Starting phenix.real_space_refine (version: dev) on Thu Mar 16 22:58:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/03_2023/6n7h_0356_neut_updated.pdb" } resolution = 3.6 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1035 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 772": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 786": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 906": "NH1" <-> "NH2" Residue "A ARG 982": "NH1" <-> "NH2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B ARG 824": "NH1" <-> "NH2" Residue "B ARG 1114": "NH1" <-> "NH2" Residue "B ARG 1150": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 153": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 17242 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7807 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7708 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 42, 'TRANS': 945} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 154 Unusual residues: {'CLR': 3, 'NAG': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'CLR': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {' CA': 2, ' ZN': 1, 'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.96, per 1000 atoms: 0.58 Number of scatterers: 17242 At special positions: 0 Unit cell: (144.82, 93.576, 152.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 88 16.00 O 3099 8.00 N 2816 7.00 C 11236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 327 " distance=2.01 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 304 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B1501 " - " ASN B 141 " " NAG B1502 " - " ASN B 312 " " NAG B1503 " - " ASN B 349 " " NAG B1504 " - " ASN B 414 " " NAG B1505 " - " ASN B 875 " " NAG D 1 " - " ASN A1000 " " NAG E 1 " - " ASN B1000 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.34 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 140 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 182 " 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 6 sheets defined 49.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 75 through 96 removed outlier: 3.753A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.819A pdb=" N ILE A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.520A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 389 through 409 Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 504 through 523 removed outlier: 3.769A pdb=" N LEU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.162A pdb=" N CYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 591 Processing helix chain 'A' and resid 593 through 604 removed outlier: 4.027A pdb=" N ARG A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 745 Proline residue: A 742 - end of helix Processing helix chain 'A' and resid 751 through 769 removed outlier: 3.603A pdb=" N VAL A 763 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.543A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 4.032A pdb=" N SER A 827 " --> pdb=" O HIS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 878 through 887 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 984 through 1003 Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1025 through 1045 removed outlier: 3.971A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A1030 " --> pdb=" O HIS A1026 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1074 removed outlier: 4.165A pdb=" N ILE A1055 " --> pdb=" O TRP A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1105 removed outlier: 4.649A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1121 Processing helix chain 'A' and resid 1124 through 1140 Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1154 through 1177 Proline residue: A1172 - end of helix Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.620A pdb=" N PHE B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 111 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.750A pdb=" N ARG B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.851A pdb=" N TYR B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.942A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 390 through 410 Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 439 through 454 Processing helix chain 'B' and resid 468 through 490 removed outlier: 3.960A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 523 removed outlier: 3.922A pdb=" N GLY B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 518 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.685A pdb=" N CYS B 540 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 542 " --> pdb=" O GLU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 562 removed outlier: 3.930A pdb=" N ALA B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 Processing helix chain 'B' and resid 593 through 604 removed outlier: 4.304A pdb=" N MET B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.932A pdb=" N ALA B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Proline residue: B 742 - end of helix Processing helix chain 'B' and resid 747 through 767 removed outlier: 3.914A pdb=" N VAL B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 797 removed outlier: 3.976A pdb=" N LYS B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 828 Processing helix chain 'B' and resid 844 through 865 removed outlier: 3.904A pdb=" N TRP B 863 " --> pdb=" O PHE B 859 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU B 864 " --> pdb=" O ASP B 860 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 880 through 887 Processing helix chain 'B' and resid 902 through 905 removed outlier: 3.958A pdb=" N GLN B 905 " --> pdb=" O LEU B 