Starting phenix.real_space_refine on Sat Feb 17 09:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2024/6n7h_0356_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2024/6n7h_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_2024/6n7h_0356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2024/6n7h_0356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2024/6n7h_0356_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7h_0356/02_2024/6n7h_0356_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5238/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 15 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: 8.76, per 1000 atoms: 0.51 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: 7.03 Conformation dependent library (CDL) restraints added in 3.4 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: 4.53 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: 5.47 Time building geometry restraints manager: 7.50 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 - 23.86: 10321 23.86 - 47.73: 436 47.73 - 71.59: 50 71.59 - 95.46: 23 95.46 - 119.32: 25 Dihedral angle restraints: 10855 sinusoidal: 4589 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 10852 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 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 5.690 Check model and map are aligned: 0.240 Set scattering table: 0.180 Process input model: 50.190 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 14.944 119.321 6811 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 % Allowed : 8.53 % Favored : 90.12 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 399 HIS 0.014 0.003 HIS B 358 PHE 0.040 0.004 PHE B1152 TYR 0.033 0.004 TYR A1181 ARG 0.011 0.001 ARG B 945 *********************** 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 : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.8375 (pp) cc_final: 0.8074 (mt) REVERT: A 131 GLU cc_start: 0.8146 (tt0) cc_final: 0.7795 (tt0) REVERT: A 420 LEU cc_start: 0.7393 (pt) cc_final: 0.5641 (mt) REVERT: A 464 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6721 (ttpt) REVERT: A 501 GLN cc_start: 0.7156 (mt0) cc_final: 0.6817 (tp-100) REVERT: A 550 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8783 (tm) REVERT: A 599 ASP cc_start: 0.7511 (t0) cc_final: 0.7100 (t70) REVERT: A 780 ILE cc_start: 0.8254 (pp) cc_final: 0.8048 (pt) REVERT: A 791 ILE cc_start: 0.9317 (mm) cc_final: 0.9090 (mt) REVERT: A 799 SER cc_start: 0.8475 (p) cc_final: 0.8263 (p) REVERT: A 850 ASP cc_start: 0.8118 (t0) cc_final: 0.7791 (t0) REVERT: A 870 PRO cc_start: 0.6715 (Cg_endo) cc_final: 0.5552 (Cg_exo) REVERT: A 956 MET cc_start: 0.8437 (ptt) cc_final: 0.8178 (ptt) REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7593 (m-80) REVERT: A 1052 THR cc_start: 0.8108 (p) cc_final: 0.7889 (t) REVERT: A 1063 MET cc_start: 0.7481 (tpt) cc_final: 0.7200 (ttt) REVERT: A 1073 LEU cc_start: 0.8536 (mt) cc_final: 0.8074 (tp) REVERT: B 82 LYS cc_start: 0.6921 (tptm) cc_final: 0.6515 (mttt) REVERT: B 88 PHE cc_start: 0.5523 (t80) cc_final: 0.4974 (t80) REVERT: B 210 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6078 (pp) REVERT: B 216 MET cc_start: 0.7841 (tpp) cc_final: 0.7373 (tpp) REVERT: B 354 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7426 (pp) REVERT: B 430 ILE cc_start: 0.8488 (tp) cc_final: 0.8258 (pt) REVERT: B 487 LEU cc_start: 0.8198 (tp) cc_final: 0.7759 (tp) REVERT: B 606 ARG cc_start: 0.5980 (mtm180) cc_final: 0.5610 (mtt-85) REVERT: B 744 LEU cc_start: 0.6111 (tt) cc_final: 0.5729 (mt) REVERT: B 760 LEU cc_start: 0.6622 (tt) cc_final: 0.6096 (mm) REVERT: B 868 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 962 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6650 (tpp80) REVERT: B 1040 PHE cc_start: 0.7792 (t80) cc_final: 0.7517 (t80) REVERT: B 1099 HIS cc_start: 0.7146 (m-70) cc_final: 0.6927 (m-70) REVERT: B 1119 LEU cc_start: 0.7999 (tp) cc_final: 0.7417 (tp) REVERT: C 72 ARG cc_start: 0.6754 (mtp-110) cc_final: 0.6409 (mtp180) REVERT: C 114 MET cc_start: 0.8318 (mtm) cc_final: 0.8098 (mtp) REVERT: C 183 CYS cc_start: 0.7974 (m) cc_final: 0.7743 (m) outliers start: 24 outliers final: 7 residues processed: 