sheet with id= BC, first strand: chain 'Q' and resid 374 through 378 removed outlier: 3.603A pdb=" N THR Q 385 " --> pdb=" O SER Q 377 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'R' and resid 66 through 68 removed outlier: 4.020A pdb=" N LYS R 211 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'R' and resid 121 through 123 removed outlier: 3.504A pdb=" N GLN R 223 " --> pdb=" O GLU R 123 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'U' and resid 257 through 263 Processing sheet with id= BG, first strand: chain 'U' and resid 265 through 269 removed outlier: 4.009A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= BI, first strand: chain 'V' and resid 110 through 116 removed outlier: 6.130A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'W' and resid 68 through 70 removed outlier: 3.864A pdb=" N TYR W 86 " --> pdb=" O HIS W 70 " (cutoff:3.500A) 2116 hydrogen bonds defined for protein. 5922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 26.46 Time building geometry restraints manager: 25.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 27036 1.42 - 1.64: 38256 1.64 - 1.85: 549 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 65853 Sorted by residual: bond pdb=" C PHE B 758 " pdb=" O PHE B 758 " ideal model delta sigma weight residual 1.233 1.218 0.015 4.80e-03 4.34e+04 9.92e+00 bond pdb=" CA VAL A1098 " pdb=" CB VAL A1098 " ideal model delta sigma weight residual 1.537 1.522 0.015 5.00e-03 4.00e+04 9.35e+00 bond pdb=" CA LYS B 451 " pdb=" C LYS B 451 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.80e-02 3.09e+03 6.54e+00 bond pdb=" SD MET Q 114 " pdb=" CE MET Q 114 " ideal model delta sigma weight residual 1.791 1.849 -0.058 2.50e-02 1.60e+03 5.34e+00 bond pdb=" CA GLU B 560 " pdb=" C GLU B 560 " ideal model delta sigma weight residual 1.523 1.486 0.038 1.80e-02 3.09e+03 4.35e+00 ... (remaining 65848 not shown) Histogram of bond angle deviations from ideal: 73.45 - 85.59: 12 85.59 - 97.72: 1 97.72 - 109.85: 9676 109.85 - 121.99: 66372 121.99 - 134.12: 13330 Bond angle restraints: 89391 Sorted by residual: angle pdb=" C ILE 4 298 " pdb=" N ILE 4 299 " pdb=" CA ILE 4 299 " ideal model delta sigma weight residual 120.24 125.55 -5.31 6.30e-01 2.52e+00 7.11e+01 angle pdb=" N ILE 1 336 " pdb=" CA ILE 1 336 " pdb=" C ILE 1 336 " ideal model delta sigma weight residual 111.62 107.45 4.17 7.90e-01 1.60e+00 2.79e+01 angle pdb=" C ILE 4 299 " pdb=" CA ILE 4 299 " pdb=" CB ILE 4 299 " ideal model delta sigma weight residual 114.35 108.90 5.45 1.06e+00 8.90e-01 2.65e+01 angle pdb=" N SER 7 322 " pdb=" CA SER 7 322 " pdb=" C SER 7 322 " ideal model delta sigma weight residual 109.56 117.03 -7.47 1.84e+00 2.95e-01 1.65e+01 angle pdb=" N SER A 466 " pdb=" CA SER A 466 " pdb=" C SER A 466 " ideal model delta sigma weight residual 108.58 115.46 -6.88 1.82e+00 3.02e-01 1.43e+01 ... (remaining 89386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.29: 35016 18.29 - 36.58: 2920 36.58 - 54.88: 1118 54.88 - 73.17: 310 73.17 - 91.46: 49 Dihedral angle restraints: 39413 sinusoidal: 16105 harmonic: 23308 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -131.31 -48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA THR 6 116 " pdb=" C THR 6 116 " pdb=" N PRO 6 117 " pdb=" CA PRO 6 117 " ideal model delta harmonic sigma weight residual -180.00 -135.23 -44.77 0 5.00e+00 4.00e-02 8.02e+01 dihedral pdb=" CA LYS M 272 " pdb=" C LYS M 272 " pdb=" N SER M 273 " pdb=" CA SER M 273 " ideal model delta harmonic sigma weight residual 180.00 -135.63 -44.37 0 5.00e+00 4.00e-02 7.87e+01 ... (remaining 39410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 7171 0.039 - 0.078: 2071 0.078 - 0.117: 734 0.117 - 0.157: 90 0.157 - 0.196: 3 Chirality restraints: 10069 Sorted by residual: chirality pdb=" CB VAL 7 323 " pdb=" CA VAL 7 323 " pdb=" CG1 VAL 7 323 " pdb=" CG2 VAL 7 323 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU 6 448 " pdb=" CB LEU 6 448 " pdb=" CD1 LEU 6 448 " pdb=" CD2 LEU 6 448 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ARG 2 450 " pdb=" N ARG 2 450 " pdb=" C ARG 2 450 " pdb=" CB ARG 2 450 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 10066 not shown) Planarity restraints: 11228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA N 11 " -0.040 2.00e-02 2.50e+03 1.69e-02 7.88e+00 pdb=" N9 DA N 11 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA N 11 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DA N 11 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA N 11 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA N 11 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA N 11 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA N 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA N 11 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 11 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA N 11 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 463 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.19e+00 pdb=" N PRO A 464 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 6 116 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO 6 117 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 6 117 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 6 117 " -0.035 5.00e-02 4.00e+02 ... (remaining 11225 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 632 2.39 - 3.02: 43013 3.02 - 3.65: 108781 3.65 - 4.27: 157206 4.27 - 4.90: 243184 Nonbonded interactions: 552816 Sorted by model distance: nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.767 3.040 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1803 " model vdw 1.961 2.170 nonbonded pdb=" OD2 ASP A 485 " pdb="MG MG A1803 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.042 2.170 nonbonded pdb=" O ILE Q 127 " pdb=" OH TYR R 133 " model vdw 2.044 2.440 ... (remaining 552811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 16.650 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 162.860 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 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 : 0.005 0.065 65853 Z= 0.300 Angle : 0.657 9.673 89391 Z= 0.378 Chirality : 0.042 0.196 10069 Planarity : 0.004 0.067 11228 Dihedral : 16.621 91.460 24467 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.12 % Rotamer Outliers : 12.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.08 % 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: -1.89 (0.09), residues: 7928 helix: -0.27 (0.10), residues: 2696 sheet: -1.72 (0.16), residues: 990 loop : -1.80 (0.09), residues: 4242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 780 poor density : 314 time to evaluate : 6.054 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 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 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 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: 780 outliers final: 332 residues processed: 1061 average time/residue: 0.6108 time to fit residues: 1099.7662 Evaluate side-chains 586 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 254 time to evaluate : 5.952 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 332 outliers final: 6 residues processed: 332 average time/residue: 0.5239 time to fit residues: 318.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 3.9990 chunk 592 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 202 optimal weight: 50.0000 chunk 399 optimal weight: 8.9990 chunk 316 optimal weight: 4.9990 chunk 612 optimal weight: 6.9990 chunk 237 optimal weight: 50.0000 chunk 372 optimal weight: 9.9990 chunk 456 optimal weight: 20.0000 chunk 710 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 138 ASN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 716 ASN ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN 2 469 ASN ** 7 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1393 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 26 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 65853 Z= 0.326 Angle : 0.712 12.586 89391 Z= 0.376 Chirality : 0.045 0.219 10069 Planarity : 0.005 0.068 11228 Dihedral : 12.948 89.973 9918 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.57 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.90 (0.09), residues: 7928 helix: -0.24 (0.09), residues: 3024 sheet: -1.66 (0.16), residues: 958 loop : -1.98 (0.10), residues: 3946 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 262 time to evaluate : 6.051 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 239 outliers final: 99 residues processed: 486 average time/residue: 0.5957 time to fit residues: 503.5596 Evaluate side-chains 349 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 250 time to evaluate : 6.053 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 4 residues processed: 99 average time/residue: 0.5197 time to fit residues: 100.9533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 591 optimal weight: 50.0000 chunk 483 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 711 optimal weight: 10.0000 chunk 768 optimal weight: 50.0000 chunk 633 optimal weight: 4.9990 chunk 705 optimal weight: 6.9990 chunk 242 optimal weight: 0.0060 chunk 570 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 555 GLN 0 614 HIS ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 ASN ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 589 GLN ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 596 GLN ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 31 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 65853 Z= 0.233 Angle : 0.638 10.717 89391 Z= 0.333 Chirality : 0.043 0.240 10069 Planarity : 0.004 0.067 11228 Dihedral : 12.869 89.313 9918 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.54 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.70 (0.09), residues: 7928 helix: -0.07 (0.09), residues: 3034 sheet: -1.50 (0.17), residues: 954 loop : -1.89 (0.10), residues: 3940 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 263 time to evaluate : 6.055 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 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: 192 outliers final: 74 residues processed: 443 average time/residue: 0.5974 time to fit residues: 462.5153 Evaluate side-chains 324 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 250 time to evaluate : 5.961 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 2 residues processed: 74 average time/residue: 0.5089 time to fit residues: 77.3431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 50.0000 chunk 534 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 339 optimal weight: 0.7980 chunk 477 optimal weight: 6.9990 chunk 713 optimal weight: 7.9990 chunk 755 optimal weight: 50.0000 chunk 373 optimal weight: 0.7980 chunk 676 optimal weight: 1.9990 chunk 203 optimal weight: 50.