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 902 through 905' Processing helix chain 'B' and resid 919 through 927 removed outlier: 4.682A pdb=" N THR B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1003 removed outlier: 3.855A pdb=" N TYR B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B1002 " --> pdb=" O CYS B 998 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B1003 " --> pdb=" O SER B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1019 through 1021 No H-bonds generated for 'chain 'B' and resid 1019 through 1021' Processing helix chain 'B' and resid 1025 through 1045 removed outlier: 4.337A pdb=" N LEU B1030 " --> pdb=" O HIS B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1074 Processing helix chain 'B' and resid 1080 through 1105 removed outlier: 3.629A pdb=" N VAL B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B1087 " --> pdb=" O VAL B1083 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS B1099 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1142 removed outlier: 5.442A pdb=" N ALA B1124 " --> pdb=" O GLU B1120 " (cutoff:3.500A) Proline residue: B1125 - end of helix removed outlier: 4.559A pdb=" N MET B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B1140 " --> pdb=" O GLY B1136 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B1141 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLY B1142 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1168 removed outlier: 4.494A pdb=" N ILE B1158 " --> pdb=" O ALA B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1176 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.882A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 159 through 167 removed outlier: 3.514A pdb=" N ARG C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 360 through 364 removed outlier: 3.536A pdb=" N LEU A 360 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 418 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.529A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.677A pdb=" N SER A 356 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 157 through 162 removed outlier: 3.930A pdb=" N PHE B 422 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 975 through 978 Processing sheet with id= F, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.851A pdb=" N TRP C 172 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 149 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 124 " --> pdb=" O THR C 149 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3608 1.33 - 1.45: 4098 1.45 - 1.57: 9815 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 17665 Sorted by residual: bond pdb=" C MET C 98 " pdb=" N THR C 99 " ideal model delta sigma weight residual 1.332 1.524 -0.192 1.40e-02 5.10e+03 1.87e+02 bond pdb=" C ARG C 123 " pdb=" N VAL C 124 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.00e-02 1.00e+04 1.43e+02 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C1 NAG B1504 " pdb=" O5 NAG B1504 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.26e+00 bond pdb=" C PRO A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.94e+00 ... (remaining 17660 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.20: 371 105.20 - 113.02: 9471 113.02 - 120.83: 8956 120.83 - 128.64: 5069 128.64 - 136.45: 172 Bond angle restraints: 24039 Sorted by residual: angle pdb=" C ASP C 83 " pdb=" N ILE C 84 " pdb=" CA ILE C 84 " ideal model delta sigma weight residual 123.10 136.45 -13.35 1.29e+00 6.01e-01 1.07e+02 angle pdb=" O ASP C 83 " pdb=" C ASP C 83 " pdb=" N ILE C 84 " ideal model delta sigma weight residual 122.19 110.99 11.20 1.21e+00 6.83e-01 8.57e+01 angle pdb=" N GLY C 196 " pdb=" CA GLY C 196 " pdb=" C GLY C 196 " ideal model delta sigma weight residual 115.21 126.82 -11.61 1.30e+00 5.92e-01 7.98e+01 angle pdb=" N ALA C 192 " pdb=" CA ALA C 192 " pdb=" C ALA C 192 " ideal model delta sigma weight residual 108.96 122.19 -13.23 1.59e+00 3.96e-01 6.93e+01 angle pdb=" N ALA C 187 " pdb=" CA ALA C 187 " pdb=" C ALA C 187 " ideal model delta sigma weight residual 112.23 121.09 -8.86 1.26e+00 6.30e-01 4.95e+01 ... (remaining 24034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 9521 17.51 - 35.03: 626 35.03 - 52.54: 111 52.54 - 70.06: 12 70.06 - 87.57: 11 Dihedral angle restraints: 10281 sinusoidal: 4015 harmonic: 6266 Sorted by residual: dihedral pdb=" CA ARG B 942 " pdb=" C ARG B 942 " pdb=" N PRO B 943 " pdb=" CA PRO B 943 " ideal model delta harmonic sigma weight residual 180.00 121.33 58.67 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA B 357 " pdb=" C ALA B 357 " pdb=" N HIS B 358 " pdb=" CA HIS B 358 " ideal model delta harmonic sigma weight residual 180.00 125.07 54.93 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLU A 836 " pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta harmonic sigma weight residual 180.00 -130.59 -49.41 0 5.00e+00 4.00e-02 9.76e+01 ... (remaining 10278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2293 0.089 - 0.178: 422 0.178 - 0.266: 51 0.266 - 0.355: 10 0.355 - 0.444: 4 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C1 NAG B1501 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1501 " pdb=" O5 NAG B1501 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA ALA C 192 " pdb=" N ALA C 192 " pdb=" C ALA C 192 " pdb=" CB ALA C 192 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG A1807 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A1807 " pdb=" O5 NAG A1807 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 2777 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 83 " 0.032 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C ASP C 