Starting phenix.real_space_refine (version: dev) on Wed Feb 22 18:05:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2023/6n7h_0356_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_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_0356/02_2023/6n7h_0356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2023/6n7h_0356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2023/6n7h_0356_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_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-4877/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: 10.43, per 1000 atoms: 0.60 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: 7.05 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: 2.51 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: 5.02 Time building geometry restraints manager: 7.57 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=" 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 bond pdb=" C7 NAG A1801 " pdb=" N2 NAG A1801 " ideal model delta sigma weight residual 1.337 1.365 -0.028 1.10e-02 8.26e+03 6.50e+00 bond pdb=" CB GLN B 242 " pdb=" CG GLN B 242 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.27e+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=" C2 NAG A1801 " pdb=" N2 NAG A1801 " pdb=" C7 NAG A1801 " ideal model delta sigma weight residual 123.12 134.14 -11.02 1.28e+00 6.08e-01 7.37e+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 ... (remaining 24034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 9852 22.04 - 44.08: 447 44.08 - 66.12: 44 66.12 - 88.15: 15 88.15 - 110.19: 7 Dihedral angle restraints: 10365 sinusoidal: 4099 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 10362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2301 0.089 - 0.178: 414 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 6.120 Check model and map are aligned: 0.260 Process input model: 46.640 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.340 ------------------------------------------------------------------------------- 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 : 0.009 0.192 17665 Z= 0.610 Angle : 1.310 15.126 24039 Z= 0.678 Chirality : 0.071 0.444 2780 Planarity : 0.009 0.073 2984 Dihedral : 12.988 110.192 6321 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 : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 545 average time/residue: 0.3147 time to fit residues: 252.3862 Evaluate side-chains 269 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1495 time to fit residues: 4.4186 ------------------------------------------------------------------------------- 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 97 ASN ** 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 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 B1099 HIS C 69 ASN C 107 ASN C 134 HIS C 180 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 17665 Z= 0.201 Angle : 0.785 13.869 24039 Z= 0.391 Chirality : 0.048 0.543 2780 Planarity : 0.006 0.065 2984 Dihedral : 9.964 103.442 2470 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.99 % Favored : 89.78 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 2143 helix: -0.95 (0.14), residues: 1163 sheet: -2.36 (0.44), residues: 114 loop : -3.06 (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 364 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 295 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 24 residues processed: 344 average time/residue: 0.2755 time to fit residues: 147.6419 Evaluate side-chains 260 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1589 time to fit residues: 9.7542 ------------------------------------------------------------------------------- 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: 0.0470 chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 496 ASN A 846 HIS A 901 GLN B 201 HIS ** 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 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 17665 Z= 0.247 Angle : 0.753 11.500 24039 Z= 0.376 Chirality : 0.048 0.557 2780 Planarity : 0.005 0.082 2984 Dihedral : 9.621 101.447 2470 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.25 % Favored : 88.61 % Rotamer Outliers : 3.93 % 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: -1.91 (0.18), residues: 2143 helix: -0.11 (0.15), residues: 1153 sheet: -1.86 (0.45), residues: 119 loop : -2.81 (0.20), residues: 871 *********************** 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 323 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 253 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 32 residues processed: 307 average time/residue: 0.2688 time to fit residues: 130.4980 Evaluate side-chains 254 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 222 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1681 time to fit residues: 12.9361 ------------------------------------------------------------------------------- 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: 0.7980 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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** C 69 ASN C 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 17665 Z= 0.225 Angle : 0.726 13.840 24039 Z= 0.360 Chirality : 0.047 0.504 2780 Planarity : 0.005 0.074 2984 Dihedral : 9.438 102.470 2470 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.27 % Favored : 89.64 % 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: -1.45 (0.18), residues: 2143 helix: 0.28 (0.15), residues: 1169 sheet: -1.49 (0.48), residues: 119 loop : -2.69 (0.21), residues: 855 *********************** 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 292 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 14 residues processed: 278 average time/residue: 0.2701 time to fit residues: 116.8558 Evaluate side-chains 232 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1692 time to fit residues: 7.3030 ------------------------------------------------------------------------------- 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: 0.9990 chunk 117 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17665 Z= 0.182 Angle : 0.698 11.643 24039 Z= 0.345 Chirality : 0.046 0.499 2780 Planarity : 0.005 0.067 2984 Dihedral : 9.263 102.227 2470 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.13 % Favored : 89.78 % Rotamer Outliers : 2.30 % 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: -1.05 (0.19), residues: 2143 helix: 0.62 (0.16), residues: 1160 sheet: -1.15 (0.51), residues: 119 loop : -2.53 (0.21), residues: 864 *********************** 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 286 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 1.998 