Starting phenix.real_space_refine on Mon Aug 25 23:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961.map" model { file = "/net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dm1_7961/08_2025/6dm1_7961_neut_trim.cif" } resolution = 4.2 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 20018 2.51 5 N 5133 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 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31097 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7730 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 957} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CYZ': 1, 'GYY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.45, per 1000 atoms: 0.21 Number of scatterers: 31097 At special positions: 0 Unit cell: (115.56, 167.4, 199.8, 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 5133 7.00 C 20018 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=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 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=2.03 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: 2.14 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 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: 132 helices and 40 sheets defined 48.2% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 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: 3.691A 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: 3.585A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.940A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.108A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 4.223A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.674A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.781A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.527A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.784A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 4.325A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.804A 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: 3.530A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.074A 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: 3.922A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.864A 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: 3.849A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 4.295A 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: 3.805A pdb=" N SER A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1160 removed outlier: 3.936A pdb=" N SER A1136 " --> pdb=" O ASN A1132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1207 removed outlier: 3.584A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1195 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.902A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 4.157A 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: 3.712A 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: 3.815A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.829A 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: 3.614A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.576A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.595A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.768A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 617 removed outlier: 4.483A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 6.263A pdb=" N ALA B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.547A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.936A 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: 3.628A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.628A 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: 3.673A pdb=" N ILE B1108 " --> pdb=" O SER B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 4.161A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.740A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.694A 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: 3.581A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.944A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.978A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 4.234A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.674A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.780A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.516A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.788A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 624 removed outlier: 4.322A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.807A 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: 3.543A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.955A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.861A 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: 3.862A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1028 removed outlier: 4.288A 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: 3.793A pdb=" N SER C1110 " --> pdb=" O PHE C1106 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C1112 " --> pdb=" O ILE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1160 removed outlier: 3.924A pdb=" N SER C1136 " --> pdb=" O ASN C1132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C1137 " --> pdb=" O ILE C1133 " (cutoff:3.500A) removed outlier: 