83 " -0.099 2.00e-02 2.50e+03 pdb=" O ASP C 83 " 0.033 2.00e-02 2.50e+03 pdb=" N ILE C 84 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 123 " -0.025 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C ARG C 123 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG C 123 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL C 124 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1179 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A1180 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1180 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1180 " -0.040 5.00e-02 4.00e+02 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 153 2.59 - 3.16: 14532 3.16 - 3.74: 26652 3.74 - 4.32: 35248 4.32 - 4.90: 57221 Nonbonded interactions: 133806 Sorted by model distance: nonbonded pdb=" O ALA C 187 " pdb=" N ASN C 189 " model vdw 2.008 2.520 nonbonded pdb=" OD2 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.125 2.230 nonbonded pdb=" OE1 GLU B 149 " pdb=" NH2 ARG C 28 " model vdw 2.159 2.520 nonbonded pdb=" OD1 ASP C 147 " pdb="ZN ZN C 202 " model vdw 2.225 2.230 nonbonded pdb=" OD2 ASP B 821 " pdb=" OH TYR B1001 " model vdw 2.242 2.440 ... (remaining 133801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 458 or (resid 459 through 466 and (name N or na \ me CA or name C or name O or name CB )) or resid 467 through 606 or resid 731 th \ rough 888 or (resid 889 and (name N or name CA or name C or name O or name CB )) \ or resid 890 through 892 or (resid 893 through 905 and (name N or name CA or na \ me C or name O or name CB )) or resid 906 through 953 or (resid 954 through 959 \ and (name N or name CA or name C or name O or name CB )) or resid 960 or (resid \ 961 and (name N or name CA or name C or name O or name CB )) or resid 962 throug \ h 1182 or (resid 1183 and (name N or name CA or name C or name O or name CB )) o \ r resid 1803 through 1807 or resid 1810)) selection = (chain 'B' and (resid 76 through 606 or (resid 731 through 737 and (name N or na \ me CA or name C or name O or name CB )) or resid 738 through 1183 or resid 1501 \ through 1503 or resid 1508)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 88 5.16 5 C 11236 2.51 5 N 2816 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 5.990 Check model and map are aligned: 0.260 Process input model: 47.200 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.010 0.192 17665 Z= 0.616 Angle : 1.316 15.126 24039 Z= 0.672 Chirality : 0.071 0.444 2780 Planarity : 0.009 0.073 2984 Dihedral : 12.335 87.573 6237 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.32 % Favored : 87.12 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.14), residues: 2143 helix: -2.49 (0.11), residues: 1142 sheet: -3.32 (0.40), residues: 115 loop : -3.44 (0.18), residues: 886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 529 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 545 average time/residue: 0.3128 time to fit residues: 250.5384 Evaluate side-chains 269 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1719 time to fit residues: 5.1080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9980 chunk 162 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 310 ASN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 823 HIS A 871 ASN A 929 ASN A1049 ASN B 120 ASN B 124 ASN B 156 GLN B 242 GLN B 310 ASN B 371 GLN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 846 HIS B 853 GLN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 929 ASN B 938 GLN B1049 ASN C 69 ASN C 107 ASN C 134 HIS C 180 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17665 Z= 0.198 Angle : 0.777 12.765 24039 Z= 0.381 Chirality : 0.047 0.305 2780 Planarity : 0.006 0.064 2984 Dihedral : 7.368 59.069 2386 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.85 % Favored : 89.92 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.17), residues: 2143 helix: -0.86 (0.14), residues: 1163 sheet: -2.32 (0.44), residues: 114 loop : -3.02 (0.19), residues: 866 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 307 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 24 residues processed: 356 average time/residue: 0.2800 time to fit residues: 155.4735 Evaluate side-chains 260 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1687 time to fit residues: 10.1546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 496 ASN A 846 HIS B 120 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 17665 Z= 0.380 Angle : 0.835 12.735 24039 Z= 0.416 Chirality : 0.051 0.572 2780 Planarity : 0.006 0.091 2984 Dihedral : 7.290 56.125 2386 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.27 % Favored : 87.59 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 2143 helix: -0.22 (0.15), residues: 1167 sheet: -1.87 (0.46), residues: 119 loop : -2.92 (0.20), residues: 857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 253 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 46 residues processed: 318 average time/residue: 0.2623 time to fit residues: 132.6033 Evaluate side-chains 272 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1626 time to fit residues: 16.7953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 195 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS A 901 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS C 69 ASN C 133 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17665 Z= 0.214 Angle : 0.739 13.751 24039 Z= 0.360 Chirality : 0.046 0.468 2780 Planarity : 0.005 0.077 2984 Dihedral : 6.916 54.714 2386 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.31 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.24 % 