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN D 216 ASN G 102 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN M 91 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 HIS ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 65853 Z= 0.194 Angle : 0.614 12.222 89391 Z= 0.318 Chirality : 0.042 0.223 10069 Planarity : 0.004 0.074 11228 Dihedral : 12.745 89.866 9918 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.14 % Favored : 91.79 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.51 (0.09), residues: 7928 helix: 0.11 (0.09), residues: 3052 sheet: -1.42 (0.16), residues: 959 loop : -1.81 (0.10), residues: 3917 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 263 time to evaluate : 6.057 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 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: 132 outliers final: 41 residues processed: 388 average time/residue: 0.5907 time to fit residues: 400.7452 Evaluate side-chains 290 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 5.973 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.5049 time to fit residues: 45.3319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 10.0000 chunk 429 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 562 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 522 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 385 optimal weight: 3.9990 chunk 678 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 151 GLN ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 375 HIS ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 65853 Z= 0.287 Angle : 0.641 10.713 89391 Z= 0.334 Chirality : 0.043 0.293 10069 Planarity : 0.004 0.071 11228 Dihedral : 12.788 89.705 9918 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.82 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.48 (0.09), residues: 7928 helix: 0.18 (0.09), residues: 3051 sheet: -1.42 (0.16), residues: 958 loop : -1.82 (0.10), residues: 3919 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 253 time to evaluate : 5.997 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 68 residues processed: 396 average time/residue: 0.6121 time to fit residues: 422.7255 Evaluate side-chains 313 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 245 time to evaluate : 6.007 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.5186 time to fit residues: 72.1646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 0.0060 chunk 680 optimal weight: 3.9990 chunk 149 optimal weight: 50.0000 chunk 443 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 756 optimal weight: 0.6980 chunk 628 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 250 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 469 ASN ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 431 GLN ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 589 GLN ** 7 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS D 179 GLN H 83 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 65853 Z= 0.164 Angle : 0.604 14.709 89391 Z= 0.310 Chirality : 0.042 0.256 10069 Planarity : 0.004 0.066 11228 Dihedral : 12.659 89.871 9918 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.46 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.27 (0.09), residues: 7928 helix: 0.38 (0.09), residues: 3061 sheet: -1.29 (0.16), residues: 956 loop : -1.74 (0.10), residues: 3911 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 257 time to evaluate : 6.183 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 36 residues processed: 333 average time/residue: 0.6485 time to fit residues: 380.3069 Evaluate side-chains 282 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 6.070 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5440 time to fit residues: 43.0825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 431 optimal weight: 0.5980 chunk 552 optimal weight: 6.9990 chunk 428 optimal weight: 0.8980 chunk 636 optimal weight: 20.0000 chunk 422 optimal weight: 8.9990 chunk 753 optimal weight: 20.0000 chunk 471 optimal weight: 5.9990 chunk 459 optimal weight: 0.9990 chunk 347 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 592 GLN 7 634 GLN ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 65853 Z= 0.177 Angle : 0.596 12.427 89391 Z= 0.305 Chirality : 0.042 0.201 10069 Planarity : 0.004 0.070 11228 Dihedral : 12.564 89.762 9918 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.71 % Favored : 92.22 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.15 (0.10), residues: 7928 helix: 0.49 (0.10), residues: 3071 sheet: -1.24 (0.17), residues: 952 loop : -1.69 (0.10), residues: 3905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 6.122 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 20 residues processed: 300 average time/residue: 0.6140 time to fit residues: 325.1113 Evaluate side-chains 266 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5479 time to fit residues: 27.6772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 450 optimal weight: 0.3980 chunk 227 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 0.0870 chunk 479 optimal weight: 0.9990 chunk 513 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 592 optimal weight: 6.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 749 ASN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 65853 Z= 0.157 Angle : 0.608 16.526 89391 Z= 0.307 Chirality : 0.042 0.346 10069 Planarity : 0.004 0.067 11228 Dihedral : 12.478 89.455 9918 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.85 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.06 (0.10), residues: 7928 helix: 0.58 (0.10), residues: 3069 sheet: -1.13 (0.16), residues: 976 loop : -1.67 (0.10), residues: 3883 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 252 time to evaluate : 6.188 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 15 residues processed: 289 average time/residue: 0.6264 time to fit residues: 320.4125 Evaluate side-chains 260 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 5.986 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6002 time to fit residues: 23.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 4.9990 chunk 722 optimal weight: 6.9990 chunk 658 optimal weight: 8.9990 chunk 702 optimal weight: 8.9990 chunk 721 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 551 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 chunk 634 optimal weight: 5.9990 chunk 664 optimal weight: 0.0970 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 198 ASN ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 422 GLN ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 65853 Z= 0.250 Angle : 0.633 14.633 89391 Z= 0.322 Chirality : 0.042 0.305 10069 Planarity : 0.004 0.069 11228 Dihedral : 12.517 89.276 9918 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.15 % Favored : 91.78 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.05 % 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: -1.08 (0.10), residues: 7928 helix: 0.59 (0.10), residues: 3072 sheet: -1.20 (0.16), residues: 978 loop : -1.69 (0.10), residues: 3878 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 249 time to evaluate : 6.037 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 277 average time/residue: 0.6270 time to fit residues: 308.4535 Evaluate side-chains 263 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 6.407 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5361 time to fit residues: 26.0317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 0.9980 chunk 461 optimal weight: 6.9990 chunk 742 optimal weight: 8.9990 chunk 453 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 chunk 516 optimal weight: 3.9990 chunk 779 optimal weight: 50.0000 chunk 717 optimal weight: 0.0470 chunk 620 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 479 optimal weight: 0.0570 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 716 ASN 0 748 GLN ** 6 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 65853 Z= 0.153 Angle : 0.620 14.434 89391 Z= 0.310 Chirality : 0.042 0.300 10069 Planarity : 0.004 0.070 11228 Dihedral : 12.381 89.628 9918 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.21 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.05 % 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: -0.98 (0.10), residues: 7928 helix: 0.65 (0.10), residues: 3081 sheet: -1.07 (0.16), residues: 991 loop : -1.64 (0.10), residues: 3856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15856 Ramachandran restraints generated. 7928 Oldfield, 0 Emsley, 7928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 6.044 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 263 average time/residue: 0.6383 time to fit residues: 298.0207 Evaluate side-chains 250 residues out of total 7221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 5.991 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4898 time to fit residues: 10.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 660 optimal weight: 0.0570 chunk 190 optimal weight: 4.9990 chunk 572 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 621 optimal weight: 0.0070 chunk 260 optimal weight: 10.0000 chunk 638 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.061030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.039490 restraints weight = 647356.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.040676 restraints weight = 409959.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.040297 restraints weight = 256241.359| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 364 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 65853 Z= 0.207 Angle : 0.622 15.119 89391 Z= 0.314 Chirality : 0.041 0.239 10069 Planarity : 0.004 0.069 11228 Dihedral : 12.387 89.497 9918 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.57 % Favored : 92.36 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.05 % 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: -0.93 (0.10), residues: 7928 helix: 0.72 (0.10), residues: 3071 sheet: -1.07 (0.16), residues: 996 loop : -1.62 (0.10), residues: 3861 =============================================================================== Job complete usr+sys time: 10387.25 seconds wall clock time: 187 minutes 7.49 seconds (11227.49 seconds total)