3.637A 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: 4.034A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1207 removed outlier: 3.560A pdb=" N GLY C1182 " --> pdb=" O SER C1178 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C1195 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C1207 " --> pdb=" O ARG C1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.907A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 4.153A 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: 3.711A 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: 3.583A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.819A 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: 3.601A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.552A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.595A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.768A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 617 removed outlier: 4.486A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 removed outlier: 6.265A pdb=" N ALA D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.539A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.897A 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: 3.605A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.715A 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: 3.630A 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: 3.666A pdb=" N ILE D1108 " --> pdb=" O SER D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1160 removed outlier: 4.165A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D1154 " --> pdb=" O ILE D1150 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.725A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.742A 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: 8.754A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.438A 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: 6.572A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.562A 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 394 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.687A pdb=" N ALA A 735 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.687A pdb=" N ALA A 735 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.376A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 49 removed outlier: 8.902A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 164 removed outlier: 6.824A pdb=" N PHE B 133 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 399 removed outlier: 5.816A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.954A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.454A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1057 through 1060 removed outlier: 3.598A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 49 removed outlier: 8.732A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 164 removed outlier: 6.579A pdb=" N PHE C 133 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 135 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC6, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'C' and resid 394 through 399 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 475 through 480 removed outlier: 3.687A pdb=" N ALA C 735 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 475 through 480 removed outlier: 3.687A pdb=" N ALA C 735 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.411A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.575A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 42 through 49 removed outlier: 8.913A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 164 removed outlier: 6.823A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD7, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AD8, first strand: chain 'D' and resid 395 through 397 removed outlier: 5.800A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE2, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.981A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.480A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1057 through 1060 removed outlier: 3.602A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1436 hydrogen bonds defined for protein. 4152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.87 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: 545 1.23 - 1.38: 11831 1.38 - 1.53: 18315 1.53 - 1.69: 799 1.69 - 1.84: 280 Bond restraints: 31770 Sorted by residual: bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.079 0.433 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C4 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.67e+02 bond pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.66e+02 bond pdb=" C4 CYZ A1302 " pdb=" C5 CYZ A1302 " ideal model delta sigma weight residual 1.512 1.081 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 31765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.19: 42787 6.19 - 12.37: 123 12.37 - 18.56: 14 18.56 - 24.74: 0 24.74 - 30.93: 8 Bond angle restraints: 42932 Sorted by residual: angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.85 -30.93 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.77 -30.85 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 137.71 -30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C3 CYZ A1302 " ideal model delta sigma weight residual 106.92 137.66 -30.74 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 105.93 132.25 -26.32 3.00e+00 1.11e-01 7.70e+01 ... (remaining 42927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.06: 18342 24.06 - 48.12: 444 48.12 - 72.19: 18 72.19 - 96.25: 16 96.25 - 120.31: 9 Dihedral angle restraints: 18829 sinusoidal: 7508 harmonic: 11321 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 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+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 -125.17 -54.83 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA PRO C 632 " pdb=" C PRO C 632 " pdb=" N ILE C 633 " pdb=" CA ILE C 633 " ideal model delta harmonic sigma weight residual -180.00 -135.68 -44.32 0 5.00e+00 4.00e-02 7.86e+01 ... (remaining 18826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 4748 0.436 - 0.872: 6 0.872 - 1.308: 0 1.308 - 1.744: 0 1.744 - 2.180: 8 Chirality restraints: 4762 Sorted by residual: 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 1.19e+02 chirality pdb=" C5 CYZ D1302 " pdb=" C4 CYZ D1302 " pdb=" C6 CYZ D1302 " pdb=" C7 CYZ D1302 " 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 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 1.18e+02 ... (remaining 4759 not shown) Planarity restraints: 5385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO C 99 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO A 99 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 99 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.043 5.00e-02 4.00e+02 ... (remaining 5382 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1661 2.72 - 3.26: 30554 3.26 - 3.81: 49686 3.81 - 4.35: 57059 4.35 - 4.90: 96544 Nonbonded interactions: 235504 Sorted by model distance: nonbonded pdb=" O ILE C1025 " pdb=" OG1 THR C1029 " model vdw 2.171 3.040 nonbonded pdb=" O ILE A1025 " pdb=" OG1 THR A1029 " model vdw 2.212 3.040 nonbonded pdb=" O ALA D1026 " pdb=" OG SER D1178 " model vdw 2.227 3.040 nonbonded pdb=" O ALA B1026 " pdb=" OG SER B1178 " model vdw 2.231 3.040 nonbonded pdb=" O GLU B 637 " pdb=" OG SER B 640 " model vdw 2.236 3.040 ... (remaining 235499 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 1208 or resid 1301 thr \ ough 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 1208 or resid 1301 through 1302)) selection = (chain 'D' and (resid 10 through 549 or resid 565 through 1208 or resid 1301 thr \ ough 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: 1.570 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.200 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 0.433 31786 Z= 0.650 Angle : 1.192 30.927 42964 Z= 0.642 Chirality : 0.104 2.180 4762 Planarity : 0.007 0.093 5385 Dihedral : 11.073 120.312 11553 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.42 % Favored : 91.17 % Rotamer: Outliers : 0.60 % Allowed : 3.93 % Favored : 95.47 % 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 aren not related in a simple way. whole: -3.78 (0.11), residues: 3897 helix: -1.99 (0.09), residues: 1788 sheet: -2.05 (0.24), residues: 410 loop : -3.17 (0.12), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 599 TYR 0.024 0.003 TYR A1031 PHE 0.023 0.003 PHE C1106 TRP 0.044 0.003 TRP A 578 HIS 0.011 0.002 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.01323 (31770) covalent geometry : angle 1.19215 (42932) SS BOND : bond 0.00451 ( 16) SS BOND : angle 1.17642 ( 32) hydrogen bonds : bond 0.14510 ( 1434) hydrogen bonds : angle 6.14731 ( 4152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 796 time to evaluate : 0.769 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: A 113 MET cc_start: 0.8951 (mmp) cc_final: 0.8696 (mmp) REVERT: A 189 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 304 ILE cc_start: 0.7994 (mt) cc_final: 0.7748 (pt) REVERT: A 483 LEU cc_start: 0.9195 (tp) cc_final: 0.8907 (tt) REVERT: A 533 TYR cc_start: 0.9124 (t80) cc_final: 0.8792 (t80) REVERT: A 1112 ILE cc_start: 0.8346 (mm) cc_final: 0.7742 (mt) REVERT: A 1141 PHE cc_start: 0.8913 (m-80) cc_final: 0.8692 (m-80) REVERT: A 1149 ILE cc_start: 0.9051 (tt) cc_final: 0.8806 (tp) REVERT: A 1181 PHE cc_start: 0.7945 (m-10) cc_final: 0.7707 (m-80) REVERT: A 1191 MET cc_start: 0.7775 (tpt) cc_final: 0.7457 (tpt) REVERT: A 1205 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8196 (tptt) REVERT: B 50 LEU cc_start: 0.8522 (mp) cc_final: 0.8316 (pt) REVERT: B 113 MET cc_start: 0.9235 (mmp) cc_final: 0.8853 (mmm) REVERT: B 184 LEU cc_start: 0.9467 (mt) cc_final: 0.9094 (mp) REVERT: B 384 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8353 (pp20) REVERT: B 463 MET cc_start: 0.8772 (mtp) cc_final: 0.8350 (ptp) REVERT: B 496 MET cc_start: 0.8995 (ttp) cc_final: 0.8517 (tmm) REVERT: B 509 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7563 (mttp) REVERT: B 670 MET cc_start: 0.9452 (mtp) cc_final: 0.8922 (mtp) REVERT: B 796 PHE cc_start: 0.9118 (m-80) cc_final: 0.8520 (m-80) REVERT: B 1091 ASP cc_start: 0.6355 (m-30) cc_final: 0.5820 (t0) REVERT: B 1106 PHE cc_start: 0.8685 (m-80) cc_final: 0.8485 (m-80) REVERT: B 1199 MET cc_start: 0.8627 (mmm) cc_final: 0.8307 (mmt) REVERT: C 304 ILE cc_start: 0.7988 (mt) cc_final: 0.7766 (pt) REVERT: C 463 MET cc_start: 0.8978 (mtp) cc_final: 0.8590 (mmm) REVERT: C 483 LEU cc_start: 0.9182 (tp) cc_final: 0.8763 (tp) REVERT: C 533 TYR cc_start: 0.9140 (t80) cc_final: 0.8771 (t80) REVERT: C 1112 ILE cc_start: 0.8404 (mm) cc_final: 0.7780 (mt) REVERT: C 1149 ILE cc_start: 0.9087 (tt) cc_final: 0.8863 (tp) REVERT: C 1181 PHE cc_start: 0.7982 (m-10) cc_final: 0.7755 (m-80) REVERT: C 1191 MET cc_start: 0.7774 (tpt) cc_final: 0.7400 (tpt) REVERT: C 1205 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8146 (tptt) REVERT: D 50 LEU cc_start: 0.8553 (mp) cc_final: 0.8342 (pt) REVERT: D 113 MET cc_start: 0.9220 (mmp) cc_final: 0.8855 (mmm) REVERT: D 184 LEU cc_start: 0.9472 (mt) cc_final: 0.9097 (mp) REVERT: D 384 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8404 (pp20) REVERT: D 463 MET cc_start: 0.8737 (mtp) cc_final: 0.8386 (mmm) REVERT: D 496 MET cc_start: 0.8995 (ttp) cc_final: 0.8560 (tmm) REVERT: D 509 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7500 (mttp) REVERT: D 670 MET cc_start: 0.9437 (mtp) cc_final: 0.8952 (mtp) REVERT: D 796 PHE cc_start: 0.9128 (m-80) cc_final: 0.8551 (m-80) REVERT: D 1091 ASP cc_start: 0.6364 (m-30) cc_final: 0.5823 (t0) REVERT: D 1106 PHE cc_start: 0.8704 (m-80) cc_final: 0.8500 (m-80) REVERT: D 1199 MET cc_start: 0.8629 (mmm) cc_final: 0.8290 (mmt) outliers start: 20 outliers final: 0 residues processed: 806 average time/residue: 0.1847 time to fit residues: 234.5718 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 : 1.055 ------------------------------------------------------------------------------- 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: 8.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 335 GLN A 587 GLN B 46 HIS B 147 GLN B 337 GLN B 412 HIS B 642 GLN C 147 GLN C 335 GLN C 587 GLN C1206 GLN D 46 HIS D 412 HIS D 435 HIS D 642 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.082418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063516 restraints weight = 143770.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065293 restraints weight = 87928.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066490 restraints weight = 63772.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067289 restraints weight = 51545.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.067724 restraints weight = 44795.848| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31786 Z= 0.123 Angle : 0.642 12.600 42964 Z= 0.334 Chirality : 0.043 0.289 4762 Planarity : 0.005 0.067 5385 Dihedral : 7.608 92.575 4391 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.03 % Favored : 93.71 % Rotamer: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % 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 aren not related in a simple way. whole: -1.93 (0.12), residues: 3897 helix: 0.12 (0.12), residues: 1768 sheet: -1.49 (0.24), residues: 452 loop : -2.81 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 661 TYR 0.025 0.001 TYR A 797 PHE 0.043 0.002 PHE A 574 TRP 0.037 0.002 TRP C 578 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00254 (31770) covalent geometry : angle 0.64096 (42932) SS BOND : bond 0.00460 ( 16) SS BOND : angle 1.46103 ( 32) hydrogen bonds : bond 0.04009 ( 1434) hydrogen bonds : angle 4.71484 ( 4152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 1.170 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 71 TYR cc_start: 0.7969 (m-80) cc_final: 0.7751 (m-10) REVERT: A 113 MET cc_start: 0.8760 (mmp) cc_final: 0.8505 (mmp) REVERT: A 292 MET cc_start: 0.8978 (mmp) cc_final: 0.8513 (ttp) REVERT: A 450 TYR cc_start: 0.8567 (m-80) cc_final: 0.8044 (m-10) REVERT: A 483 LEU cc_start: 0.9200 (tp) cc_final: 0.8931 (tt) REVERT: A 577 LEU cc_start: 0.9335 (mm) cc_final: 0.8979 (mm) REVERT: A 797 TYR cc_start: 0.8968 (m-80) cc_final: 0.8754 (m-80) REVERT: A 1057 MET cc_start: 0.6563 (mmp) cc_final: 0.6111 (mtm) REVERT: A 1069 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 1097 LEU cc_start: 0.9035 (tt) cc_final: 0.8691 (pp) REVERT: A 1116 MET cc_start: 0.9330 (tpt) cc_final: 0.9012 (tpp) REVERT: A 1141 PHE cc_start: 0.9126 (m-80) cc_final: 0.8613 (m-80) REVERT: A 1190 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8865 (mm-30) REVERT: A 1191 MET cc_start: 0.7971 (tpt) cc_final: 0.7745 (tpp) REVERT: A 1205 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8240 (tptt) REVERT: B 116 ASP cc_start: 0.7826 (t0) cc_final: 0.7435 (t70) REVERT: B 407 MET cc_start: 0.8966 (mmm) cc_final: 0.8730 (mmm) REVERT: B 463 MET cc_start: 0.8520 (mtp) cc_final: 0.8048 (ttm) REVERT: B 500 ILE cc_start: 0.8431 (mt) cc_final: 0.8081 (mm) REVERT: B 503 MET cc_start: 0.8975 (tmm) cc_final: 0.8404 (tmm) REVERT: B 670 MET cc_start: 0.9447 (mtp) cc_final: 0.8988 (mtp) REVERT: B 721 MET cc_start: 0.8421 (ttm) cc_final: 0.8121 (ttm) REVERT: C 292 MET cc_start: 0.8931 (mmp) cc_final: 0.8466 (ttm) REVERT: C 577 LEU cc_start: 0.9365 (mm) cc_final: 0.8984 (mm) REVERT: C 797 TYR cc_start: 0.8949 (m-80) cc_final: 0.8736 (m-80) REVERT: C 1069 GLU cc_start: 0.7556 (tt0) cc_final: 0.7270 (tm-30) REVERT: C 1116 MET cc_start: 0.9274 (tpt) cc_final: 0.9049 (tpp) REVERT: C 1190 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8853 (mm-30) REVERT: C 1191 MET cc_start: 0.7907 (tpt) cc_final: 0.7683 (tpt) REVERT: C 1205 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8224 (tptt) REVERT: D 116 ASP cc_start: 0.7840 (t0) cc_final: 0.7414 (t70) REVERT: D 407 MET cc_start: 0.8971 (mmm) cc_final: 0.8747 (mmm) REVERT: D 416 GLU cc_start: 0.8343 (tp30) cc_final: 0.8110 (pm20) REVERT: D 463 MET cc_start: 0.8601 (mtp) cc_final: 0.8143 (ttm) REVERT: D 500 ILE cc_start: 0.8447 (mt) cc_final: 0.8078 (mm) REVERT: D 503 MET cc_start: 0.9002 (tmm) cc_final: 0.8443 (tmm) REVERT: D 670 MET cc_start: 0.9451 (mtp) cc_final: 0.8991 (mtp) REVERT: D 768 TYR cc_start: 0.8164 (t80) cc_final: 0.7816 (t80) REVERT: D 789 LEU cc_start: 0.9262 (mt) cc_final: 0.9031 (mt) outliers start: 2 outliers final: 0 residues processed: 489 average time/residue: 0.1658 time to fit residues: 133.1037 Evaluate side-chains 300 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 382 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 207 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 412 HIS A 435 HIS A 642 GLN B 24 GLN B 337 GLN B 355 ASN B1159 ASN C 46 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 207 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 435 HIS C 642 GLN D 24 GLN D 246 GLN D 355 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.074706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056510 restraints weight = 149312.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058026 restraints weight = 93615.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059049 restraints weight = 69330.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059727 restraints weight = 56958.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060161 restraints weight = 50025.734| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 31786 Z= 0.305 Angle : 0.788 11.470 42964 Z= 0.415 Chirality : 0.046 0.234 4762 Planarity : 0.005 0.078 5385 Dihedral : 7.135 87.296 4391 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.93 % Favored : 91.76 % Rotamer: Outliers : 0.15 % Allowed : 3.75 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: -1.42 (0.13), residues: 3897 helix: 0.58 (0.12), residues: 1797 sheet: -1.31 (0.25), residues: 432 loop : -2.63 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 661 TYR 0.025 0.002 TYR D 647 PHE 0.028 0.003 PHE D1181 TRP 0.033 0.002 TRP A 578 HIS 0.007 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00657 (31770) covalent geometry : angle 0.78704 (42932) SS BOND : bond 0.01424 ( 16) SS BOND : angle 1.48522 ( 32) hydrogen bonds : bond 0.04931 ( 1434) hydrogen bonds : angle 5.10267 ( 4152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9110 (ptt) cc_final: 0.8837 (ptt) REVERT: A 292 MET cc_start: 0.9000 (mmp) cc_final: 0.8538 (ttp) REVERT: A 408 MET cc_start: 0.7974 (tpt) cc_final: 0.7767 (tpp) REVERT: A 527 MET cc_start: 0.9046 (ptp) cc_final: 0.8763 (ppp) REVERT: A 674 MET cc_start: 0.8443 (mmm) cc_final: 0.8217 (mmm) REVERT: A 797 TYR cc_start: 0.9072 (m-80) cc_final: 0.8784 (m-80) REVERT: A 803 LEU cc_start: 0.9437 (mp) cc_final: 0.9130 (mp) REVERT: A 1029 THR cc_start: 0.3980 (OUTLIER) cc_final: 0.3516 (m) REVERT: A 1057 MET cc_start: 0.6900 (mmp) cc_final: 0.6363 (mtm) REVERT: A 1069 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 1115 PHE cc_start: 0.8079 (p90) cc_final: 0.7578 (p90) REVERT: A 1116 MET cc_start: 0.9374 (tpt) cc_final: 0.9165 (tpp) REVERT: A 1141 PHE cc_start: 0.9440 (m-80) cc_final: 0.8976 (m-80) REVERT: A 1190 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8900 (mm-30) REVERT: A 1205 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8187 (tptt) REVERT: B 25 GLU cc_start: 0.9049 (mp0) cc_final: 0.8706 (mp0) REVERT: B 113 MET cc_start: 0.8998 (mmp) cc_final: 0.8677 (mmm) REVERT: B 138 ASP cc_start: 0.8404 (t0) cc_final: 0.8070 (t0) REVERT: B 496 MET cc_start: 0.8454 (tmm) cc_final: 0.8117 (tmm) REVERT: B 503 MET cc_start: 0.8832 (tmm) cc_final: 0.8436 (tmm) REVERT: B 600 ILE cc_start: 0.9288 (pt) cc_final: 0.9047 (tt) REVERT: B 670 MET cc_start: 0.9419 (mtp) cc_final: 0.9054 (mtp) REVERT: C 33 MET cc_start: 0.9119 (ptt) cc_final: 0.8855 (ptt) REVERT: C 113 MET cc_start: 0.8937 (mmp) cc_final: 0.8670 (mmp) REVERT: C 292 MET cc_start: 0.8963 (mmp) cc_final: 0.8495 (ttp) REVERT: C 450 TYR cc_start: 0.8601 (m-80) cc_final: 0.8383 (m-10) REVERT: C 463 MET cc_start: 0.8819 (mmm) cc_final: 0.8571 (mmm) REVERT: C 674 MET cc_start: 0.8436 (mmm) cc_final: 0.8232 (mmm) REVERT: C 1032 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6702 (m-10) REVERT: C 1069 GLU cc_start: 0.7638 (tt0) cc_final: 0.7365 (tm-30) REVERT: C 1116 MET cc_start: 0.9324 (tpt) cc_final: 0.9112 (tpp) REVERT: C 1141 PHE cc_start: 0.9397 (m-80) cc_final: 0.8958 (m-80) REVERT: C 1190 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8898 (mm-30) REVERT: C 1191 MET cc_start: 0.8111 (tpt) cc_final: 0.7906 (tpp) REVERT: C 1205 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8210 (tptt) REVERT: D 25 GLU cc_start: 0.9042 (mp0) cc_final: 0.8715 (mp0) REVERT: D 113 MET cc_start: 0.8971 (mmp) cc_final: 0.8668 (mmm) REVERT: D 416 GLU cc_start: 0.8631 (tp30) cc_final: 0.8418 (pm20) REVERT: D 496 MET cc_start: 0.8473 (tmm) cc_final: 0.8112 (tmm) REVERT: D 503 MET cc_start: 0.8859 (tmm) cc_final: 0.8462 (tmm) REVERT: D 600 ILE cc_start: 0.9303 (pt) cc_final: 0.9058 (tt) REVERT: D 670 MET cc_start: 0.9429 (mtp) cc_final: 0.9046 (mtp) REVERT: D 808 LEU cc_start: 0.8995 (tt) cc_final: 0.8467 (mp) REVERT: B 1301 GLU cc_start: 0.7013 (tp30) cc_final: 0.6700 (tp30) REVERT: D 1301 GLU cc_start: 0.6993 (tp30) cc_final: 0.6680 (tp30) outliers start: 5 outliers final: 2 residues processed: 319 average time/residue: 0.1574 time to fit residues: 83.6083 Evaluate side-chains 238 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 48 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 354 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 270 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 214 HIS A 302 GLN A 619 ASN B 355 ASN C 83 ASN C 147 GLN C 214 HIS D 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060542 restraints weight = 143548.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062241 restraints weight = 86453.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063384 restraints weight = 62170.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064129 restraints weight = 50016.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064611 restraints weight = 43361.928| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 31786 Z= 0.112 Angle : 0.596 9.036 42964 Z= 0.306 Chirality : 0.042 0.243 4762 Planarity : 0.004 0.057 5385 Dihedral : 5.996 70.050 4391 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.39 % Favored : 93.41 % Rotamer: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: -0.74 (0.13), residues: 3897 helix: 1.28 (0.12), residues: 1805 sheet: -0.97 (0.25), residues: 430 loop : -2.48 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 661 TYR 0.018 0.001 TYR D1031 PHE 0.018 0.001 PHE A1115 TRP 0.027 0.002 TRP C1032 HIS 0.003 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00239 (31770) covalent geometry : angle 0.59530 (42932) SS BOND : bond 0.00461 ( 16) SS BOND : angle 1.00501 ( 32) hydrogen bonds : bond 0.03314 ( 1434) hydrogen bonds : angle 4.29632 ( 4152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 1.144 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 33 MET cc_start: 0.9014 (ptt) cc_final: 0.8567 (ptt) REVERT: A 292 MET cc_start: 0.8952 (mmp) cc_final: 0.8469 (ttp) REVERT: A 380 MET cc_start: 0.8487 (tmm) cc_final: 0.8223 (tmm) REVERT: A 577 LEU cc_start: 0.9411 (mm) cc_final: 0.9064 (mm) REVERT: A 674 MET cc_start: 0.8516 (mmm) cc_final: 0.8240 (mmm) REVERT: A 704 LEU cc_start: 0.9255 (pp) cc_final: 0.9050 (pp) REVERT: A 797 TYR cc_start: 0.9124 (m-80) cc_final: 0.8789 (m-80) REVERT: A 1057 MET cc_start: 0.6873 (mmp) cc_final: 0.6438 (mtm) REVERT: A 1069 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 1116 MET cc_start: 0.9404 (tpt) cc_final: 0.9178 (tpp) REVERT: A 1141 PHE cc_start: 0.9358 (m-80) cc_final: 0.8798 (m-80) REVERT: A 1190 GLU cc_start: 0.9433 (mm-30) cc_final: 0.8983 (mm-30) REVERT: A 1205 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8183 (tptt) REVERT: B 25 GLU cc_start: 0.8965 (mp0) cc_final: 0.8701 (mp0) REVERT: B 113 MET cc_start: 0.8982 (mmp) cc_final: 0.8592 (mmm) REVERT: B 138 ASP cc_start: 0.8337 (t0) cc_final: 0.7765 (t0) REVERT: B 408 MET cc_start: 0.8364 (ppp) cc_final: 0.8017 (ppp) REVERT: B 496 MET cc_start: 0.8488 (tmm) cc_final: 0.7795 (tmm) REVERT: B 503 MET cc_start: 0.8880 (tmm) cc_final: 0.8356 (tmm) REVERT: B 670 MET cc_start: 0.9386 (mtp) cc_final: 0.8987 (mtp) REVERT: B 808 LEU cc_start: 0.8887 (tt) cc_final: 0.8440 (mt) REVERT: C 33 MET cc_start: 0.9018 (ptt) cc_final: 0.8566 (ptt) REVERT: C 292 MET cc_start: 0.8922 (mmp) cc_final: 0.8424 (ttp) REVERT: C 380 MET cc_start: 0.8503 (tmm) cc_final: 0.8254 (tmm) REVERT: C 408 MET cc_start: 0.8146 (tpt) cc_final: 0.7919 (tpp) REVERT: C 463 MET cc_start: 0.8799 (mmm) cc_final: 0.8551 (mmm) REVERT: C 527 MET cc_start: 0.9114 (ppp) cc_final: 0.8736 (ppp) REVERT: C 577 LEU cc_start: 0.9423 (mm) cc_final: 0.9053 (mm) REVERT: C 629 MET cc_start: -0.1191 (mtt) cc_final: -0.1482 (mmt) REVERT: C 674 MET cc_start: 0.8560 (mmm) cc_final: 0.8302 (mmm) REVERT: C 797 TYR cc_start: 0.8958 (m-80) cc_final: 0.8572 (m-80) REVERT: C 803 LEU cc_start: 0.9542 (mt) cc_final: 0.9225 (mt) REVERT: C 1069 GLU cc_start: 0.7626 (tt0) cc_final: 0.7417 (tm-30) REVERT: C 1115 PHE cc_start: 0.8076 (p90) cc_final: 0.7600 (p90) REVERT: C 1141 PHE cc_start: 0.9349 (m-80) cc_final: 0.8831 (m-80) REVERT: C 1177 TRP cc_start: 0.7670 (m100) cc_final: 0.7032 (m-90) REVERT: C 1190 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9000 (mm-30) REVERT: C 1205 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8205 (tptt) REVERT: D 25 GLU cc_start: 0.8980 (mp0) cc_final: 0.8704 (mp0) REVERT: D 113 MET cc_start: 0.8949 (mmp) cc_final: 0.8583 (mmm) REVERT: D 138 ASP cc_start: 0.8329 (t0) cc_final: 0.7771 (t0) REVERT: D 408 MET cc_start: 0.8357 (ppp) cc_final: 0.7949 (ppp) REVERT: D 416 GLU cc_start: 0.8601 (tp30) cc_final: 0.8309 (pm20) REVERT: D 496 MET cc_start: 0.8440 (tmm) cc_final: 0.7772 (tmm) REVERT: D 503 MET cc_start: 0.8901 (tmm) cc_final: 0.8360 (tmm) REVERT: D 600 ILE cc_start: 0.9165 (pt) cc_final: 0.8924 (tt) REVERT: D 670 MET cc_start: 0.9374 (mtp) cc_final: 0.8991 (mtp) REVERT: D 808 LEU cc_start: 0.8909 (tt) cc_final: 0.8451 (mt) outliers start: 3 outliers final: 0 residues processed: 373 average time/residue: 0.1571 time to fit residues: 97.9046 Evaluate side-chains 262 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 146 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 213 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 302 GLN B 355 ASN C 619 ASN D 355 ASN D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059024 restraints weight = 146550.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060648 restraints weight = 90297.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061766 restraints weight = 65758.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062495 restraints weight = 53232.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062975 restraints weight = 46376.292| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31786 Z= 0.127 Angle : 0.592 12.879 42964 Z= 0.305 Chirality : 0.042 0.263 4762 Planarity : 0.004 0.063 5385 Dihedral : 5.337 49.609 4391 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.93 % Favored : 92.84 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -0.42 (0.14), residues: 3897 helix: 1.51 (0.12), residues: 1815 sheet: -0.69 (0.25), residues: 472 loop : -2.36 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.018 0.001 TYR B 647 PHE 0.021 0.001 PHE A1181 TRP 0.025 0.001 TRP C1032 HIS 0.003 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00282 (31770) covalent geometry : angle 0.59181 (42932) SS BOND : bond 0.00389 ( 16) SS BOND : angle 1.09968 ( 32) hydrogen bonds : bond 0.03418 ( 1434) hydrogen bonds : angle 4.27561 ( 4152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.311 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: A 113 MET cc_start: 0.8729 (mmp) cc_final: 0.8443 (mmt) REVERT: A 292 MET cc_start: 0.9028 (mmp) cc_final: 0.8445 (ttp) REVERT: A 380 MET cc_start: 0.8534 (tmm) cc_final: 0.8254 (tmm) REVERT: A 450 TYR cc_start: 0.8547 (m-80) cc_final: 0.8205 (m-10) REVERT: A 577 LEU cc_start: 0.9488 (mm) cc_final: 0.9130 (mm) REVERT: A 797 TYR cc_start: 0.9128 (m-80) cc_final: 0.8689 (m-80) REVERT: A 1057 MET cc_start: 0.6884 (mmp) cc_final: 0.6656 (mtm) REVERT: A 1069 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 1141 PHE cc_start: 0.9395 (m-80) cc_final: 0.8909 (m-80) REVERT: A 1190 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 1205 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8195 (tptt) REVERT: B 25 GLU cc_start: 0.8983 (mp0) cc_final: 0.8715 (mp0) REVERT: B 113 MET cc_start: 0.8947 (mmp) cc_final: 0.8679 (mmm) REVERT: B 138 ASP cc_start: 0.8320 (t0) cc_final: 0.7715 (t0) REVERT: B 408 MET cc_start: 0.8435 (ppp) cc_final: 0.7986 (ppp) REVERT: B 503 MET cc_start: 0.8882 (tmm) cc_final: 0.8272 (tmm) REVERT: B 600 ILE cc_start: 0.9245 (pt) cc_final: 0.9002 (tt) REVERT: B 670 MET cc_start: 0.9409 (mtp) cc_final: 0.9062 (mtp) REVERT: B 808 LEU cc_start: 0.8902 (tt) cc_final: 0.8460 (mt) REVERT: C 113 MET cc_start: 0.8711 (mmp) cc_final: 0.8506 (mmt) REVERT: C 292 MET cc_start: 0.8945 (mmp) cc_final: 0.8393 (ttm) REVERT: C 380 MET cc_start: 0.8552 (tmm) cc_final: 0.8165 (tmm) REVERT: C 408 MET cc_start: 0.8110 (tpt) cc_final: 0.7813 (tpp) REVERT: C 527 MET cc_start: 0.9132 (ppp) cc_final: 0.8737 (ppp) REVERT: C 577 LEU cc_start: 0.9421 (mm) cc_final: 0.9061 (mm) REVERT: C 797 TYR cc_start: 0.8927 (m-80) cc_final: 0.8406 (m-80) REVERT: C 1141 PHE cc_start: 0.9404 (m-80) cc_final: 0.8979 (m-80) REVERT: C 1190 GLU cc_start: 0.9425 (mm-30) cc_final: 0.8957 (mm-30) REVERT: C 1205 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8211 (tptt) REVERT: D 25 GLU cc_start: 0.9034 (mp0) cc_final: 0.8727 (mp0) REVERT: D 113 MET cc_start: 0.8941 (mmp) cc_final: 0.8668 (mmm) REVERT: D 116 ASP cc_start: 0.8032 (t0) cc_final: 0.7825 (t0) REVERT: D 138 ASP cc_start: 0.8328 (t0) cc_final: 0.7761 (t0) REVERT: D 408 MET cc_start: 0.8408 (ppp) cc_final: 0.7933 (ppp) REVERT: D 416 GLU cc_start: 0.8687 (tp30) cc_final: 0.8367 (pm20) REVERT: D 463 MET cc_start: 0.8745 (ptp) cc_final: 0.8509 (ptp) REVERT: D 503 MET cc_start: 0.8901 (tmm) cc_final: 0.8305 (tmm) REVERT: D 600 ILE cc_start: 0.9276 (pt) cc_final: 0.9021 (tt) REVERT: D 670 MET cc_start: 0.9391 (mtp) cc_final: 0.9006 (mtp) REVERT: D 808 LEU cc_start: 0.8871 (tt) cc_final: 0.8487 (mp) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.1876 time to fit residues: 103.0416 Evaluate side-chains 249 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 192 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 214 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 642 GLN B 246 GLN B 355 ASN C 46 HIS C 147 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 355 ASN D1159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056463 restraints weight = 148079.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.057931 restraints weight = 93493.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058964 restraints weight = 68882.