545 average time/residue: 0.3039 time to fit residues: 242.7584 Evaluate side-chains 284 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 273 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1171 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 188 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.7980 chunk 162 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2898 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 : 0.796 13.466 24039 Z= 0.387 Chirality : 0.048 0.466 2780 Planarity : 0.005 0.062 2984 Dihedral : 12.241 82.350 2983 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.27 % Favored : 89.45 % Rotamer: Outliers : 4.15 % Allowed : 14.42 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.17), residues: 2143 helix: -0.91 (0.14), residues: 1161 sheet: -2.37 (0.44), residues: 114 loop : -3.06 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1027 HIS 0.010 0.001 HIS B 739 PHE 0.020 0.002 PHE B 790 TYR 0.023 0.002 TYR A 224 ARG 0.007 0.000 ARG B 138 *********************** 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 381 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 307 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: A 292 MET cc_start: 0.8010 (mmt) cc_final: 0.7722 (mmt) REVERT: A 397 GLU cc_start: 0.7216 (tt0) cc_final: 0.6929 (tm-30) REVERT: A 422 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6305 (p90) REVERT: A 434 PHE cc_start: 0.7029 (t80) cc_final: 0.6779 (t80) REVERT: A 464 LYS cc_start: 0.7342 (mmtm) cc_final: 0.6676 (ttpt) REVERT: A 550 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8772 (tm) REVERT: A 587 MET cc_start: 0.7742 (tmm) cc_final: 0.7505 (tmm) REVERT: A 799 SER cc_start: 0.8297 (p) cc_final: 0.7992 (p) REVERT: A 862 ASP cc_start: 0.7397 (t70) cc_final: 0.6989 (t0) REVERT: A 956 MET cc_start: 0.8291 (ptt) cc_final: 0.8068 (ptt) REVERT: A 1034 VAL cc_start: 0.7349 (p) cc_final: 0.7148 (p) REVERT: A 1051 TRP cc_start: 0.6936 (t-100) cc_final: 0.6424 (t60) REVERT: A 1122 MET cc_start: 0.8148 (ttm) cc_final: 0.7460 (ttm) REVERT: A 1175 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8716 (mt) REVERT: B 82 LYS cc_start: 0.6911 (tptm) cc_final: 0.6553 (mptt) REVERT: B 101 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5625 (t80) REVERT: B 102 LEU cc_start: 0.5249 (mp) cc_final: 0.4914 (tt) REVERT: B 210 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.5914 (pp) REVERT: B 354 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7398 (pp) REVERT: B 599 ASP cc_start: 0.7917 (t70) cc_final: 0.7477 (t70) REVERT: B 606 ARG cc_start: 0.5950 (mtm180) cc_final: 0.5593 (mtt-85) REVERT: B 760 LEU cc_start: 0.6481 (tt) cc_final: 0.5775 (mm) REVERT: B 868 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5890 (tp) REVERT: B 962 ARG cc_start: 0.7133 (ttt180) cc_final: 0.6696 (tpp80) REVERT: B 1040 PHE cc_start: 0.7747 (t80) cc_final: 0.7466 (t80) REVERT: B 1111 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7641 (tppt) outliers start: 74 outliers final: 28 residues processed: 359 average time/residue: 0.2926 time to fit residues: 163.7604 Evaluate side-chains 273 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 129 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 501 GLN A 846 HIS A 901 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17665 Z= 0.316 Angle : 0.804 12.773 24039 Z= 0.396 Chirality : 0.049 0.536 2780 Planarity : 0.006 0.083 2984 Dihedral : 9.574 59.848 2976 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.62 % Favored : 88.29 % Rotamer: Outliers : 6.06 % Allowed : 15.82 % Favored : 78.11 % 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: -2.01 (0.18), residues: 2143 helix: -0.21 (0.15), residues: 1164 sheet: -1.81 (0.47), residues: 119 loop : -2.88 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 278 HIS 0.009 0.001 HIS B 358 PHE 0.024 0.002 PHE A 848 TYR 0.026 0.002 TYR A 224 ARG 0.005 0.001 ARG B 138 *********************** 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 362 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 254 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: A 422 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6427 (p90) REVERT: A 550 