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: -1.49 (0.18), residues: 2143 helix: 0.23 (0.15), residues: 1170 sheet: -1.53 (0.48), residues: 119 loop : -2.69 (0.21), residues: 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 1.995 Fit side-chains outliers start: 50 outliers final: 18 residues processed: 286 average time/residue: 0.2822 time to fit residues: 125.9766 Evaluate side-chains 242 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1708 time to fit residues: 8.2728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 823 HIS B 872 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 17665 Z= 0.165 Angle : 0.706 15.372 24039 Z= 0.340 Chirality : 0.046 0.466 2780 Planarity : 0.005 0.079 2984 Dihedral : 6.588 58.710 2386 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.50 % Favored : 89.41 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.24 % 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: -1.01 (0.19), residues: 2143 helix: 0.68 (0.16), residues: 1148 sheet: -1.15 (0.49), residues: 119 loop : -2.52 (0.21), residues: 876 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 265 time to evaluate : 1.849 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 286 average time/residue: 0.2890 time to fit residues: 128.5681 Evaluate side-chains 231 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1750 time to fit residues: 6.8010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 901 GLN B 168 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS C 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17665 Z= 0.175 Angle : 0.692 13.374 24039 Z= 0.337 Chirality : 0.045 0.445 2780 Planarity : 0.005 0.062 2984 Dihedral : 6.304 48.369 2386 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.99 % Favored : 89.92 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % 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: -0.83 (0.19), residues: 2143 helix: 0.79 (0.16), residues: 1151 sheet: -1.08 (0.51), residues: 114 loop : -2.39 (0.21), residues: 878 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 263 average time/residue: 0.2876 time to fit residues: 118.0682 Evaluate side-chains 231 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1757 time to fit residues: 6.3246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17665 Z= 0.186 Angle : 0.692 12.717 24039 Z= 0.336 Chirality : 0.045 0.456 2780 Planarity : 0.005 0.063 2984 Dihedral : 6.097 51.667 2386 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.17 % Favored : 89.73 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % 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: -0.67 (0.19), residues: 2143 helix: 0.91 (0.16), residues: 1153 sheet: -0.94 (0.50), residues: 119 loop : -2.31 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 2.088 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 247 average time/residue: 0.2755 time to fit residues: 107.2897 Evaluate side-chains 220 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 214 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1595 time to fit residues: 4.3879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17665 Z= 0.185 Angle : 0.696 11.582 24039 Z= 0.341 Chirality : 0.045 0.450 2780 Planarity : 0.005 0.064 2984 Dihedral : 6.068 59.026 2386 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.27 % Favored : 89.64 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % 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: -0.55 (0.19), residues: 2143 helix: 1.02 (0.16), residues: 1145 sheet: -0.84 (0.50), residues: 119 loop : -2.25 (0.21), residues: 879 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 2.136 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 230 average time/residue: 0.2775 time to fit residues: 101.8742 Evaluate side-chains 220 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1764 time to fit residues: 5.2975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 194 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 17665 Z= 0.199 Angle : 0.704 11.968 24039 Z= 0.343 Chirality : 0.046 0.457 2780 Planarity : 0.005 0.065 2984 Dihedral : 6.065 53.652 2386 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.41 % Favored : 89.50 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % 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: -0.57 (0.19), residues: 2143 helix: 1.00 (0.16), residues: 1150 sheet: -0.89 (0.49), residues: 119 loop : -2.27 (0.21), residues: 874 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 230 average time/residue: 0.2783 time to fit residues: 101.8125 Evaluate side-chains 217 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1656 time to fit residues: 4.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 141 optimal weight: 0.0970 chunk 213 optimal weight: 5.9990 chunk 196 optimal weight: 0.0470 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 17665 Z= 0.163 Angle : 0.700 11.869 24039 Z= 0.339 Chirality : 0.044 0.448 2780 Planarity : 0.005 0.059 2984 Dihedral : 5.877 56.147 2386 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.57 % Favored : 90.39 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.15 % 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: -0.43 (0.19), residues: 2143 helix: 1.15 (0.16), residues: 1147 sheet: -0.90 (0.49), residues: 119 loop : -2.23 (0.21), residues: 877 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 246 average time/residue: 0.2855 time to fit residues: 109.1547 Evaluate side-chains 222 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1795 time to fit residues: 4.0880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: