Starting phenix.real_space_refine on Mon Sep 14 15:46:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.map" model { file = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dm0_7960/09_2026/6dm0_7960.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 20017 2.51 5 N 5132 2.21 5 O 5770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31095 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7734 Classifications: {'peptide': 984} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 958} Chain breaks: 4 Chain: "B" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7734 Classifications: {'peptide': 984} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 958} Chain breaks: 4 Chain: "D" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CYZ': 1, 'GZD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.31, per 1000 atoms: 0.24 Number of scatterers: 31095 At special positions: 0 Unit cell: (115.56, 167.4, 198.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5770 8.00 N 5132 7.00 C 20017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.04 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 38 sheets defined 48.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.603A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.595A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.681A pdb=" N LYS A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.797A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.051A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 4.132A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.667A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 removed outlier: 4.052A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.664A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.598A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 4.199A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 4.034A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.876A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 removed outlier: 3.720A pdb=" N ASN A 791 " --> pdb=" O SER A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 788 through 791' Processing helix chain 'A' and resid 792 through 820 removed outlier: 4.119A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 4.304A pdb=" N LEU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1094 Processing helix chain 'A' and resid 1095 through 1102 Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.839A pdb=" N SER A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1160 removed outlier: 4.027A pdb=" N SER A1136 " --> pdb=" O ASN A1132 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1207 removed outlier: 3.514A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1195 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.961A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.625A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.585A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.955A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.677A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.679A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.727A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.553A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.580A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 617 removed outlier: 4.433A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.522A pdb=" N LEU B 624 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.946A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.591A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 793 through 817 Processing helix chain 'B' and resid 1007 through 1028 removed outlier: 3.578A pdb=" N LEU B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1103 Processing helix chain 'B' and resid 1104 through 1123 removed outlier: 3.808A pdb=" N ILE B1108 " --> pdb=" O SER B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1161 removed outlier: 4.215A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.781A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.608A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.592A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.679A pdb=" N LYS C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.802A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.945A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 4.137A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.665A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.824A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.652A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.608A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 624 removed outlier: 4.196A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 4.034A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.897A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 removed outlier: 3.709A pdb=" N ASN C 791 " --> pdb=" O SER C 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 788 through 791' Processing helix chain 'C' and resid 792 through 820 removed outlier: 4.125A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1028 removed outlier: 4.293A pdb=" N LEU C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1094 Processing helix chain 'C' and resid 1095 through 1102 Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.829A pdb=" N SER C1110 " --> pdb=" O PHE C1106 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1160 removed outlier: 4.003A pdb=" N SER C1136 " --> pdb=" O ASN C1132 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C1137 " --> pdb=" O ILE C1133 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C1138 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1207 removed outlier: 3.599A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C1195 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C1207 " --> pdb=" O ARG C1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.964A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.625A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.586A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.944A pdb=" N LYS D 172 " --> pdb=" O ASN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.666A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.667A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.714A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.557A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.580A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 617 removed outlier: 4.438A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.519A pdb=" N LEU D 624 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.911A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.577A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 793 through 817 Processing helix chain 'D' and resid 1007 through 1028 removed outlier: 3.578A pdb=" N LEU D1022 " --> pdb=" O ALA D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1103 Processing helix chain 'D' and resid 1104 through 1123 removed outlier: 3.797A pdb=" N ILE D1108 " --> pdb=" O SER D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 4.220A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D1154 " --> pdb=" O ILE D1150 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.759A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D1198 " --> pdb=" O VAL D1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 49 removed outlier: 3.806A pdb=" N ALA A 72 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.183A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 735 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.555A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 476 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 735 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.382A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.687A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A1077 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.456A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.312A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB5, first strand: chain 'B' and resid 395 through 399 removed outlier: 5.775A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB8, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.971A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.546A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1057 through 1060 removed outlier: 3.542A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 49 removed outlier: 3.786A pdb=" N ALA C 72 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.181A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC6, first strand: chain 'C' and resid 439 through 444 removed outlier: 3.542A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 735 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 439 through 444 removed outlier: 3.542A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 476 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 735 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.401A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.689A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C1077 " --> pdb=" O THR C1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.448A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.310A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD5, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AD6, first strand: chain 'D' and resid 395 through 399 removed outlier: 5.753A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AD9, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.005A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.568A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1057 through 1060 removed outlier: 3.548A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1482 hydrogen bonds defined for protein. 4320 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: 7.44 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 422 1.23 - 1.38: 11526 1.38 - 1.53: 18294 1.53 - 1.68: 1247 1.68 - 1.83: 280 Bond restraints: 31769 Sorted by residual: bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C4 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.64e+02 bond pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.64e+02 ... (remaining 31764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 42797 6.09 - 12.19: 119 12.19 - 18.28: 14 18.28 - 24.38: 0 24.38 - 30.47: 8 Bond angle restraints: 42938 Sorted by residual: angle pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C3 CYZ A1302 " ideal model delta sigma weight residual 106.92 137.39 -30.47 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.36 -30.44 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.34 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 137.34 -30.42 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 105.93 132.26 -26.33 3.00e+00 1.11e-01 7.70e+01 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17911 17.69 - 35.39: 671 35.39 - 53.08: 122 53.08 - 70.77: 12 70.77 - 88.47: 11 Dihedral angle restraints: 18727 sinusoidal: 7405 harmonic: 11322 Sorted by residual: dihedral pdb=" CA SER D 635 " pdb=" C SER D 635 " pdb=" N ALA D 636 " pdb=" CA ALA D 636 " ideal model delta harmonic sigma weight residual -180.00 -127.76 -52.24 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -127.86 -52.14 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLY A 313 " pdb=" C GLY A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual -180.00 -137.30 -42.70 0 5.00e+00 4.00e-02 7.29e+01 ... (remaining 18724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 4750 0.436 - 0.872: 8 0.872 - 1.308: 0 1.308 - 1.744: 0 1.744 - 2.180: 8 Chirality restraints: 4766 Sorted by residual: chirality pdb=" C5 CYZ C1302 " pdb=" C4 CYZ C1302 " pdb=" C6 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ A1302 " pdb=" C4 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ B1302 " pdb=" C4 CYZ B1302 " pdb=" C6 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.18e+02 ... (remaining 4763 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.062 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO A 99 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO C 99 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.057 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO B 99 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.047 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1875 2.73 - 3.27: 30915 3.27 - 3.81: 50180 3.81 - 4.36: 56935 4.36 - 4.90: 96111 Nonbonded interactions: 236016 Sorted by model distance: nonbonded pdb=" O ILE C1025 " pdb=" OG1 THR C1029 " model vdw 2.183 3.040 nonbonded pdb=" O ILE B1025 " pdb=" OG1 THR B1029 " model vdw 2.194 3.040 nonbonded pdb=" O ILE D1025 " pdb=" OG1 THR D1029 " model vdw 2.194 3.040 nonbonded pdb=" O GLU D 637 " pdb=" OG SER D 640 " model vdw 2.217 3.040 nonbonded pdb=" O GLU B 637 " pdb=" OG SER B 640 " model vdw 2.217 3.040 ... (remaining 236011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1302)) selection = (chain 'B' and (resid 10 through 549 or resid 565 through 1302)) selection = (chain 'C' and (resid 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1302)) selection = (chain 'D' and (resid 10 through 549 or resid 565 through 1302)) } 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.680 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.013 0.432 31785 Z= 0.633 Angle : 1.104 30.472 42970 Z= 0.558 Chirality : 0.103 2.180 4766 Planarity : 0.007 0.095 5384 Dihedral : 10.159 88.467 11451 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.39 % Favored : 91.20 % Rotamer: Outliers : 0.30 % Allowed : 3.96 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.11), residues: 3898 helix: -1.43 (0.10), residues: 1784 sheet: -2.14 (0.23), residues: 432 loop : -3.13 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 599 TYR 0.027 0.003 TYR B1031 PHE 0.022 0.003 PHE B 36 TRP 0.054 0.003 TRP A 578 HIS 0.011 0.002 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.01279 / 0.63 (31769) covalent geometry : angle 1.10435 / 0.56 (42938) SS BOND : bond 0.00502 / 0.33 ( 16) SS BOND : angle 1.20110 / 0.83 ( 32) hydrogen bonds : bond 0.12079 / 7.93 ( 1468) hydrogen bonds : angle 6.06298 / 4.17 ( 4320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 807 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8566 (mmp) cc_final: 0.8338 (mmp) REVERT: A 131 ASP cc_start: 0.8977 (p0) cc_final: 0.8559 (t0) REVERT: A 140 ASP cc_start: 0.9221 (m-30) cc_final: 0.8867 (p0) REVERT: A 249 ASP cc_start: 0.8925 (m-30) cc_final: 0.8651 (t0) REVERT: A 306 ILE cc_start: 0.7247 (pp) cc_final: 0.6681 (mm) REVERT: A 362 GLU cc_start: 0.9223 (tt0) cc_final: 0.8981 (tm-30) REVERT: A 408 MET cc_start: 0.9084 (mmm) cc_final: 0.8584 (tpp) REVERT: A 463 MET cc_start: 0.9305 (mtp) cc_final: 0.8968 (ttm) REVERT: A 518 LEU cc_start: 0.9666 (mt) cc_final: 0.9036 (tt) REVERT: A 569 ASN cc_start: 0.8335 (t0) cc_final: 0.8014 (t0) REVERT: A 605 TRP cc_start: 0.9409 (t-100) cc_final: 0.9157 (t-100) REVERT: A 670 MET cc_start: 0.9776 (mtp) cc_final: 0.9078 (mmm) REVERT: A 674 MET cc_start: 0.9370 (mtm) cc_final: 0.9090 (mtt) REVERT: A 713 GLU cc_start: 0.9023 (tt0) cc_final: 0.8652 (mm-30) REVERT: A 1012 THR cc_start: 0.8674 (t) cc_final: 0.8424 (p) REVERT: A 1023 MET cc_start: 0.9192 (tpp) cc_final: 0.8909 (ttm) REVERT: A 1036 ARG cc_start: 0.7628 (mtm180) cc_final: 0.6943 (tpt170) REVERT: A 1110 SER cc_start: 0.9047 (t) cc_final: 0.8668 (p) REVERT: A 1192 VAL cc_start: 0.9346 (t) cc_final: 0.8282 (t) REVERT: B 18 PHE cc_start: 0.8920 (m-80) cc_final: 0.8703 (m-80) REVERT: B 394 THR cc_start: 0.8126 (p) cc_final: 0.7809 (p) REVERT: B 405 TYR cc_start: 0.9504 (m-10) cc_final: 0.8957 (m-80) REVERT: B 407 MET cc_start: 0.8797 (mtm) cc_final: 0.8331 (mpp) REVERT: B 416 GLU cc_start: 0.8466 (tp30) cc_final: 0.7881 (mp0) REVERT: B 424 TYR cc_start: 0.9357 (t80) cc_final: 0.8888 (t80) REVERT: B 439 LYS cc_start: 0.9189 (mttt) cc_final: 0.8795 (mptt) REVERT: B 517 PHE cc_start: 0.9232 (p90) cc_final: 0.8859 (p90) REVERT: B 521 LEU cc_start: 0.9198 (mm) cc_final: 0.8867 (tp) REVERT: B 531 PHE cc_start: 0.9461 (m-10) cc_final: 0.9224 (m-80) REVERT: B 568 THR cc_start: 0.7814 (m) cc_final: 0.7505 (p) REVERT: B 585 MET cc_start: 0.8956 (mtm) cc_final: 0.8669 (mtm) REVERT: B 709 ASN cc_start: 0.9234 (t0) cc_final: 0.8928 (t0) REVERT: B 768 TYR cc_start: 0.9257 (m-10) cc_final: 0.8727 (m-80) REVERT: B 795 VAL cc_start: 0.9255 (t) cc_final: 0.8982 (t) REVERT: B 1097 LEU cc_start: 0.8703 (mm) cc_final: 0.8449 (tt) REVERT: B 1153 ILE cc_start: 0.9424 (mt) cc_final: 0.9200 (pt) REVERT: C 113 MET cc_start: 0.8552 (mmp) cc_final: 0.8309 (mmp) REVERT: C 131 ASP cc_start: 0.9009 (p0) cc_final: 0.8538 (t0) REVERT: C 140 ASP cc_start: 0.9198 (m-30) cc_final: 0.8839 (p0) REVERT: C 249 ASP cc_start: 0.8955 (m-30) cc_final: 0.8572 (t0) REVERT: C 306 ILE cc_start: 0.7386 (pp) cc_final: 0.6833 (mm) REVERT: C 362 GLU cc_start: 0.9204 (tt0) cc_final: 0.8989 (tm-30) REVERT: C 408 MET cc_start: 0.9062 (mmm) cc_final: 0.8555 (tpp) REVERT: C 463 MET cc_start: 0.9278 (mtp) cc_final: 0.8959 (ttm) REVERT: C 500 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9266 (tp) REVERT: C 518 LEU cc_start: 0.9677 (mt) cc_final: 0.9011 (tt) REVERT: C 569 ASN cc_start: 0.8426 (t0) cc_final: 0.8114 (t0) REVERT: C 605 TRP cc_start: 0.9401 (t-100) cc_final: 0.8944 (t-100) REVERT: C 670 MET cc_start: 0.9774 (mtp) cc_final: 0.9086 (mmm) REVERT: C 674 MET cc_start: 0.9359 (mtm) cc_final: 0.9089 (mtt) REVERT: C 713 GLU cc_start: 0.9058 (tt0) cc_final: 0.8687 (mm-30) REVERT: C 803 LEU cc_start: 0.9719 (mt) cc_final: 0.9497 (mt) REVERT: C 1012 THR cc_start: 0.8664 (t) cc_final: 0.8426 (p) REVERT: C 1036 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6997 (tpt170) REVERT: C 1110 SER cc_start: 0.9050 (t) cc_final: 0.8755 (p) REVERT: C 1116 MET cc_start: 0.8230 (tpt) cc_final: 0.7773 (tpt) REVERT: C 1192 VAL cc_start: 0.9359 (t) cc_final: 0.8235 (t) REVERT: D 18 PHE cc_start: 0.8965 (m-80) cc_final: 0.8762 (m-80) REVERT: D 206 ASP cc_start: 0.8690 (t70) cc_final: 0.8439 (m-30) REVERT: D 394 THR cc_start: 0.8061 (p) cc_final: 0.7826 (p) REVERT: D 405 TYR cc_start: 0.9499 (m-10) cc_final: 0.8958 (m-80) REVERT: D 407 MET cc_start: 0.8780 (mtm) cc_final: 0.8344 (mpp) REVERT: D 416 GLU cc_start: 0.8551 (tp30) cc_final: 0.8018 (pm20) REVERT: D 424 TYR cc_start: 0.9361 (t80) cc_final: 0.8916 (t80) REVERT: D 439 LYS cc_start: 0.9203 (mttt) cc_final: 0.8838 (mptt) REVERT: D 517 PHE cc_start: 0.9266 (p90) cc_final: 0.8976 (p90) REVERT: D 521 LEU cc_start: 0.9215 (mm) cc_final: 0.8849 (tp) REVERT: D 568 THR cc_start: 0.7895 (m) cc_final: 0.7485 (p) REVERT: D 569 ASN cc_start: 0.7594 (m-40) cc_final: 0.7185 (m110) REVERT: D 709 ASN cc_start: 0.9234 (t0) cc_final: 0.8984 (t0) REVERT: D 768 TYR cc_start: 0.9252 (m-10) cc_final: 0.8639 (m-80) REVERT: D 795 VAL cc_start: 0.9239 (t) cc_final: 0.8944 (t) REVERT: D 1097 LEU cc_start: 0.8631 (mm) cc_final: 0.8401 (tt) REVERT: D 1153 ILE cc_start: 0.9427 (mt) cc_final: 0.9167 (pt) outliers start: 10 outliers final: 2 residues processed: 814 average time/residue: 0.2015 time to fit residues: 258.3685 Evaluate side-chains 401 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN B 46 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 412 HIS B 747 ASN C 587 GLN C1206 GLN D 24 GLN D 46 HIS ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 412 HIS D 747 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.075200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058853 restraints weight = 165038.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060796 restraints weight = 96181.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062137 restraints weight = 66369.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063052 restraints weight = 51140.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063678 restraints weight = 42629.991| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31785 Z= 0.118 Angle : 0.613 10.445 42970 Z= 0.327 Chirality : 0.041 0.190 4766 Planarity : 0.005 0.075 5384 Dihedral : 6.071 74.631 4289 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3898 helix: 0.36 (0.12), residues: 1794 sheet: -1.80 (0.24), residues: 422 loop : -2.63 (0.13), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.014 0.001 TYR B1031 PHE 0.042 0.001 PHE C 574 TRP 0.038 0.002 TRP C 578 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (31769) covalent geometry : angle 0.61152 / 0.33 (42938) SS BOND : bond 0.00302 / 0.20 ( 16) SS BOND : angle 1.42265 / 0.94 ( 32) hydrogen bonds : bond 0.03759 / 2.46 ( 1468) hydrogen bonds : angle 4.67639 / 3.24 ( 4320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 537 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9373 (t80) cc_final: 0.8971 (t80) REVERT: A 113 MET cc_start: 0.8348 (mmp) cc_final: 0.7663 (mpp) REVERT: A 140 ASP cc_start: 0.9079 (m-30) cc_final: 0.8781 (p0) REVERT: A 189 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 249 ASP cc_start: 0.9057 (m-30) cc_final: 0.8657 (t0) REVERT: A 408 MET cc_start: 0.9014 (mmm) cc_final: 0.8599 (tpp) REVERT: A 463 MET cc_start: 0.9325 (mtp) cc_final: 0.8955 (ttm) REVERT: A 503 MET cc_start: 0.8118 (tpp) cc_final: 0.7850 (tpp) REVERT: A 569 ASN cc_start: 0.8631 (t0) cc_final: 0.8385 (t0) REVERT: A 610 LEU cc_start: 0.9628 (mt) cc_final: 0.8510 (mp) REVERT: A 670 MET cc_start: 0.9711 (mtp) cc_final: 0.9215 (mpp) REVERT: A 713 GLU cc_start: 0.8808 (tt0) cc_final: 0.8532 (mm-30) REVERT: A 807 MET cc_start: 0.9387 (ptp) cc_final: 0.9186 (ptp) REVERT: A 1023 MET cc_start: 0.9107 (tpp) cc_final: 0.8892 (ttp) REVERT: A 1109 LEU cc_start: 0.9072 (tt) cc_final: 0.8761 (tt) REVERT: A 1192 VAL cc_start: 0.9286 (t) cc_final: 0.8307 (t) REVERT: B 55 SER cc_start: 0.9682 (m) cc_final: 0.9372 (p) REVERT: B 133 PHE cc_start: 0.9205 (p90) cc_final: 0.8993 (p90) REVERT: B 247 ILE cc_start: 0.9566 (pt) cc_final: 0.9156 (tp) REVERT: B 405 TYR cc_start: 0.9430 (m-10) cc_final: 0.9116 (m-80) REVERT: B 414 MET cc_start: 0.8183 (ptp) cc_final: 0.7744 (ptp) REVERT: B 416 GLU cc_start: 0.8429 (tp30) cc_final: 0.7960 (mp0) REVERT: B 503 MET cc_start: 0.8549 (tmm) cc_final: 0.8210 (tmm) REVERT: B 517 PHE cc_start: 0.9163 (p90) cc_final: 0.8808 (p90) REVERT: B 521 LEU cc_start: 0.9178 (mm) cc_final: 0.8893 (tp) REVERT: B 674 MET cc_start: 0.8680 (mtm) cc_final: 0.8236 (mtp) REVERT: B 768 TYR cc_start: 0.9218 (m-10) cc_final: 0.8510 (m-80) REVERT: B 807 MET cc_start: 0.9456 (ptt) cc_final: 0.9216 (ppp) REVERT: B 1109 LEU cc_start: 0.8912 (tp) cc_final: 0.8684 (tp) REVERT: B 1159 ASN cc_start: 0.9146 (t0) cc_final: 0.8703 (m-40) REVERT: C 74 PHE cc_start: 0.9332 (t80) cc_final: 0.8943 (t80) REVERT: C 113 MET cc_start: 0.8339 (mmp) cc_final: 0.7626 (mpp) REVERT: C 140 ASP cc_start: 0.9105 (m-30) cc_final: 0.8795 (p0) REVERT: C 189 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 249 ASP cc_start: 0.9058 (m-30) cc_final: 0.8607 (t0) REVERT: C 408 MET cc_start: 0.8977 (mmm) cc_final: 0.8560 (tpp) REVERT: C 463 MET cc_start: 0.9312 (mtp) cc_final: 0.8936 (ttm) REVERT: C 503 MET cc_start: 0.8117 (tpp) cc_final: 0.7833 (tpp) REVERT: C 569 ASN cc_start: 0.8594 (t0) cc_final: 0.8350 (t0) REVERT: C 605 TRP cc_start: 0.9156 (t-100) cc_final: 0.8923 (t-100) REVERT: C 670 MET cc_start: 0.9711 (mtp) cc_final: 0.9202 (mpp) REVERT: C 713 GLU cc_start: 0.8830 (tt0) cc_final: 0.8558 (mm-30) REVERT: C 1023 MET cc_start: 0.9545 (mtt) cc_final: 0.9207 (ptm) REVERT: C 1036 ARG cc_start: 0.7361 (mtm180) cc_final: 0.6993 (tpt170) REVERT: C 1173 TYR cc_start: 0.8056 (p90) cc_final: 0.7834 (p90) REVERT: C 1192 VAL cc_start: 0.9268 (t) cc_final: 0.8258 (t) REVERT: D 55 SER cc_start: 0.9659 (m) cc_final: 0.9355 (p) REVERT: D 133 PHE cc_start: 0.9228 (p90) cc_final: 0.9004 (p90) REVERT: D 206 ASP cc_start: 0.8380 (t70) cc_final: 0.8120 (m-30) REVERT: D 247 ILE cc_start: 0.9556 (pt) cc_final: 0.9235 (tp) REVERT: D 405 TYR cc_start: 0.9419 (m-10) cc_final: 0.9101 (m-80) REVERT: D 414 MET cc_start: 0.7988 (ptp) cc_final: 0.7317 (ptp) REVERT: D 416 GLU cc_start: 0.8437 (tp30) cc_final: 0.8035 (pm20) REVERT: D 503 MET cc_start: 0.8541 (tmm) cc_final: 0.7978 (tmm) REVERT: D 517 PHE cc_start: 0.9179 (p90) cc_final: 0.8796 (p90) REVERT: D 521 LEU cc_start: 0.9129 (mm) cc_final: 0.8819 (tp) REVERT: D 585 MET cc_start: 0.8774 (mtp) cc_final: 0.8505 (mtp) REVERT: D 674 MET cc_start: 0.8702 (mtm) cc_final: 0.8287 (mtp) REVERT: D 721 MET cc_start: 0.8837 (tpt) cc_final: 0.8637 (ppp) REVERT: D 747 ASN cc_start: 0.9263 (m-40) cc_final: 0.8891 (m-40) REVERT: D 768 TYR cc_start: 0.9161 (m-10) cc_final: 0.8483 (m-80) REVERT: D 1109 LEU cc_start: 0.8913 (tp) cc_final: 0.8687 (tp) outliers start: 4 outliers final: 2 residues processed: 541 average time/residue: 0.1807 time to fit residues: 159.5790 Evaluate side-chains 373 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 747 ASN ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.072145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055791 restraints weight = 168096.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057599 restraints weight = 99374.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058850 restraints weight = 69435.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059708 restraints weight = 54008.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060295 restraints weight = 45250.402| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31785 Z= 0.140 Angle : 0.603 9.312 42970 Z= 0.319 Chirality : 0.040 0.167 4766 Planarity : 0.004 0.069 5384 Dihedral : 5.769 80.362 4289 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.62 % Favored : 93.12 % Rotamer: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3898 helix: 1.10 (0.12), residues: 1810 sheet: -1.58 (0.24), residues: 430 loop : -2.44 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.017 0.001 TYR D1031 PHE 0.029 0.001 PHE C 574 TRP 0.044 0.002 TRP C 578 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (31769) covalent geometry : angle 0.60175 / 0.32 (42938) SS BOND : bond 0.00358 / 0.24 ( 16) SS BOND : angle 1.57260 / 0.94 ( 32) hydrogen bonds : bond 0.03433 / 2.23 ( 1468) hydrogen bonds : angle 4.52059 / 3.13 ( 4320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 454 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9385 (t80) cc_final: 0.8935 (t80) REVERT: A 113 MET cc_start: 0.8487 (mmp) cc_final: 0.7675 (mpp) REVERT: A 249 ASP cc_start: 0.9117 (m-30) cc_final: 0.8804 (t0) REVERT: A 362 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 408 MET cc_start: 0.8958 (mmm) cc_final: 0.8726 (tpp) REVERT: A 414 MET cc_start: 0.9306 (tmm) cc_final: 0.9082 (tmm) REVERT: A 450 TYR cc_start: 0.7944 (m-80) cc_final: 0.7728 (m-80) REVERT: A 463 MET cc_start: 0.9270 (mtp) cc_final: 0.8839 (ttm) REVERT: A 503 MET cc_start: 0.7913 (tpp) cc_final: 0.7676 (tpp) REVERT: A 527 MET cc_start: 0.9291 (mtp) cc_final: 0.9015 (mtp) REVERT: A 569 ASN cc_start: 0.8619 (t0) cc_final: 0.8346 (t0) REVERT: A 610 LEU cc_start: 0.9580 (mt) cc_final: 0.8230 (mp) REVERT: A 670 MET cc_start: 0.9804 (mtp) cc_final: 0.9276 (mtp) REVERT: A 1109 LEU cc_start: 0.9088 (tt) cc_final: 0.8886 (tt) REVERT: A 1192 VAL cc_start: 0.9296 (t) cc_final: 0.8400 (t) REVERT: B 55 SER cc_start: 0.9687 (m) cc_final: 0.9378 (p) REVERT: B 247 ILE cc_start: 0.9562 (pt) cc_final: 0.9315 (tp) REVERT: B 405 TYR cc_start: 0.9374 (m-10) cc_final: 0.8992 (m-80) REVERT: B 414 MET cc_start: 0.8331 (ptp) cc_final: 0.8117 (ptp) REVERT: B 416 GLU cc_start: 0.8396 (tp30) cc_final: 0.7948 (mp0) REVERT: B 503 MET cc_start: 0.8633 (tmm) cc_final: 0.8046 (tmm) REVERT: B 517 PHE cc_start: 0.9151 (p90) cc_final: 0.8760 (p90) REVERT: B 620 LEU cc_start: 0.9065 (mt) cc_final: 0.8811 (tt) REVERT: B 674 MET cc_start: 0.8639 (mtm) cc_final: 0.8127 (mtt) REVERT: B 710 GLU cc_start: 0.8791 (pt0) cc_final: 0.8588 (tm-30) REVERT: B 721 MET cc_start: 0.9085 (tmm) cc_final: 0.8683 (ppp) REVERT: B 747 ASN cc_start: 0.9270 (m-40) cc_final: 0.8891 (m-40) REVERT: B 768 TYR cc_start: 0.9258 (m-10) cc_final: 0.8624 (m-80) REVERT: B 807 MET cc_start: 0.9409 (ptt) cc_final: 0.9141 (ppp) REVERT: B 1159 ASN cc_start: 0.9136 (t0) cc_final: 0.8678 (m-40) REVERT: C 74 PHE cc_start: 0.9384 (t80) cc_final: 0.8942 (t80) REVERT: C 113 MET cc_start: 0.8493 (mmp) cc_final: 0.7677 (mpp) REVERT: C 249 ASP cc_start: 0.9133 (m-30) cc_final: 0.8795 (t0) REVERT: C 408 MET cc_start: 0.8966 (mmm) cc_final: 0.8719 (tpp) REVERT: C 450 TYR cc_start: 0.7961 (m-80) cc_final: 0.7750 (m-80) REVERT: C 463 MET cc_start: 0.9273 (mtp) cc_final: 0.8829 (ttm) REVERT: C 503 MET cc_start: 0.8005 (tpp) cc_final: 0.7605 (tpp) REVERT: C 527 MET cc_start: 0.9222 (mtp) cc_final: 0.8967 (mtp) REVERT: C 569 ASN cc_start: 0.8637 (t0) cc_final: 0.8326 (t0) REVERT: C 590 ASP cc_start: 0.8381 (p0) cc_final: 0.8163 (p0) REVERT: C 670 MET cc_start: 0.9805 (mtp) cc_final: 0.9264 (mtp) REVERT: C 713 GLU cc_start: 0.8961 (tt0) cc_final: 0.8646 (mm-30) REVERT: C 1036 ARG cc_start: 0.7288 (mtm180) cc_final: 0.7017 (tpt170) REVERT: C 1173 TYR cc_start: 0.8261 (p90) cc_final: 0.8053 (p90) REVERT: C 1192 VAL cc_start: 0.9277 (t) cc_final: 0.8402 (t) REVERT: D 55 SER cc_start: 0.9672 (m) cc_final: 0.9366 (p) REVERT: D 247 ILE cc_start: 0.9570 (pt) cc_final: 0.9329 (tp) REVERT: D 405 TYR cc_start: 0.9363 (m-10) cc_final: 0.8953 (m-80) REVERT: D 414 MET cc_start: 0.8339 (ptp) cc_final: 0.7828 (ptp) REVERT: D 416 GLU cc_start: 0.8424 (tp30) cc_final: 0.8048 (pm20) REVERT: D 463 MET cc_start: 0.8480 (tpt) cc_final: 0.8157 (mmm) REVERT: D 503 MET cc_start: 0.8624 (tmm) cc_final: 0.8281 (tmm) REVERT: D 517 PHE cc_start: 0.9190 (p90) cc_final: 0.8811 (p90) REVERT: D 613 ILE cc_start: 0.9714 (pt) cc_final: 0.9511 (pt) REVERT: D 620 LEU cc_start: 0.9118 (mt) cc_final: 0.8847 (tt) REVERT: D 674 MET cc_start: 0.8713 (mtm) cc_final: 0.8276 (mtt) REVERT: D 747 ASN cc_start: 0.9365 (m-40) cc_final: 0.8744 (m110) REVERT: D 768 TYR cc_start: 0.9174 (m-10) cc_final: 0.8503 (m-80) REVERT: D 807 MET cc_start: 0.9447 (ppp) cc_final: 0.9222 (ppp) REVERT: D 1159 ASN cc_start: 0.9134 (t0) cc_final: 0.8747 (m-40) REVERT: D 1199 MET cc_start: 0.9168 (mmt) cc_final: 0.8921 (mtp) REVERT: D 1200 PHE cc_start: 0.9439 (t80) cc_final: 0.9076 (t80) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.1857 time to fit residues: 136.7264 Evaluate side-chains 328 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 224 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 354 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 791 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.071966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.055652 restraints weight = 167487.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057432 restraints weight = 99528.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058669 restraints weight = 69716.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059511 restraints weight = 54287.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060102 restraints weight = 45638.212| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31785 Z= 0.119 Angle : 0.565 8.637 42970 Z= 0.299 Chirality : 0.040 0.191 4766 Planarity : 0.004 0.056 5384 Dihedral : 5.558 80.390 4289 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.61 % Rotamer: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3898 helix: 1.50 (0.12), residues: 1808 sheet: -1.23 (0.24), residues: 458 loop : -2.35 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 331 TYR 0.019 0.001 TYR D1031 PHE 0.026 0.001 PHE C1115 TRP 0.022 0.001 TRP C1032 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (31769) covalent geometry : angle 0.56399 / 0.30 (42938) SS BOND : bond 0.00335 / 0.24 ( 16) SS BOND : angle 1.46163 / 0.91 ( 32) hydrogen bonds : bond 0.03174 / 2.06 ( 1468) hydrogen bonds : angle 4.33243 / 3.00 ( 4320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9383 (t80) cc_final: 0.8914 (t80) REVERT: A 113 MET cc_start: 0.8305 (mmp) cc_final: 0.7617 (mpp) REVERT: A 249 ASP cc_start: 0.9092 (m-30) cc_final: 0.8806 (t70) REVERT: A 414 MET cc_start: 0.9371 (tmm) cc_final: 0.9155 (tmm) REVERT: A 463 MET cc_start: 0.9318 (mtp) cc_final: 0.8937 (mmm) REVERT: A 569 ASN cc_start: 0.8589 (t0) cc_final: 0.8294 (t0) REVERT: A 670 MET cc_start: 0.9823 (mtp) cc_final: 0.9295 (mtp) REVERT: A 782 GLU cc_start: 0.8338 (pt0) cc_final: 0.7976 (pm20) REVERT: A 1023 MET cc_start: 0.9623 (mtt) cc_final: 0.9205 (ptt) REVERT: A 1115 PHE cc_start: 0.8799 (m-80) cc_final: 0.8481 (m-80) REVERT: A 1192 VAL cc_start: 0.9292 (t) cc_final: 0.8471 (t) REVERT: B 25 GLU cc_start: 0.8689 (mp0) cc_final: 0.8055 (tm-30) REVERT: B 55 SER cc_start: 0.9696 (m) cc_final: 0.9398 (p) REVERT: B 210 THR cc_start: 0.9325 (m) cc_final: 0.9098 (p) REVERT: B 405 TYR cc_start: 0.9415 (m-10) cc_final: 0.8730 (m-80) REVERT: B 406 VAL cc_start: 0.9468 (t) cc_final: 0.9185 (t) REVERT: B 416 GLU cc_start: 0.8425 (tp30) cc_final: 0.8039 (pm20) REVERT: B 503 MET cc_start: 0.8593 (tmm) cc_final: 0.8067 (tmm) REVERT: B 517 PHE cc_start: 0.9177 (p90) cc_final: 0.8797 (p90) REVERT: B 541 PHE cc_start: 0.8824 (t80) cc_final: 0.8551 (t80) REVERT: B 620 LEU cc_start: 0.9053 (mt) cc_final: 0.8850 (tt) REVERT: B 674 MET cc_start: 0.8758 (mtm) cc_final: 0.8387 (mtt) REVERT: B 708 MET cc_start: 0.9301 (mtp) cc_final: 0.8682 (mmm) REVERT: B 710 GLU cc_start: 0.8827 (pt0) cc_final: 0.8606 (tm-30) REVERT: B 721 MET cc_start: 0.9057 (tmm) cc_final: 0.8632 (ppp) REVERT: B 747 ASN cc_start: 0.9395 (m-40) cc_final: 0.8790 (m110) REVERT: B 768 TYR cc_start: 0.9182 (m-10) cc_final: 0.8579 (m-80) REVERT: B 807 MET cc_start: 0.9426 (ptt) cc_final: 0.9225 (ppp) REVERT: B 1114 LEU cc_start: 0.8977 (tp) cc_final: 0.8754 (tp) REVERT: B 1159 ASN cc_start: 0.9076 (t0) cc_final: 0.8623 (m-40) REVERT: C 74 PHE cc_start: 0.9374 (t80) cc_final: 0.8895 (t80) REVERT: C 113 MET cc_start: 0.8298 (mmp) cc_final: 0.7586 (mpp) REVERT: C 249 ASP cc_start: 0.9104 (m-30) cc_final: 0.8772 (t70) REVERT: C 414 MET cc_start: 0.9370 (tmm) cc_final: 0.9156 (tmm) REVERT: C 450 TYR cc_start: 0.8023 (m-80) cc_final: 0.7815 (m-80) REVERT: C 463 MET cc_start: 0.9272 (mtp) cc_final: 0.8941 (ttm) REVERT: C 518 LEU cc_start: 0.9618 (mt) cc_final: 0.9333 (mt) REVERT: C 569 ASN cc_start: 0.8597 (t0) cc_final: 0.8286 (t0) REVERT: C 670 MET cc_start: 0.9821 (mtp) cc_final: 0.9097 (mmt) REVERT: C 713 GLU cc_start: 0.8900 (tt0) cc_final: 0.8695 (tp30) REVERT: C 1023 MET cc_start: 0.9595 (mtt) cc_final: 0.9275 (mtm) REVERT: C 1115 PHE cc_start: 0.8742 (m-80) cc_final: 0.8435 (m-80) REVERT: C 1192 VAL cc_start: 0.9326 (t) cc_final: 0.8374 (t) REVERT: D 55 SER cc_start: 0.9669 (m) cc_final: 0.9342 (p) REVERT: D 405 TYR cc_start: 0.9375 (m-10) cc_final: 0.8989 (m-80) REVERT: D 406 VAL cc_start: 0.9413 (t) cc_final: 0.9110 (t) REVERT: D 416 GLU cc_start: 0.8530 (tp30) cc_final: 0.8219 (pm20) REVERT: D 463 MET cc_start: 0.8523 (tpt) cc_final: 0.8091 (mmm) REVERT: D 503 MET cc_start: 0.8531 (tmm) cc_final: 0.8063 (tmm) REVERT: D 517 PHE cc_start: 0.9231 (p90) cc_final: 0.8834 (p90) REVERT: D 620 LEU cc_start: 0.9074 (mt) cc_final: 0.8863 (tt) REVERT: D 674 MET cc_start: 0.8795 (mtm) cc_final: 0.8400 (mtt) REVERT: D 721 MET cc_start: 0.9067 (tmm) cc_final: 0.8699 (ppp) REVERT: D 747 ASN cc_start: 0.9396 (m-40) cc_final: 0.8887 (m-40) REVERT: D 768 TYR cc_start: 0.9182 (m-10) cc_final: 0.8483 (m-80) REVERT: D 807 MET cc_start: 0.9456 (ppp) cc_final: 0.9211 (ppp) REVERT: D 1159 ASN cc_start: 0.9112 (t0) cc_final: 0.8712 (m-40) REVERT: D 1200 PHE cc_start: 0.9470 (t80) cc_final: 0.9104 (t80) outliers start: 2 outliers final: 0 residues processed: 434 average time/residue: 0.1755 time to fit residues: 127.1104 Evaluate side-chains 326 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 263 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 381 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A1159 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.071490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055288 restraints weight = 165499.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057059 restraints weight = 97830.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058285 restraints weight = 68386.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059148 restraints weight = 53089.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059755 restraints weight = 44304.333| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31785 Z= 0.115 Angle : 0.556 8.304 42970 Z= 0.293 Chirality : 0.039 0.164 4766 Planarity : 0.004 0.056 5384 Dihedral : 5.438 81.790 4289 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.41 % Favored : 93.41 % Rotamer: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3898 helix: 1.72 (0.12), residues: 1798 sheet: -1.04 (0.24), residues: 428 loop : -2.30 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.021 0.001 TYR D1031 PHE 0.018 0.001 PHE D1200 TRP 0.021 0.001 TRP A1032 HIS 0.003 0.001 HIS A1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (31769) covalent geometry : angle 0.55486 / 0.29 (42938) SS BOND : bond 0.00557 / 0.34 ( 16) SS BOND : angle 1.57640 / 1.02 ( 32) hydrogen bonds : bond 0.03101 / 2.01 ( 1468) hydrogen bonds : angle 4.29324 / 2.97 ( 4320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9359 (t80) cc_final: 0.8867 (t80) REVERT: A 113 MET cc_start: 0.8291 (mmp) cc_final: 0.7618 (mpp) REVERT: A 414 MET cc_start: 0.9358 (tmm) cc_final: 0.9096 (tmm) REVERT: A 440 TYR cc_start: 0.8292 (p90) cc_final: 0.8064 (p90) REVERT: A 450 TYR cc_start: 0.8425 (m-80) cc_final: 0.8117 (m-80) REVERT: A 463 MET cc_start: 0.9321 (mtp) cc_final: 0.8957 (mmm) REVERT: A 503 MET cc_start: 0.8047 (tpp) cc_final: 0.7698 (tpp) REVERT: A 518 LEU cc_start: 0.9595 (mt) cc_final: 0.9319 (tp) REVERT: A 569 ASN cc_start: 0.8630 (t0) cc_final: 0.8345 (t0) REVERT: A 610 LEU cc_start: 0.9610 (mp) cc_final: 0.9241 (mp) REVERT: A 670 MET cc_start: 0.9832 (mtp) cc_final: 0.9289 (mtp) REVERT: A 782 GLU cc_start: 0.8370 (pt0) cc_final: 0.8142 (pm20) REVERT: A 1023 MET cc_start: 0.9602 (mtt) cc_final: 0.9256 (ptt) REVERT: A 1115 PHE cc_start: 0.8808 (m-80) cc_final: 0.8267 (m-80) REVERT: A 1116 MET cc_start: 0.9181 (mmp) cc_final: 0.8564 (tpt) REVERT: A 1192 VAL cc_start: 0.9336 (t) cc_final: 0.8471 (t) REVERT: B 25 GLU cc_start: 0.8718 (mp0) cc_final: 0.8092 (tm-30) REVERT: B 55 SER cc_start: 0.9706 (m) cc_final: 0.9403 (p) REVERT: B 210 THR cc_start: 0.9316 (m) cc_final: 0.9102 (p) REVERT: B 361 MET cc_start: 0.7423 (tpt) cc_final: 0.7154 (tpp) REVERT: B 405 TYR cc_start: 0.9300 (m-10) cc_final: 0.8882 (m-80) REVERT: B 406 VAL cc_start: 0.9418 (t) cc_final: 0.9173 (t) REVERT: B 414 MET cc_start: 0.8452 (ptp) cc_final: 0.7929 (ptp) REVERT: B 416 GLU cc_start: 0.8398 (tp30) cc_final: 0.8065 (pm20) REVERT: B 503 MET cc_start: 0.8491 (tmm) cc_final: 0.7978 (tmm) REVERT: B 517 PHE cc_start: 0.9189 (p90) cc_final: 0.8829 (p90) REVERT: B 585 MET cc_start: 0.9358 (mmp) cc_final: 0.9102 (mmp) REVERT: B 620 LEU cc_start: 0.9077 (mt) cc_final: 0.8837 (tt) REVERT: B 631 SER cc_start: 0.8736 (m) cc_final: 0.8274 (p) REVERT: B 674 MET cc_start: 0.8701 (mtm) cc_final: 0.8384 (mtt) REVERT: B 710 GLU cc_start: 0.8829 (pt0) cc_final: 0.8599 (tm-30) REVERT: B 721 MET cc_start: 0.9104 (tmm) cc_final: 0.8680 (ppp) REVERT: B 768 TYR cc_start: 0.9181 (m-10) cc_final: 0.8606 (m-80) REVERT: B 807 MET cc_start: 0.9442 (ptt) cc_final: 0.9237 (ppp) REVERT: B 1159 ASN cc_start: 0.9081 (t0) cc_final: 0.8838 (t0) REVERT: C 74 PHE cc_start: 0.9369 (t80) cc_final: 0.8888 (t80) REVERT: C 113 MET cc_start: 0.8291 (mmp) cc_final: 0.7598 (mpp) REVERT: C 196 CYS cc_start: 0.9067 (m) cc_final: 0.8798 (p) REVERT: C 201 VAL cc_start: 0.9422 (p) cc_final: 0.9123 (p) REVERT: C 414 MET cc_start: 0.9371 (tmm) cc_final: 0.9157 (tmm) REVERT: C 440 TYR cc_start: 0.8294 (p90) cc_final: 0.8063 (p90) REVERT: C 463 MET cc_start: 0.9281 (mtp) cc_final: 0.8779 (ttm) REVERT: C 503 MET cc_start: 0.8031 (tpp) cc_final: 0.7665 (tpp) REVERT: C 569 ASN cc_start: 0.8542 (t0) cc_final: 0.8234 (t0) REVERT: C 670 MET cc_start: 0.9818 (mtp) cc_final: 0.9351 (mtt) REVERT: C 713 GLU cc_start: 0.8949 (tt0) cc_final: 0.8737 (tp30) REVERT: C 782 GLU cc_start: 0.8365 (pt0) cc_final: 0.8088 (pm20) REVERT: C 1023 MET cc_start: 0.9569 (mtt) cc_final: 0.9164 (ptt) REVERT: C 1115 PHE cc_start: 0.8821 (m-80) cc_final: 0.8406 (m-80) REVERT: C 1192 VAL cc_start: 0.9228 (t) cc_final: 0.8343 (t) REVERT: D 25 GLU cc_start: 0.8694 (mp0) cc_final: 0.8075 (tm-30) REVERT: D 55 SER cc_start: 0.9716 (m) cc_final: 0.9415 (p) REVERT: D 195 ASP cc_start: 0.8567 (t0) cc_final: 0.8256 (t0) REVERT: D 405 TYR cc_start: 0.9278 (m-10) cc_final: 0.8850 (m-80) REVERT: D 406 VAL cc_start: 0.9418 (t) cc_final: 0.9116 (t) REVERT: D 414 MET cc_start: 0.8387 (ptp) cc_final: 0.7822 (ptp) REVERT: D 416 GLU cc_start: 0.8422 (tp30) cc_final: 0.8176 (pm20) REVERT: D 503 MET cc_start: 0.8502 (tmm) cc_final: 0.8013 (tmm) REVERT: D 517 PHE cc_start: 0.9224 (p90) cc_final: 0.8836 (p90) REVERT: D 586 GLN cc_start: 0.8062 (mp10) cc_final: 0.7808 (mp10) REVERT: D 620 LEU cc_start: 0.9067 (mt) cc_final: 0.8827 (tt) REVERT: D 674 MET cc_start: 0.8737 (mtm) cc_final: 0.8402 (mtt) REVERT: D 721 MET cc_start: 0.9131 (tmm) cc_final: 0.8701 (ppp) REVERT: D 768 TYR cc_start: 0.9167 (m-10) cc_final: 0.8478 (m-80) REVERT: D 807 MET cc_start: 0.9461 (ppp) cc_final: 0.9203 (ppp) REVERT: D 1159 ASN cc_start: 0.9067 (t0) cc_final: 0.8653 (m-40) REVERT: D 1200 PHE cc_start: 0.9414 (t80) cc_final: 0.8949 (t80) outliers start: 1 outliers final: 1 residues processed: 420 average time/residue: 0.1777 time to fit residues: 124.5955 Evaluate side-chains 314 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 388 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 333 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 747 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055600 restraints weight = 167615.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057380 restraints weight = 99771.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058620 restraints weight = 69986.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059471 restraints weight = 54534.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060071 restraints weight = 45788.836| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31785 Z= 0.106 Angle : 0.551 8.141 42970 Z= 0.288 Chirality : 0.040 0.215 4766 Planarity : 0.004 0.055 5384 Dihedral : 5.305 82.449 4289 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.05 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3898 helix: 1.71 (0.12), residues: 1826 sheet: -1.01 (0.24), residues: 428 loop : -2.18 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1203 TYR 0.019 0.001 TYR B1031 PHE 0.019 0.001 PHE C1115 TRP 0.018 0.001 TRP A1032 HIS 0.003 0.001 HIS A1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (31769) covalent geometry : angle 0.54959 / 0.29 (42938) SS BOND : bond 0.00334 / 0.22 ( 16) SS BOND : angle 1.51524 / 0.97 ( 32) hydrogen bonds : bond 0.02975 / 1.93 ( 1468) hydrogen bonds : angle 4.20655 / 2.90 ( 4320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9374 (t80) cc_final: 0.9122 (t80) REVERT: A 113 MET cc_start: 0.8257 (mmp) cc_final: 0.7521 (mpp) REVERT: A 414 MET cc_start: 0.9336 (tmm) cc_final: 0.9090 (tmm) REVERT: A 440 TYR cc_start: 0.8282 (p90) cc_final: 0.8049 (p90) REVERT: A 450 TYR cc_start: 0.8444 (m-80) cc_final: 0.8113 (m-80) REVERT: A 463 MET cc_start: 0.9338 (mtp) cc_final: 0.8965 (mmm) REVERT: A 503 MET cc_start: 0.8355 (tpp) cc_final: 0.7883 (tpp) REVERT: A 518 LEU cc_start: 0.9629 (mt) cc_final: 0.9398 (tp) REVERT: A 670 MET cc_start: 0.9832 (mtp) cc_final: 0.9416 (mtp) REVERT: A 674 MET cc_start: 0.9338 (mtm) cc_final: 0.9110 (ptp) REVERT: A 1023 MET cc_start: 0.9594 (mtt) cc_final: 0.9235 (ptt) REVERT: A 1115 PHE cc_start: 0.8831 (m-80) cc_final: 0.8244 (m-80) REVERT: A 1116 MET cc_start: 0.9194 (mmp) cc_final: 0.8562 (tpt) REVERT: A 1159 ASN cc_start: 0.8931 (t0) cc_final: 0.8681 (m110) REVERT: A 1192 VAL cc_start: 0.9257 (t) cc_final: 0.8422 (t) REVERT: B 25 GLU cc_start: 0.8723 (mp0) cc_final: 0.8142 (mp0) REVERT: B 133 PHE cc_start: 0.9221 (p90) cc_final: 0.9000 (p90) REVERT: B 210 THR cc_start: 0.9299 (m) cc_final: 0.9087 (p) REVERT: B 331 ARG cc_start: 0.9333 (ttt-90) cc_final: 0.9027 (mtt180) REVERT: B 405 TYR cc_start: 0.9325 (m-10) cc_final: 0.9034 (m-80) REVERT: B 406 VAL cc_start: 0.9380 (t) cc_final: 0.9150 (t) REVERT: B 414 MET cc_start: 0.8462 (ptp) cc_final: 0.7909 (ptp) REVERT: B 416 GLU cc_start: 0.8382 (tp30) cc_final: 0.8094 (pm20) REVERT: B 503 MET cc_start: 0.8476 (tmm) cc_final: 0.7985 (tmm) REVERT: B 517 PHE cc_start: 0.9178 (p90) cc_final: 0.8844 (p90) REVERT: B 620 LEU cc_start: 0.9057 (mt) cc_final: 0.8774 (tt) REVERT: B 631 SER cc_start: 0.8699 (m) cc_final: 0.8230 (p) REVERT: B 674 MET cc_start: 0.8686 (mtm) cc_final: 0.8364 (mtt) REVERT: B 710 GLU cc_start: 0.8819 (pt0) cc_final: 0.8571 (tm-30) REVERT: B 721 MET cc_start: 0.9108 (tmm) cc_final: 0.8703 (ppp) REVERT: B 747 ASN cc_start: 0.9262 (m-40) cc_final: 0.8913 (m-40) REVERT: B 768 TYR cc_start: 0.9195 (m-10) cc_final: 0.8587 (m-80) REVERT: B 807 MET cc_start: 0.9459 (ptt) cc_final: 0.9216 (ppp) REVERT: B 1159 ASN cc_start: 0.9070 (t0) cc_final: 0.8837 (t0) REVERT: C 74 PHE cc_start: 0.9376 (t80) cc_final: 0.9112 (t80) REVERT: C 113 MET cc_start: 0.8279 (mmp) cc_final: 0.7539 (mpp) REVERT: C 196 CYS cc_start: 0.9075 (m) cc_final: 0.8829 (p) REVERT: C 201 VAL cc_start: 0.9436 (p) cc_final: 0.9123 (p) REVERT: C 414 MET cc_start: 0.9378 (tmm) cc_final: 0.9087 (tmm) REVERT: C 440 TYR cc_start: 0.8325 (p90) cc_final: 0.8081 (p90) REVERT: C 463 MET cc_start: 0.9345 (mtp) cc_final: 0.8956 (mmm) REVERT: C 503 MET cc_start: 0.8020 (tpp) cc_final: 0.7794 (tpp) REVERT: C 518 LEU cc_start: 0.9602 (mt) cc_final: 0.9296 (tp) REVERT: C 670 MET cc_start: 0.9824 (mtp) cc_final: 0.9135 (mmt) REVERT: C 782 GLU cc_start: 0.8499 (pt0) cc_final: 0.8187 (pm20) REVERT: C 797 TYR cc_start: 0.8479 (m-80) cc_final: 0.8247 (m-80) REVERT: C 1023 MET cc_start: 0.9564 (mtt) cc_final: 0.9196 (ptt) REVERT: C 1115 PHE cc_start: 0.8843 (m-80) cc_final: 0.8424 (m-80) REVERT: C 1191 MET cc_start: 0.9083 (ppp) cc_final: 0.8871 (ppp) REVERT: C 1192 VAL cc_start: 0.9302 (t) cc_final: 0.8423 (t) REVERT: D 25 GLU cc_start: 0.8703 (mp0) cc_final: 0.8099 (mp0) REVERT: D 55 SER cc_start: 0.9719 (m) cc_final: 0.9423 (p) REVERT: D 195 ASP cc_start: 0.8582 (t0) cc_final: 0.8279 (t0) REVERT: D 405 TYR cc_start: 0.9288 (m-10) cc_final: 0.8990 (m-80) REVERT: D 406 VAL cc_start: 0.9337 (t) cc_final: 0.9122 (t) REVERT: D 414 MET cc_start: 0.8388 (ptp) cc_final: 0.8099 (ptp) REVERT: D 416 GLU cc_start: 0.8471 (tp30) cc_final: 0.8141 (pm20) REVERT: D 503 MET cc_start: 0.8484 (tmm) cc_final: 0.7998 (tmm) REVERT: D 517 PHE cc_start: 0.9222 (p90) cc_final: 0.8822 (p90) REVERT: D 586 GLN cc_start: 0.7977 (mp10) cc_final: 0.7764 (mp10) REVERT: D 620 LEU cc_start: 0.9048 (mt) cc_final: 0.8739 (tt) REVERT: D 674 MET cc_start: 0.8704 (mtm) cc_final: 0.8444 (mtt) REVERT: D 721 MET cc_start: 0.9150 (tmm) cc_final: 0.8739 (ppp) REVERT: D 747 ASN cc_start: 0.9268 (m-40) cc_final: 0.8921 (m-40) REVERT: D 768 TYR cc_start: 0.9130 (m-10) cc_final: 0.8485 (m-80) REVERT: D 807 MET cc_start: 0.9454 (ppp) cc_final: 0.9187 (ppp) REVERT: D 1159 ASN cc_start: 0.9069 (t0) cc_final: 0.8813 (t0) REVERT: D 1200 PHE cc_start: 0.9429 (t80) cc_final: 0.8993 (t80) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.1685 time to fit residues: 115.2741 Evaluate side-chains 314 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 95 optimal weight: 0.7980 chunk 264 optimal weight: 6.9990 chunk 94 optimal weight: 0.0010 chunk 368 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 379 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 GLN B 337 GLN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.072510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056064 restraints weight = 167971.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057889 restraints weight = 99669.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.059130 restraints weight = 69687.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059986 restraints weight = 54344.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060567 restraints weight = 45662.636| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31785 Z= 0.098 Angle : 0.545 8.243 42970 Z= 0.282 Chirality : 0.039 0.170 4766 Planarity : 0.004 0.053 5384 Dihedral : 5.202 80.658 4289 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3898 helix: 1.86 (0.13), residues: 1816 sheet: -0.89 (0.25), residues: 408 loop : -2.10 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 309 TYR 0.017 0.001 TYR D1031 PHE 0.015 0.001 PHE C1115 TRP 0.034 0.001 TRP A 578 HIS 0.003 0.001 HIS C1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (31769) covalent geometry : angle 0.54354 / 0.28 (42938) SS BOND : bond 0.00489 / 0.31 ( 16) SS BOND : angle 1.44307 / 0.92 ( 32) hydrogen bonds : bond 0.02778 / 1.80 ( 1468) hydrogen bonds : angle 4.07016 / 2.81 ( 4320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9395 (t80) cc_final: 0.9125 (t80) REVERT: A 113 MET cc_start: 0.8274 (mmp) cc_final: 0.7439 (mpp) REVERT: A 414 MET cc_start: 0.9375 (tmm) cc_final: 0.9172 (tmm) REVERT: A 440 TYR cc_start: 0.8292 (p90) cc_final: 0.8082 (p90) REVERT: A 450 TYR cc_start: 0.8557 (m-80) cc_final: 0.8168 (m-80) REVERT: A 463 MET cc_start: 0.9327 (mtp) cc_final: 0.8971 (mmm) REVERT: A 503 MET cc_start: 0.8097 (tpp) cc_final: 0.7878 (tpp) REVERT: A 518 LEU cc_start: 0.9616 (mt) cc_final: 0.9392 (tp) REVERT: A 670 MET cc_start: 0.9831 (mtp) cc_final: 0.9125 (mmt) REVERT: A 1023 MET cc_start: 0.9599 (mtt) cc_final: 0.9244 (ptt) REVERT: A 1115 PHE cc_start: 0.8871 (m-80) cc_final: 0.8255 (m-80) REVERT: A 1116 MET cc_start: 0.9178 (mmp) cc_final: 0.8630 (tpt) REVERT: A 1191 MET cc_start: 0.9115 (ppp) cc_final: 0.8909 (ppp) REVERT: A 1192 VAL cc_start: 0.9275 (t) cc_final: 0.8399 (t) REVERT: B 25 GLU cc_start: 0.8731 (mp0) cc_final: 0.8139 (mp0) REVERT: B 55 SER cc_start: 0.9729 (m) cc_final: 0.9446 (p) REVERT: B 133 PHE cc_start: 0.9192 (p90) cc_final: 0.8965 (p90) REVERT: B 195 ASP cc_start: 0.8627 (t0) cc_final: 0.8236 (t0) REVERT: B 210 THR cc_start: 0.9247 (m) cc_final: 0.9019 (p) REVERT: B 331 ARG cc_start: 0.9329 (ttt-90) cc_final: 0.9018 (mtt180) REVERT: B 414 MET cc_start: 0.8456 (ptp) cc_final: 0.8162 (ptp) REVERT: B 416 GLU cc_start: 0.8410 (tp30) cc_final: 0.8070 (pm20) REVERT: B 503 MET cc_start: 0.8313 (tmm) cc_final: 0.7916 (tmm) REVERT: B 517 PHE cc_start: 0.9152 (p90) cc_final: 0.8812 (p90) REVERT: B 581 LEU cc_start: 0.9490 (tp) cc_final: 0.9279 (tt) REVERT: B 614 SER cc_start: 0.9799 (m) cc_final: 0.9598 (p) REVERT: B 620 LEU cc_start: 0.9003 (mt) cc_final: 0.8761 (tp) REVERT: B 631 SER cc_start: 0.8635 (m) cc_final: 0.8190 (p) REVERT: B 670 MET cc_start: 0.9727 (mtp) cc_final: 0.9516 (mtp) REVERT: B 710 GLU cc_start: 0.8906 (pt0) cc_final: 0.8607 (tm-30) REVERT: B 768 TYR cc_start: 0.9168 (m-10) cc_final: 0.8595 (m-80) REVERT: B 807 MET cc_start: 0.9484 (ptt) cc_final: 0.9245 (ppp) REVERT: B 1159 ASN cc_start: 0.9092 (t0) cc_final: 0.8891 (t0) REVERT: C 74 PHE cc_start: 0.9413 (t80) cc_final: 0.9138 (t80) REVERT: C 113 MET cc_start: 0.8261 (mmp) cc_final: 0.7427 (mpp) REVERT: C 196 CYS cc_start: 0.9050 (m) cc_final: 0.8775 (p) REVERT: C 201 VAL cc_start: 0.9432 (p) cc_final: 0.9109 (p) REVERT: C 440 TYR cc_start: 0.8282 (p90) cc_final: 0.8067 (p90) REVERT: C 463 MET cc_start: 0.9288 (mtp) cc_final: 0.8916 (mmm) REVERT: C 518 LEU cc_start: 0.9608 (mt) cc_final: 0.9271 (tp) REVERT: C 527 MET cc_start: 0.9195 (mtp) cc_final: 0.7984 (mtp) REVERT: C 531 PHE cc_start: 0.9426 (m-10) cc_final: 0.9053 (m-80) REVERT: C 670 MET cc_start: 0.9825 (mtp) cc_final: 0.9121 (mmt) REVERT: C 721 MET cc_start: 0.8303 (ptt) cc_final: 0.7828 (ptt) REVERT: C 782 GLU cc_start: 0.8359 (pt0) cc_final: 0.7985 (pm20) REVERT: C 1023 MET cc_start: 0.9532 (mtt) cc_final: 0.9158 (ptt) REVERT: C 1115 PHE cc_start: 0.8852 (m-80) cc_final: 0.8243 (m-80) REVERT: C 1116 MET cc_start: 0.9227 (mmp) cc_final: 0.8668 (tpt) REVERT: C 1191 MET cc_start: 0.9082 (ppp) cc_final: 0.8866 (ppp) REVERT: C 1192 VAL cc_start: 0.9223 (t) cc_final: 0.8399 (t) REVERT: D 25 GLU cc_start: 0.8656 (mp0) cc_final: 0.8071 (mp0) REVERT: D 55 SER cc_start: 0.9718 (m) cc_final: 0.9431 (p) REVERT: D 195 ASP cc_start: 0.8542 (t0) cc_final: 0.8237 (t0) REVERT: D 331 ARG cc_start: 0.9338 (ttt-90) cc_final: 0.9031 (mtt180) REVERT: D 406 VAL cc_start: 0.9294 (t) cc_final: 0.9080 (t) REVERT: D 414 MET cc_start: 0.8358 (ptp) cc_final: 0.8048 (ptp) REVERT: D 416 GLU cc_start: 0.8565 (tp30) cc_final: 0.8148 (pm20) REVERT: D 503 MET cc_start: 0.8527 (tmm) cc_final: 0.8084 (tmm) REVERT: D 517 PHE cc_start: 0.9182 (p90) cc_final: 0.8836 (p90) REVERT: D 614 SER cc_start: 0.9795 (m) cc_final: 0.9592 (p) REVERT: D 620 LEU cc_start: 0.9013 (mt) cc_final: 0.8750 (tp) REVERT: D 631 SER cc_start: 0.8707 (m) cc_final: 0.8193 (p) REVERT: D 670 MET cc_start: 0.9711 (mtp) cc_final: 0.9494 (mtp) REVERT: D 674 MET cc_start: 0.8607 (mtm) cc_final: 0.8404 (mtt) REVERT: D 721 MET cc_start: 0.9167 (tmm) cc_final: 0.8835 (ppp) REVERT: D 768 TYR cc_start: 0.9114 (m-10) cc_final: 0.8477 (m-80) REVERT: D 807 MET cc_start: 0.9460 (ppp) cc_final: 0.9199 (ppp) REVERT: D 1159 ASN cc_start: 0.9029 (t0) cc_final: 0.8800 (t0) REVERT: D 1199 MET cc_start: 0.9201 (mmt) cc_final: 0.8997 (mtp) REVERT: D 1200 PHE cc_start: 0.9436 (t80) cc_final: 0.9066 (t80) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1634 time to fit residues: 113.9981 Evaluate side-chains 315 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 32 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 297 optimal weight: 0.0770 chunk 372 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN B 24 GLN B 337 GLN B 642 GLN B 709 ASN ** B1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.070382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054098 restraints weight = 169734.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055829 restraints weight = 101084.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057035 restraints weight = 71013.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057860 restraints weight = 55430.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058434 restraints weight = 46646.233| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31785 Z= 0.145 Angle : 0.593 8.222 42970 Z= 0.309 Chirality : 0.040 0.183 4766 Planarity : 0.004 0.055 5384 Dihedral : 5.374 85.278 4289 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3898 helix: 1.76 (0.12), residues: 1830 sheet: -0.92 (0.25), residues: 402 loop : -2.07 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 178 TYR 0.017 0.001 TYR B1031 PHE 0.016 0.001 PHE C1115 TRP 0.055 0.002 TRP A 578 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31769) covalent geometry : angle 0.59099 / 0.31 (42938) SS BOND : bond 0.00430 / 0.26 ( 16) SS BOND : angle 1.74294 / 1.14 ( 32) hydrogen bonds : bond 0.03194 / 2.07 ( 1468) hydrogen bonds : angle 4.31252 / 2.98 ( 4320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8327 (mmp) cc_final: 0.7475 (mpp) REVERT: A 414 MET cc_start: 0.9339 (tmm) cc_final: 0.9127 (tmm) REVERT: A 440 TYR cc_start: 0.8341 (p90) cc_final: 0.8138 (p90) REVERT: A 450 TYR cc_start: 0.8480 (m-80) cc_final: 0.7878 (m-80) REVERT: A 463 MET cc_start: 0.9320 (mtp) cc_final: 0.9030 (mtt) REVERT: A 670 MET cc_start: 0.9833 (mtp) cc_final: 0.9176 (mmt) REVERT: A 674 MET cc_start: 0.9333 (mtm) cc_final: 0.9112 (ptp) REVERT: A 1023 MET cc_start: 0.9598 (mtt) cc_final: 0.9241 (ptt) REVERT: A 1030 ASP cc_start: 0.7220 (p0) cc_final: 0.6977 (t70) REVERT: A 1115 PHE cc_start: 0.8846 (m-80) cc_final: 0.8212 (m-80) REVERT: A 1116 MET cc_start: 0.9211 (mmp) cc_final: 0.8656 (tpt) REVERT: A 1192 VAL cc_start: 0.9283 (t) cc_final: 0.8489 (t) REVERT: B 25 GLU cc_start: 0.8631 (mp0) cc_final: 0.7981 (mp0) REVERT: B 195 ASP cc_start: 0.8504 (t0) cc_final: 0.8201 (t0) REVERT: B 331 ARG cc_start: 0.9357 (ttt-90) cc_final: 0.9049 (mtm180) REVERT: B 406 VAL cc_start: 0.9278 (t) cc_final: 0.9077 (t) REVERT: B 416 GLU cc_start: 0.8575 (tp30) cc_final: 0.8146 (pm20) REVERT: B 453 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8955 (ptm-80) REVERT: B 503 MET cc_start: 0.8295 (tmm) cc_final: 0.7911 (tmm) REVERT: B 517 PHE cc_start: 0.9151 (p90) cc_final: 0.8943 (p90) REVERT: B 581 LEU cc_start: 0.9489 (tp) cc_final: 0.9251 (tt) REVERT: B 620 LEU cc_start: 0.9049 (mt) cc_final: 0.8775 (tp) REVERT: B 631 SER cc_start: 0.8706 (m) cc_final: 0.8282 (p) REVERT: B 710 GLU cc_start: 0.8887 (pt0) cc_final: 0.8545 (tm-30) REVERT: B 721 MET cc_start: 0.9013 (ppp) cc_final: 0.8739 (ppp) REVERT: B 768 TYR cc_start: 0.9227 (m-10) cc_final: 0.8740 (m-80) REVERT: C 113 MET cc_start: 0.8330 (mmp) cc_final: 0.7479 (mpp) REVERT: C 196 CYS cc_start: 0.9112 (m) cc_final: 0.8837 (p) REVERT: C 201 VAL cc_start: 0.9452 (p) cc_final: 0.9144 (p) REVERT: C 463 MET cc_start: 0.9340 (mtp) cc_final: 0.9063 (mtt) REVERT: C 518 LEU cc_start: 0.9594 (mt) cc_final: 0.9371 (tp) REVERT: C 670 MET cc_start: 0.9821 (mtp) cc_final: 0.9120 (mmt) REVERT: C 721 MET cc_start: 0.8499 (ptt) cc_final: 0.8012 (ptt) REVERT: C 1023 MET cc_start: 0.9549 (mtt) cc_final: 0.9165 (mtp) REVERT: C 1115 PHE cc_start: 0.8859 (m-80) cc_final: 0.8272 (m-80) REVERT: C 1116 MET cc_start: 0.9243 (mmp) cc_final: 0.8658 (tpt) REVERT: C 1191 MET cc_start: 0.9102 (ppp) cc_final: 0.8896 (ppp) REVERT: C 1192 VAL cc_start: 0.9303 (t) cc_final: 0.8414 (t) REVERT: D 25 GLU cc_start: 0.8650 (mp0) cc_final: 0.8061 (mp0) REVERT: D 195 ASP cc_start: 0.8511 (t0) cc_final: 0.8254 (t0) REVERT: D 331 ARG cc_start: 0.9385 (ttt-90) cc_final: 0.9083 (mtm180) REVERT: D 414 MET cc_start: 0.8482 (ptp) cc_final: 0.8165 (ptp) REVERT: D 416 GLU cc_start: 0.8571 (tp30) cc_final: 0.8143 (pm20) REVERT: D 503 MET cc_start: 0.8440 (tmm) cc_final: 0.8026 (tmm) REVERT: D 517 PHE cc_start: 0.9199 (p90) cc_final: 0.8960 (p90) REVERT: D 585 MET cc_start: 0.9385 (mmm) cc_final: 0.9109 (mmm) REVERT: D 620 LEU cc_start: 0.9061 (mt) cc_final: 0.8779 (tp) REVERT: D 631 SER cc_start: 0.8720 (m) cc_final: 0.8213 (p) REVERT: D 670 MET cc_start: 0.9686 (mtp) cc_final: 0.9458 (mtp) REVERT: D 674 MET cc_start: 0.8693 (mtm) cc_final: 0.8477 (mtt) REVERT: D 721 MET cc_start: 0.9239 (tmm) cc_final: 0.8927 (ppp) REVERT: D 768 TYR cc_start: 0.9171 (m-10) cc_final: 0.8553 (m-80) REVERT: D 807 MET cc_start: 0.9443 (ppp) cc_final: 0.9154 (ppp) REVERT: D 1200 PHE cc_start: 0.9440 (t80) cc_final: 0.9021 (t80) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1611 time to fit residues: 105.1287 Evaluate side-chains 303 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 75 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 158 optimal weight: 0.0050 chunk 345 optimal weight: 0.1980 chunk 359 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN B 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.071435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055206 restraints weight = 166871.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056956 restraints weight = 99065.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058158 restraints weight = 69545.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059009 restraints weight = 54356.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059578 restraints weight = 45583.605| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31785 Z= 0.103 Angle : 0.566 8.897 42970 Z= 0.291 Chirality : 0.040 0.178 4766 Planarity : 0.004 0.052 5384 Dihedral : 5.231 82.511 4289 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3898 helix: 1.90 (0.12), residues: 1826 sheet: -0.78 (0.27), residues: 368 loop : -1.96 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 599 TYR 0.020 0.001 TYR C1127 PHE 0.018 0.001 PHE D 541 TRP 0.044 0.001 TRP A 578 HIS 0.003 0.001 HIS A1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (31769) covalent geometry : angle 0.56414 / 0.29 (42938) SS BOND : bond 0.00475 / 0.29 ( 16) SS BOND : angle 1.81433 / 1.17 ( 32) hydrogen bonds : bond 0.02933 / 1.89 ( 1468) hydrogen bonds : angle 4.14705 / 2.84 ( 4320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9268 (t80) cc_final: 0.8914 (t80) REVERT: A 113 MET cc_start: 0.8259 (mmp) cc_final: 0.7388 (mpp) REVERT: A 363 LEU cc_start: 0.8937 (tp) cc_final: 0.8403 (tp) REVERT: A 450 TYR cc_start: 0.8471 (m-80) cc_final: 0.7984 (m-80) REVERT: A 463 MET cc_start: 0.9318 (mtp) cc_final: 0.9063 (mmm) REVERT: A 503 MET cc_start: 0.8318 (tpp) cc_final: 0.8089 (tpp) REVERT: A 670 MET cc_start: 0.9821 (mtp) cc_final: 0.9148 (mmt) REVERT: A 1023 MET cc_start: 0.9583 (mtt) cc_final: 0.9245 (ptt) REVERT: A 1115 PHE cc_start: 0.8868 (m-80) cc_final: 0.8228 (m-80) REVERT: A 1116 MET cc_start: 0.9181 (mmp) cc_final: 0.8622 (tpt) REVERT: A 1192 VAL cc_start: 0.9218 (t) cc_final: 0.8358 (t) REVERT: B 25 GLU cc_start: 0.8657 (mp0) cc_final: 0.8037 (mp0) REVERT: B 195 ASP cc_start: 0.8479 (t0) cc_final: 0.8126 (t0) REVERT: B 414 MET cc_start: 0.7685 (pmm) cc_final: 0.7067 (pmm) REVERT: B 416 GLU cc_start: 0.8590 (tp30) cc_final: 0.8206 (pm20) REVERT: B 503 MET cc_start: 0.8402 (tmm) cc_final: 0.8000 (tmm) REVERT: B 517 PHE cc_start: 0.9136 (p90) cc_final: 0.8920 (p90) REVERT: B 620 LEU cc_start: 0.9039 (mt) cc_final: 0.8768 (tp) REVERT: B 631 SER cc_start: 0.8617 (m) cc_final: 0.8238 (p) REVERT: B 710 GLU cc_start: 0.8864 (pt0) cc_final: 0.8577 (tm-30) REVERT: B 721 MET cc_start: 0.9017 (ppp) cc_final: 0.8720 (ppp) REVERT: B 768 TYR cc_start: 0.9184 (m-10) cc_final: 0.8690 (m-80) REVERT: C 74 PHE cc_start: 0.9262 (t80) cc_final: 0.8892 (t80) REVERT: C 113 MET cc_start: 0.8247 (mmp) cc_final: 0.7359 (mpp) REVERT: C 196 CYS cc_start: 0.9041 (m) cc_final: 0.8779 (p) REVERT: C 201 VAL cc_start: 0.9413 (p) cc_final: 0.9096 (p) REVERT: C 414 MET cc_start: 0.9318 (tmm) cc_final: 0.9044 (tmm) REVERT: C 450 TYR cc_start: 0.8445 (m-10) cc_final: 0.8023 (m-80) REVERT: C 463 MET cc_start: 0.9289 (mtp) cc_final: 0.8799 (ttm) REVERT: C 518 LEU cc_start: 0.9564 (mt) cc_final: 0.9312 (tp) REVERT: C 527 MET cc_start: 0.9314 (mtp) cc_final: 0.9042 (mtp) REVERT: C 610 LEU cc_start: 0.9654 (mm) cc_final: 0.9205 (mp) REVERT: C 670 MET cc_start: 0.9818 (mtp) cc_final: 0.9082 (mmt) REVERT: C 721 MET cc_start: 0.8494 (ptt) cc_final: 0.8034 (ptt) REVERT: C 1023 MET cc_start: 0.9534 (mtt) cc_final: 0.9188 (ptt) REVERT: C 1115 PHE cc_start: 0.8862 (m-80) cc_final: 0.8238 (m-80) REVERT: C 1116 MET cc_start: 0.9232 (mmp) cc_final: 0.8650 (tpt) REVERT: C 1191 MET cc_start: 0.9097 (ppp) cc_final: 0.8859 (ppp) REVERT: C 1192 VAL cc_start: 0.9216 (t) cc_final: 0.8375 (t) REVERT: D 25 GLU cc_start: 0.8653 (mp0) cc_final: 0.8044 (mp0) REVERT: D 196 CYS cc_start: 0.7563 (m) cc_final: 0.7352 (m) REVERT: D 331 ARG cc_start: 0.9345 (ttt-90) cc_final: 0.9051 (mtm180) REVERT: D 406 VAL cc_start: 0.9197 (t) cc_final: 0.8986 (t) REVERT: D 414 MET cc_start: 0.8364 (ptp) cc_final: 0.8027 (ptp) REVERT: D 416 GLU cc_start: 0.8598 (tp30) cc_final: 0.8200 (pm20) REVERT: D 503 MET cc_start: 0.8494 (tmm) cc_final: 0.8079 (tmm) REVERT: D 517 PHE cc_start: 0.9150 (p90) cc_final: 0.8932 (p90) REVERT: D 585 MET cc_start: 0.9333 (mmm) cc_final: 0.8991 (mmm) REVERT: D 620 LEU cc_start: 0.9056 (mt) cc_final: 0.8785 (tp) REVERT: D 631 SER cc_start: 0.8666 (m) cc_final: 0.8137 (p) REVERT: D 670 MET cc_start: 0.9680 (mtp) cc_final: 0.9477 (mtp) REVERT: D 674 MET cc_start: 0.8660 (mtm) cc_final: 0.8457 (mtt) REVERT: D 721 MET cc_start: 0.9174 (tmm) cc_final: 0.8907 (ppp) REVERT: D 768 TYR cc_start: 0.9140 (m-10) cc_final: 0.8587 (m-80) REVERT: D 807 MET cc_start: 0.9451 (ppp) cc_final: 0.9198 (ppp) REVERT: D 1200 PHE cc_start: 0.9431 (t80) cc_final: 0.9030 (t80) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1642 time to fit residues: 109.0500 Evaluate side-chains 302 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 156 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 chunk 264 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 66 optimal weight: 0.0030 chunk 138 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS B 337 GLN B 709 ASN B1159 ASN C 224 ASN C1204 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052671 restraints weight = 170022.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054426 restraints weight = 100131.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055623 restraints weight = 70143.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.056432 restraints weight = 54916.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057001 restraints weight = 46425.908| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31785 Z= 0.153 Angle : 0.614 8.969 42970 Z= 0.319 Chirality : 0.040 0.166 4766 Planarity : 0.004 0.065 5384 Dihedral : 5.345 86.617 4289 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3898 helix: 1.73 (0.12), residues: 1826 sheet: -0.84 (0.26), residues: 382 loop : -2.00 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 369 TYR 0.017 0.001 TYR B1031 PHE 0.018 0.001 PHE A1115 TRP 0.043 0.002 TRP A 578 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (31769) covalent geometry : angle 0.61209 / 0.32 (42938) SS BOND : bond 0.00517 / 0.30 ( 16) SS BOND : angle 1.70684 / 1.10 ( 32) hydrogen bonds : bond 0.03386 / 2.20 ( 1468) hydrogen bonds : angle 4.37483 / 3.01 ( 4320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7796 Ramachandran restraints generated. 3898 Oldfield, 0 Emsley, 3898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.9299 (t80) cc_final: 0.8899 (t80) REVERT: A 113 MET cc_start: 0.8437 (mmp) cc_final: 0.7473 (mpp) REVERT: A 414 MET cc_start: 0.9373 (tmm) cc_final: 0.9168 (tmm) REVERT: A 450 TYR cc_start: 0.8521 (m-80) cc_final: 0.7854 (m-80) REVERT: A 463 MET cc_start: 0.9330 (mtp) cc_final: 0.9056 (mtt) REVERT: A 610 LEU cc_start: 0.9674 (mp) cc_final: 0.9467 (mp) REVERT: A 670 MET cc_start: 0.9833 (mtp) cc_final: 0.9198 (mmt) REVERT: A 1023 MET cc_start: 0.9602 (mtt) cc_final: 0.9239 (ptt) REVERT: A 1116 MET cc_start: 0.9254 (mmp) cc_final: 0.8863 (tpt) REVERT: A 1140 PHE cc_start: 0.8077 (m-80) cc_final: 0.7860 (m-80) REVERT: A 1191 MET cc_start: 0.9155 (ppp) cc_final: 0.8950 (ppp) REVERT: A 1192 VAL cc_start: 0.9279 (t) cc_final: 0.8480 (t) REVERT: B 195 ASP cc_start: 0.8668 (t0) cc_final: 0.8317 (t0) REVERT: B 331 ARG cc_start: 0.9406 (ttt-90) cc_final: 0.9085 (mtm180) REVERT: B 414 MET cc_start: 0.7897 (pmm) cc_final: 0.7533 (pmm) REVERT: B 416 GLU cc_start: 0.8563 (tp30) cc_final: 0.8173 (pm20) REVERT: B 503 MET cc_start: 0.8390 (tmm) cc_final: 0.7996 (tmm) REVERT: B 620 LEU cc_start: 0.9104 (mt) cc_final: 0.8830 (tp) REVERT: B 629 MET cc_start: 0.7070 (mmm) cc_final: 0.6784 (mmm) REVERT: B 631 SER cc_start: 0.8719 (m) cc_final: 0.8325 (p) REVERT: B 710 GLU cc_start: 0.8907 (pt0) cc_final: 0.8557 (tm-30) REVERT: B 721 MET cc_start: 0.9065 (ppp) cc_final: 0.8817 (ppp) REVERT: B 768 TYR cc_start: 0.9282 (m-10) cc_final: 0.8803 (m-80) REVERT: C 74 PHE cc_start: 0.9283 (t80) cc_final: 0.8893 (t80) REVERT: C 113 MET cc_start: 0.8497 (mmp) cc_final: 0.7499 (mpp) REVERT: C 196 CYS cc_start: 0.9091 (m) cc_final: 0.8833 (p) REVERT: C 201 VAL cc_start: 0.9494 (p) cc_final: 0.9186 (p) REVERT: C 414 MET cc_start: 0.9390 (tmm) cc_final: 0.9100 (tmm) REVERT: C 463 MET cc_start: 0.9355 (mtp) cc_final: 0.9071 (mtt) REVERT: C 610 LEU cc_start: 0.9718 (mm) cc_final: 0.9173 (mp) REVERT: C 670 MET cc_start: 0.9835 (mtp) cc_final: 0.9191 (mmt) REVERT: C 721 MET cc_start: 0.8503 (ptt) cc_final: 0.8069 (ptt) REVERT: C 1023 MET cc_start: 0.9552 (mtt) cc_final: 0.9176 (ptt) REVERT: C 1115 PHE cc_start: 0.8881 (m-80) cc_final: 0.8432 (m-80) REVERT: C 1191 MET cc_start: 0.9087 (ppp) cc_final: 0.8880 (ppp) REVERT: C 1192 VAL cc_start: 0.9293 (t) cc_final: 0.8385 (t) REVERT: C 1199 MET cc_start: 0.9396 (mmp) cc_final: 0.9187 (mmm) REVERT: D 331 ARG cc_start: 0.9437 (ttt-90) cc_final: 0.9102 (mtm180) REVERT: D 406 VAL cc_start: 0.9322 (t) cc_final: 0.9112 (t) REVERT: D 414 MET cc_start: 0.8531 (ptp) cc_final: 0.7992 (ptp) REVERT: D 416 GLU cc_start: 0.8524 (tp30) cc_final: 0.8208 (pm20) REVERT: D 503 MET cc_start: 0.8419 (tmm) cc_final: 0.7969 (tmm) REVERT: D 585 MET cc_start: 0.9483 (mmm) cc_final: 0.8851 (mmm) REVERT: D 620 LEU cc_start: 0.9098 (mt) cc_final: 0.8855 (tp) REVERT: D 631 SER cc_start: 0.8766 (m) cc_final: 0.8255 (p) REVERT: D 670 MET cc_start: 0.9695 (mtp) cc_final: 0.9449 (mtp) REVERT: D 674 MET cc_start: 0.8800 (mtm) cc_final: 0.8559 (mtt) REVERT: D 721 MET cc_start: 0.9235 (tmm) cc_final: 0.8925 (ppp) REVERT: D 768 TYR cc_start: 0.9276 (m-10) cc_final: 0.8625 (m-80) REVERT: D 807 MET cc_start: 0.9442 (ppp) cc_final: 0.9177 (ppp) REVERT: D 1200 PHE cc_start: 0.9511 (t80) cc_final: 0.9010 (t80) outliers start: 2 outliers final: 2 residues processed: 366 average time/residue: 0.1747 time to fit residues: 110.0594 Evaluate side-chains 291 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 339 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 152 optimal weight: 0.4980 chunk 248 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN B 709 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052855 restraints weight = 167086.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054600 restraints weight = 98603.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055808 restraints weight = 69106.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056631 restraints weight = 53856.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057219 restraints weight = 45301.952| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31785 Z= 0.129 Angle : 0.593 9.087 42970 Z= 0.307 Chirality : 0.040 0.165 4766 Planarity : 0.004 0.059 5384 Dihedral : 5.313 85.509 4289 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3898 helix: 1.76 (0.12), residues: 1842 sheet: -0.84 (0.27), residues: 382 loop : -1.94 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 369 TYR 0.017 0.001 TYR C1127 PHE 0.015 0.001 PHE C1115 TRP 0.040 0.002 TRP A 578 HIS 0.002 0.001 HIS B1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (31769) covalent geometry : angle 0.59146 / 0.31 (42938) SS BOND : bond 0.00489 / 0.30 ( 16) SS BOND : angle 1.66027 / 1.08 ( 32) hydrogen bonds : bond 0.03205 / 2.07 ( 1468) hydrogen bonds : angle 4.31147 / 2.96 ( 4320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4955.50 seconds wall clock time: 86 minutes 45.04 seconds (5205.04 seconds total)