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8833 (tm) REVERT: A 575 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 587 MET cc_start: 0.7602 (tmm) cc_final: 0.7268 (tmm) REVERT: A 799 SER cc_start: 0.8441 (p) cc_final: 0.8134 (p) REVERT: A 862 ASP cc_start: 0.7572 (t70) cc_final: 0.7198 (t0) REVERT: A 956 MET cc_start: 0.8416 (ptt) cc_final: 0.8157 (ptt) REVERT: A 1051 TRP cc_start: 0.7182 (t-100) cc_final: 0.6296 (t60) REVERT: A 1175 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8670 (mt) REVERT: B 82 LYS cc_start: 0.6914 (tptm) cc_final: 0.6531 (mptt) REVERT: B 101 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 131 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6908 (tm-30) REVERT: B 140 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 210 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6282 (pp) REVERT: B 227 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8627 (tt) REVERT: B 354 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7665 (pp) REVERT: B 429 ASP cc_start: 0.7477 (t0) cc_final: 0.6973 (t0) REVERT: B 560 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 606 ARG cc_start: 0.5910 (mtm180) cc_final: 0.5412 (mtt-85) REVERT: B 760 LEU cc_start: 0.6440 (tt) cc_final: 0.5731 (mm) REVERT: B 1111 LYS cc_start: 0.7954 (ttpp) cc_final: 0.7669 (tppt) REVERT: C 67 SER cc_start: 0.8063 (p) cc_final: 0.7668 (m) REVERT: C 69 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7619 (p0) outliers start: 108 outliers final: 54 residues processed: 331 average time/residue: 0.2595 time to fit residues: 136.7875 Evaluate side-chains 301 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1059 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 69 ASN 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: 6.9990 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 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: 0.7572 moved from start: 0.4071 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= 0.188 Angle : 0.723 12.143 24039 Z= 0.348 Chirality : 0.046 0.487 2780 Planarity : 0.005 0.069 2984 Dihedral : 8.318 57.292 2972 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.13 % Favored : 89.78 % Rotamer: Outliers : 4.60 % Allowed : 17.79 % Favored : 77.61 % 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: -1.43 (0.18), residues: 2143 helix: 0.28 (0.15), residues: 1170 sheet: -1.48 (0.48), residues: 119 loop : -2.66 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1027 HIS 0.006 0.001 HIS B 358 PHE 0.022 0.001 PHE B 88 TYR 0.024 0.001 TYR A 224 ARG 0.003 0.000 ARG A 893 *********************** 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 336 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 254 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7171 (pt0) cc_final: 0.6951 (mm-30) REVERT: A 173 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: A 276 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6976 (p0) REVERT: A 315 LYS cc_start: 0.6439 (pptt) cc_final: 0.6215 (tptp) REVERT: A 422 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6250 (p90) REVERT: A 447 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7116 (tp) REVERT: A 550 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8788 (tm) REVERT: A 587 MET cc_start: 0.7717 (tmm) cc_final: 0.7294 (tmm) REVERT: A 799 SER cc_start: 0.8394 (p) cc_final: 0.8098 (p) REVERT: A 862 ASP cc_start: 0.7396 (t70) cc_final: 0.7122 (t0) REVERT: A 870 PRO cc_start: 0.6362 (Cg_exo) cc_final: 0.6038 (Cg_endo) REVERT: A 956 MET cc_start: 0.8471 (ptt) cc_final: 0.8182 (ptt) REVERT: A 1034 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7295 (p) REVERT: A 1049 ASN cc_start: 0.7457 (m110) cc_final: 0.7028 (t0) REVERT: A 1051 TRP cc_start: 0.7257 (t-100) cc_final: 0.6373 (t60) REVERT: A 1113 ARG cc_start: 0.7391 (tmm160) cc_final: 0.7093 (tmm160) REVERT: A 1122 MET cc_start: 0.8009 (ttm) cc_final: 0.7538 (ttm) REVERT: A 1175 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 82 LYS cc_start: 0.6934 (tptm) cc_final: 0.6565 (mptt) REVERT: B 102 LEU cc_start: 0.5338 (mm) cc_final: 0.4560 (tt) REVERT: B 131 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6790 (tm-30) REVERT: B 140 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 157 LEU cc_start: 0.9181 (mp) cc_final: 0.8933 (mt) REVERT: B 210 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6081 (pp) REVERT: B 227 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 429 ASP cc_start: 0.7457 (t0) cc_final: 0.6967 (t0) REVERT: B 560 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: B 606 ARG cc_start: 0.5898 (mtm180) cc_final: 0.5520 (mtt-85) REVERT: B 744 LEU cc_start: 0.6873 (pp) cc_final: 0.6389 (mt) REVERT: B 760 LEU cc_start: 0.6320 (tt) cc_final: 0.5701 (mm) REVERT: B 1111 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7781 (tppt) REVERT: C 67 SER cc_start: 0.8022 (p) cc_final: 0.7665 (m) outliers start: 82 outliers final: 40 residues processed: 313 average time/residue: 0.2715 time to fit residues: 132.9958 Evaluate side-chains 295 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 6.9990 chunk 117 optimal weight: 0.0020 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 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 ** 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: 0.7613 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17665 Z= 0.233 Angle : 0.733 14.553 24039 Z= 0.355 Chirality : 0.047 0.492 2780 Planarity : 0.005 0.068 2984 Dihedral : 8.017 56.860 2972 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.11 % Favored : 88.85 % Rotamer: Outliers : 5.11 % Allowed : 18.97 % Favored : 75.93 % 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: -1.22 (0.19), residues: 2143 helix: 0.46 (0.16), residues: 1172 sheet: -1.27 (0.49), residues: 119 loop : -2.61 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 278 HIS 0.008 0.001 HIS A 328 PHE 0.017 0.001 PHE A 848 TYR 0.026 0.001 TYR A 224 ARG 0.004 0.000 ARG A 893 *********************** 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 340 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 249 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: A 276 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7033 (p0) REVERT: A 315 LYS cc_start: 0.6517 (pptt) cc_final: 0.6261 (tptp) REVERT: A 422 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6369 (p90) REVERT: A 447 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7199 (tp) REVERT: A 550 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8828 (tm) REVERT: A 587 MET cc_start: 0.7645 (tmm) cc_final: 0.7218 (tmm) REVERT: A 799 SER cc_start: 0.8407 (p) cc_final: 0.8105 (p) REVERT: A 862 ASP cc_start: 0.7459 (t70) cc_final: 0.7190 (t0) REVERT: A 956 MET cc_start: 0.8610 (ptt) cc_final: 0.8327 (ptt) REVERT: A 1020 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: A 1049 ASN cc_start: 0.7326 (m110) cc_final: 0.7035 (t0) REVERT: A 1051 TRP cc_start: 0.7200 (t-100) cc_final: 0.6303 (t60) REVERT: A 1175 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8676 (mt) REVERT: B 82 LYS cc_start: 0.6913 (tptm) cc_final: 0.6537 (mptt) REVERT: B 85 ARG cc_start: 0.7241 (tpt-90) cc_final: 0.6949 (tpt-90) REVERT: B 102 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.4798 (tt) REVERT: B 136 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8386 (t) REVERT: B 140 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 157 LEU cc_start: 0.9211 (mp) cc_final: 0.8951 (mt) REVERT: B 210 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6659 (pt) REVERT: B 227 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (tt) REVERT: B 429 ASP cc_start: 0.7412 (t0) cc_final: 0.6918 (t0) REVERT: B 449 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: B 560 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: B 606 ARG cc_start: 0.5862 (mtm180) cc_final: 0.5504 (mtt-85) REVERT: B 744 LEU cc_start: 0.6869 (pp) cc_final: 0.6393 (mt) REVERT: B 760 LEU cc_start: 0.6339 (tt) cc_final: 0.5767 (mm) REVERT: C 67 SER cc_start: 0.8329 (p) cc_final: 0.8101 (m) outliers start: 91 outliers final: 56 residues processed: 310 average time/residue: 0.2645 time to fit residues: 129.3786 Evaluate side-chains 297 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 227 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 799 SER Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1058 MET Chi-restraints excluded: chain B residue 1059 VAL Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 171 optimal weight: 0.0770 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 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 ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17665 Z= 0.171 Angle : 0.693 12.984 24039 Z= 0.334 Chirality : 0.045 0.449 2780 Planarity : 0.005 0.070 2984 Dihedral : 7.684 58.754 2972 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.94 % Favored : 89.97 % Rotamer: Outliers : 4.15 % Allowed : 20.09 % Favored : 75.76 % 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: -0.83 (0.19), residues: 2143 helix: 0.80 (0.16), residues: 1158 sheet: -1.07 (0.50), residues: 119 loop : -2.42 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 278 HIS 0.008 0.001 HIS B 358 PHE 0.020 0.001 PHE B1178 TYR 0.023 0.001 TYR A 224 ARG 0.004 0.000 ARG A 893 *********************** 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 337 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 263 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6289 (p90) REVERT: A 447 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7125 (tp) REVERT: A 460 TRP cc_start: 0.5934 (m-10) cc_final: 0.5734 (m-10) REVERT: A 550 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8738 (tm) REVERT: A 587 MET cc_start: 0.7712 (tmm) cc_final: 0.7266 (tmm) REVERT: A 780 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7861 (pt) REVERT: A 799 SER cc_start: 0.8366 (p) cc_final: 0.8089 (p) REVERT: A 856 GLN cc_start: 0.6178 (tm-30) cc_final: 0.5963 (tm-30) REVERT: A 1034 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7387 (p) REVERT: A 1051 TRP cc_start: 0.7239 (t-100) cc_final: 0.6298 (t60) REVERT: A 1175 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8640 (mt) REVERT: B 82 LYS cc_start: 0.6841 (tptm) cc_final: 0.6507 (mptt) REVERT: B 85 ARG cc_start: 0.7237 (tpt-90) cc_final: 0.6973 (tpt-90) REVERT: B 102 LEU cc_start: 0.5288 (mm) cc_final: 0.4669 (tt) REVERT: B 112 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5801 (m-10) REVERT: B 136 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 140 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 157 LEU cc_start: 0.9160 (mp) cc_final: 0.8887 (mt) REVERT: B 210 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6648 (pt) REVERT: B 227 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8528 (tt) REVERT: B 365 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: B 429 ASP cc_start: 0.7338 (t0) cc_final: 0.6949 (t0) REVERT: B 560 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: B 606 ARG cc_start: 0.5843 (mtm180) cc_final: 0.5424 (mtt-85) REVERT: B 744 LEU cc_start: 0.6854 (pp) cc_final: 0.6446 (mt) REVERT: B 748 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.5934 (mttt) REVERT: B 760 LEU cc_start: 0.6339 (tt) cc_final: 0.5742 (mm) REVERT: C 67 SER cc_start: 0.8242 (p) cc_final: 0.7986 (m) outliers start: 74 outliers final: 39 residues processed: 312 average time/residue: 0.2754 time to fit residues: 134.1976 Evaluate side-chains 281 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1058 MET Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 206 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 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 B 872 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17665 Z= 0.163 Angle : 0.683 12.418 24039 Z= 0.329 Chirality : 0.044 0.440 2780 Planarity : 0.005 0.079 2984 Dihedral : 7.524 58.595 2970 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.85 % Favored : 90.11 % Rotamer: Outliers : 4.43 % Allowed : 21.49 % Favored : 74.07 % 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: -0.70 (0.19), residues: 2143 helix: 0.89 (0.16), residues: 1155 sheet: -1.03 (0.49), residues: 119 loop : -2.34 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 278 HIS 0.008 0.001 HIS B 358 PHE 0.021 0.001 PHE B 88 TYR 0.024 0.001 TYR A 224 ARG 0.004 0.000 ARG A 893 *********************** 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 317 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 238 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6170 (p90) REVERT: A 447 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7131 (tp) REVERT: A 460 TRP cc_start: 0.6017 (m-10) cc_final: 0.5765 (m-10) REVERT: A 550 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8719 (tm) REVERT: A 799 SER cc_start: 0.8349 (p) cc_final: 0.8062 (p) REVERT: A 1020 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: A 1034 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 1051 TRP cc_start: 0.7277 (t-100) cc_final: 0.6288 (t60) REVERT: A 1175 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8693 (mt) REVERT: B 82 LYS cc_start: 0.6870 (tptm) cc_final: 0.6484 (mptt) REVERT: B 102 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.4719 (tt) REVERT: B 112 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.5661 (m-10) REVERT: B 136 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8424 (t) REVERT: B 140 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8338 (mp) REVERT: B 157 LEU cc_start: 0.9105 (mp) cc_final: 0.8812 (mt) REVERT: B 210 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6599 (pt) REVERT: B 227 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8478 (tt) REVERT: B 365 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: B 429 ASP cc_start: 0.7343 (t0) cc_final: 0.7007 (t0) REVERT: B 457 MET cc_start: 0.4714 (mpt) cc_final: 0.4406 (mpp) REVERT: B 560 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: B 606 ARG cc_start: 0.5870 (mtm180) cc_final: 0.5451 (mtt-85) REVERT: B 744 LEU cc_start: 0.6815 (pp) cc_final: 0.6357 (mt) REVERT: B 748 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.5991 (mttt) REVERT: B 760 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5935 (mm) REVERT: C 67 SER cc_start: 0.8192 (p) cc_final: 0.7951 (m) outliers start: 79 outliers final: 44 residues processed: 296 average time/residue: 0.2666 time to fit residues: 125.1232 Evaluate side-chains 284 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 HIS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.2980 chunk 123 optimal weight: 0.0570 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 187 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 168 ASN B 189 HIS B 310 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17665 Z= 0.161 Angle : 0.676 11.583 24039 Z= 0.324 Chirality : 0.044 0.415 2780 Planarity : 0.005 0.079 2984 Dihedral : 7.412 57.079 2970 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.75 % Favored : 90.20 % Rotamer: Outliers : 3.87 % Allowed : 22.00 % Favored : 74.13 % 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: -0.56 (0.19), residues: 2143 helix: 1.00 (0.16), residues: 1152 sheet: -1.04 (0.49), residues: 119 loop : -2.23 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 278 HIS 0.009 0.001 HIS B 358 PHE 0.018 0.001 PHE A 522 TYR 0.024 0.001 TYR A 224 ARG 0.004 0.000 ARG A 893 *********************** 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 321 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6252 (p90) REVERT: A 447 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7006 (tp) REVERT: A 550 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8729 (tm) REVERT: A 587 MET cc_start: 0.7542 (ppp) cc_final: 0.7140 (tmm) REVERT: A 799 SER cc_start: 0.8327 (p) cc_final: 0.8049 (p) REVERT: A 1020 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: A 1034 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7417 (p) REVERT: A 1051 TRP cc_start: 0.7232 (t-100) cc_final: 0.6288 (t60) REVERT: A 1175 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 82 LYS cc_start: 0.6859 (tptm) cc_final: 0.6367 (mttp) REVERT: B 102 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4689 (tt) REVERT: B 112 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5599 (m-10) REVERT: B 131 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6590 (tm-30) REVERT: B 140 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 157 LEU cc_start: 0.9054 (mp) cc_final: 0.8736 (mt) REVERT: B 210 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6595 (pt) REVERT: B 227 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8494 (tt) REVERT: B 365 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.8768 (mp10) REVERT: B 374 GLU cc_start: 0.8076 (tt0) cc_final: 0.7872 (mm-30) REVERT: B 429 ASP cc_start: 0.7317 (t0) cc_final: 0.7001 (t0) REVERT: B 457 MET cc_start: 0.4728 (mpt) cc_final: 0.4377 (mpp) REVERT: B 560 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: B 744 LEU cc_start: 0.6789 (pp) cc_final: 0.6335 (mt) REVERT: B 748 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6124 (mttt) REVERT: B 760 LEU cc_start: 0.6294 (tt) cc_final: 0.5924 (mm) REVERT: B 1020 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7868 (pp30) REVERT: C 83 ASP cc_start: 0.8605 (m-30) cc_final: 0.8277 (t0) outliers start: 69 outliers final: 42 residues processed: 299 average time/residue: 0.2702 time to fit residues: 126.9080 Evaluate side-chains 291 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 234 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5103 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= 0.180 Angle : 0.694 11.305 24039 Z= 0.336 Chirality : 0.044 0.403 2780 Planarity : 0.005 0.080 2984 Dihedral : 7.444 59.589 2970 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.08 % Favored : 89.87 % Rotamer: Outliers : 4.04 % Allowed : 22.00 % Favored : 73.96 % 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: 1.01 (0.16), residues: 1154 sheet: -1.04 (0.48), residues: 119 loop : -2.24 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 278 HIS 0.012 0.001 HIS A 328 PHE 0.021 0.001 PHE A 522 TYR 0.024 0.001 TYR A 224 ARG 0.006 0.000 ARG A 893 *********************** 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 305 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6306 (p90) REVERT: A 447 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7135 (tp) REVERT: A 550 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (tm) REVERT: A 587 MET cc_start: 0.7579 (ppp) cc_final: 0.7100 (tmm) REVERT: A 799 SER cc_start: 0.8314 (p) cc_final: 0.8037 (p) REVERT: A 843 MET cc_start: 0.8370 (ttp) cc_final: 0.8138 (ttp) REVERT: A 856 GLN cc_start: 0.6268 (tm-30) cc_final: 0.5833 (tm-30) REVERT: A 1020 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: A 1034 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7420 (p) REVERT: A 1051 TRP cc_start: 0.7150 (t-100) cc_final: 0.6246 (t60) REVERT: A 1071 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7663 (ptm) REVERT: A 1175 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 82 LYS cc_start: 0.6801 (tptm) cc_final: 0.6408 (mttt) REVERT: B 102 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.4657 (tt) REVERT: B 112 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5743 (m-10) REVERT: B 140 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 157 LEU cc_start: 0.9088 (mp) cc_final: 0.8780 (mt) REVERT: B 210 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6526 (pt) REVERT: B 365 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.8761 (mp10) REVERT: B 374 GLU cc_start: 0.8053 (tt0) cc_final: 0.7828 (mm-30) REVERT: B 429 ASP cc_start: 0.7318 (t0) cc_final: 0.6997 (t0) REVERT: B 457 MET cc_start: 0.4774 (mpt) cc_final: 0.4390 (mpp) REVERT: B 560 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7436 (m-10) REVERT: B 744 LEU cc_start: 0.6800 (pp) cc_final: 0.6317 (mt) REVERT: B 748 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6130 (mttt) REVERT: B 760 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6025 (mm) REVERT: B 1020 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7830 (pp30) REVERT: C 83 ASP cc_start: 0.8602 (m-30) cc_final: 0.8315 (t0) outliers start: 72 outliers final: 50 residues processed: 284 average time/residue: 0.2640 time to fit residues: 117.8343 Evaluate side-chains 291 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1079 SER Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain B residue 1165 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 0.0370 chunk 213 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 169 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 0.0670 chunk 134 optimal weight: 2.