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 14 residues processed: 270 average time/residue: 0.2869 time to fit residues: 121.1961 Evaluate side-chains 234 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1711 time to fit residues: 7.3154 ------------------------------------------------------------------------------- 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: 0.0370 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 0.0170 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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 218 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17665 Z= 0.166 Angle : 0.681 14.654 24039 Z= 0.335 Chirality : 0.045 0.466 2780 Planarity : 0.005 0.062 2984 Dihedral : 9.108 102.487 2470 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.66 % Favored : 90.25 % 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: -0.81 (0.19), residues: 2143 helix: 0.81 (0.16), residues: 1159 sheet: -1.03 (0.50), residues: 119 loop : -2.41 (0.21), residues: 865 *********************** 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 278 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 271 average time/residue: 0.2865 time to fit residues: 120.5417 Evaluate side-chains 231 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1656 time to fit residues: 5.9007 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 0.0970 chunk 151 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 0.0020 chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 ** 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 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: 0.7678 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 17665 Z= 0.159 Angle : 0.670 12.970 24039 Z= 0.329 Chirality : 0.044 0.464 2780 Planarity : 0.005 0.060 2984 Dihedral : 9.002 102.747 2470 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.99 % Favored : 89.92 % Rotamer Outliers : 1.01 % 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: -0.58 (0.19), residues: 2143 helix: 1.01 (0.16), residues: 1149 sheet: -1.08 (0.51), residues: 114 loop : -2.27 (0.21), residues: 880 *********************** 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 266 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.094 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 260 average time/residue: 0.2787 time to fit residues: 114.4192 Evaluate side-chains 228 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1626 time to fit residues: 4.8116 ------------------------------------------------------------------------------- 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: 3.9990 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 ** 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS C 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17665 Z= 0.185 Angle : 0.684 12.242 24039 Z= 0.340 Chirality : 0.044 0.457 2780 Planarity : 0.005 0.085 2984 Dihedral : 9.021 102.739 2470 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.99 % Favored : 89.97 % Rotamer Outliers : 0.79 % 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: -0.53 (0.19), residues: 2143 helix: 1.07 (0.16), residues: 1151 sheet: -1.00 (0.49), residues: 119 loop : -2.29 (0.21), residues: 873 *********************** 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: 14 poor density : 225 time to evaluate : 2.006 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 233 average time/residue: 0.2657 time to fit residues: 98.9958 Evaluate side-chains 217 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1557 time to fit residues: 4.5225 ------------------------------------------------------------------------------- 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: 0.4980 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 0.0870 chunk 181 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 856 GLN ** 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17665 Z= 0.178 Angle : 0.679 11.968 24039 Z= 0.335 Chirality : 0.044 0.465 2780 Planarity : 0.005 0.080 2984 Dihedral : 8.997 102.957 2470 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.71 % Favored : 90.25 % Rotamer Outliers : 0.67 % 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: -0.41 (0.19), residues: 2143 helix: 1.15 (0.16), residues: 1145 sheet: -0.97 (0.49), residues: 119 loop : -2.19 (0.21), residues: 879 *********************** 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 240 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 237 average time/residue: 0.2805 time to fit residues: 104.1194 Evaluate side-chains 216 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1596 time to fit residues: 4.2137 ------------------------------------------------------------------------------- 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: 0.3980 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS C 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17665 Z= 0.247 Angle : 0.732 11.704 24039 Z= 0.361 Chirality : 0.047 0.426 2780 Planarity : 0.005 0.085 2984 Dihedral : 9.079 103.061 2470 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.83 % Favored : 89.08 % Rotamer Outliers : 0.56 % 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: -0.46 (0.19), residues: 2143 helix: 1.07 (0.16), residues: 1150 sheet: -0.95 (0.49), residues: 119 loop : -2.17 (0.21), residues: 874 ********************** 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 232 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 222 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 227 average time/residue: 0.2864 time to fit residues: 102.8337 Evaluate side-chains 214 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1682 time to fit residues: 5.0209 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114885 restraints weight = 29495.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118433 restraints weight = 17473.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119270 restraints weight = 11020.359| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17665 Z= 0.215 Angle : 0.719 11.971 24039 Z= 0.353 Chirality : 0.046 0.456 2780 Planarity : 0.005 0.083 2984 Dihedral : 9.069 103.226 2470 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.89 % Favored : 89.97 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.19 % 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: -0.44 (0.19), residues: 2143 helix: 1.10 (0.16), residues: 1152 sheet: -1.13 (0.48), residues: 121 loop : -2.15 (0.21), residues: 870 =============================================================================== Job complete usr+sys time: 3246.77 seconds wall clock time: 60 minutes 14.14 seconds (3614.14 seconds total)