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5229 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= 0.177 Angle : 0.685 11.158 24039 Z= 0.329 Chirality : 0.044 0.410 2780 Planarity : 0.005 0.082 2984 Dihedral : 7.246 56.817 2970 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.31 % Favored : 89.64 % Rotamer: Outliers : 3.65 % Allowed : 22.39 % Favored : 73.96 % 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: -0.44 (0.19), residues: 2143 helix: 1.10 (0.16), residues: 1146 sheet: -1.03 (0.49), residues: 119 loop : -2.15 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 278 HIS 0.010 0.001 HIS B 358 PHE 0.021 0.001 PHE A 522 TYR 0.024 0.001 TYR A 224 ARG 0.005 0.000 ARG A 893 ********************** 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 301 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6296 (p90) REVERT: A 447 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7141 (tp) REVERT: A 550 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (tm) REVERT: A 799 SER cc_start: 0.8315 (p) cc_final: 0.8037 (p) REVERT: A 843 MET cc_start: 0.8434 (ttp) cc_final: 0.8229 (ttp) REVERT: A 856 GLN cc_start: 0.6234 (tm-30) cc_final: 0.5728 (tm-30) REVERT: A 1020 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: A 1034 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (p) REVERT: A 1051 TRP cc_start: 0.7203 (t-100) cc_final: 0.6215 (t60) REVERT: A 1071 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7643 (ptm) REVERT: A 1175 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8712 (mt) REVERT: B 82 LYS cc_start: 0.6802 (tptm) cc_final: 0.6403 (mttt) REVERT: B 102 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4667 (tt) REVERT: B 112 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5755 (m-10) REVERT: B 140 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 157 LEU cc_start: 0.9082 (mp) cc_final: 0.8784 (mt) REVERT: B 165 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6352 (tp30) REVERT: B 210 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6466 (pt) REVERT: B 429 ASP cc_start: 0.7390 (t0) cc_final: 0.6984 (t0) REVERT: B 560 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: B 603 ARG cc_start: 0.7808 (tpp80) cc_final: 0.6263 (mmm160) REVERT: B 744 LEU cc_start: 0.6833 (pp) cc_final: 0.6343 (mt) REVERT: B 748 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6195 (mttt) REVERT: B 1020 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7755 (pp30) REVERT: C 83 ASP cc_start: 0.8595 (m-30) cc_final: 0.8333 (t0) outliers start: 65 outliers final: 45 residues processed: 283 average time/residue: 0.2687 time to fit residues: 118.6680 Evaluate side-chains 279 residues out of total 1830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 560 PHE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain B residue 834 LEU Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1020 GLN Chi-restraints excluded: chain B residue 1071 MET Chi-restraints excluded: chain B residue 1164 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 98 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 170 optimal weight: 0.0030 chunk 71 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 149 optimal weight: 0.8980 overall best weight: 0.7510 ------------------------------------------------------------------------------- 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 576 GLN ** A1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117135 restraints weight = 29583.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120382 restraints weight = 17015.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121071 restraints weight = 11073.259| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5371 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= 0.172 Angle : 0.687 11.451 24039 Z= 0.330 Chirality : 0.044 0.405 2780 Planarity : 0.005 0.081 2984 Dihedral : 7.057 56.835 2970 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.03 % Favored : 89.92 % Rotamer: Outliers : 3.70 % Allowed : 22.95 % Favored : 73.34 % 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: 1.11 (0.16), residues: 1151 sheet: -1.00 (0.49), residues: 119 loop : -2.16 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 278 HIS 0.008 0.001 HIS A 328 PHE 0.022 0.001 PHE A 522 TYR 0.024 0.001 TYR A 224 ARG 0.006 0.000 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.21 seconds wall clock time: 65 minutes 47.26 seconds (3947.26 seconds total)