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059646 restraints weight = 55987.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060085 restraints weight = 48918.264| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31786 Z= 0.240 Angle : 0.693 10.558 42964 Z= 0.364 Chirality : 0.044 0.266 4762 Planarity : 0.005 0.064 5385 Dihedral : 5.429 55.308 4391 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.13 % Favored : 91.63 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % 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 aren not related in a simple way. whole: -0.63 (0.13), residues: 3897 helix: 1.28 (0.12), residues: 1814 sheet: -1.09 (0.25), residues: 418 loop : -2.25 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 309 TYR 0.034 0.002 TYR B 647 PHE 0.025 0.002 PHE C1115 TRP 0.036 0.002 TRP A 578 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00519 (31770) covalent geometry : angle 0.69288 (42932) SS BOND : bond 0.00581 ( 16) SS BOND : angle 0.93872 ( 32) hydrogen bonds : bond 0.04321 ( 1434) hydrogen bonds : angle 4.73894 ( 4152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.9101 (ptt) cc_final: 0.8533 (ptt) REVERT: A 182 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: A 292 MET cc_start: 0.8992 (mmp) cc_final: 0.8462 (ttp) REVERT: A 380 MET cc_start: 0.8847 (tmm) cc_final: 0.8343 (tmm) REVERT: A 577 LEU cc_start: 0.9474 (mm) cc_final: 0.9147 (mm) REVERT: A 586 GLN cc_start: 0.9166 (mp10) cc_final: 0.8616 (mp10) REVERT: A 1057 MET cc_start: 0.7019 (mmp) cc_final: 0.6733 (mtm) REVERT: A 1115 PHE cc_start: 0.8234 (p90) cc_final: 0.7969 (p90) REVERT: A 1141 PHE cc_start: 0.9449 (m-80) cc_final: 0.9093 (m-80) REVERT: A 1190 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8916 (mm-30) REVERT: A 1205 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8212 (tptt) REVERT: B 25 GLU cc_start: 0.9067 (mp0) cc_final: 0.8665 (mp0) REVERT: B 33 MET cc_start: 0.8049 (ptp) cc_final: 0.7836 (ptp) REVERT: B 113 MET cc_start: 0.8993 (mmp) cc_final: 0.8682 (mmm) REVERT: B 138 ASP cc_start: 0.8401 (t0) cc_final: 0.8022 (t0) REVERT: B 408 MET cc_start: 0.8578 (ppp) cc_final: 0.8079 (ppp) REVERT: B 496 MET cc_start: 0.8472 (tmm) cc_final: 0.7991 (tmm) REVERT: B 503 MET cc_start: 0.8845 (tmm) cc_final: 0.8417 (tmm) REVERT: B 670 MET cc_start: 0.9411 (mtp) cc_final: 0.9053 (mtp) REVERT: B 808 LEU cc_start: 0.8979 (tt) cc_final: 0.8561 (mt) REVERT: C 33 MET cc_start: 0.9112 (ptt) cc_final: 0.8538 (ptt) REVERT: C 292 MET cc_start: 0.8973 (mmp) cc_final: 0.8442 (ttp) REVERT: C 380 MET cc_start: 0.8830 (tmm) cc_final: 0.8330 (tmm) REVERT: C 450 TYR cc_start: 0.8632 (m-80) cc_final: 0.8426 (m-10) REVERT: C 527 MET cc_start: 0.9085 (ppp) cc_final: 0.8848 (ppp) REVERT: C 577 LEU cc_start: 0.9450 (mm) cc_final: 0.9116 (mm) REVERT: C 674 MET cc_start: 0.8521 (mmm) cc_final: 0.8185 (mmm) REVERT: C 1069 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 1115 PHE cc_start: 0.7990 (p90) cc_final: 0.7629 (p90) REVERT: C 1141 PHE cc_start: 0.9454 (m-80) cc_final: 0.9160 (m-80) REVERT: C 1190 GLU cc_start: 0.9450 (mm-30) cc_final: 0.8928 (mm-30) REVERT: C 1205 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8257 (tptt) REVERT: D 25 GLU cc_start: 0.9021 (mp0) cc_final: 0.8596 (mp0) REVERT: D 113 MET cc_start: 0.9009 (mmp) cc_final: 0.8671 (mmm) REVERT: D 138 ASP cc_start: 0.8446 (t0) cc_final: 0.8055 (t0) REVERT: D 407 MET cc_start: 0.8856 (mmm) cc_final: 0.8630 (mmm) REVERT: D 408 MET cc_start: 0.8589 (ppp) cc_final: 0.8125 (ppp) REVERT: D 463 MET cc_start: 0.8653 (ptp) cc_final: 0.8242 (ptt) REVERT: D 496 MET cc_start: 0.8473 (tmm) cc_final: 0.7986 (tmm) REVERT: D 503 MET cc_start: 0.8848 (tmm) cc_final: 0.8423 (tmm) REVERT: D 670 MET cc_start: 0.9361 (mtp) cc_final: 0.9008 (mtp) REVERT: D 808 LEU cc_start: 0.8955 (tt) cc_final: 0.8602 (mp) outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.1836 time to fit residues: 94.4284 Evaluate side-chains 235 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 330 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 302 GLN A 642 GLN B 355 ASN C 24 GLN C 147 GLN C 619 ASN D 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058170 restraints weight = 147610.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059714 restraints weight = 92062.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060770 restraints weight = 67640.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061435 restraints weight = 55157.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061794 restraints weight = 48336.028| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31786 Z= 0.130 Angle : 0.583 8.076 42964 Z= 0.305 Chirality : 0.042 0.209 4762 Planarity : 0.004 0.055 5385 Dihedral : 5.046 49.156 4391 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.95 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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 aren not related in a simple way. whole: -0.28 (0.14), residues: 3897 helix: 1.60 (0.12), residues: 1822 sheet: -0.90 (0.25), residues: 436 loop : -2.14 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 661 TYR 0.029 0.001 TYR D 647 PHE 0.022 0.001 PHE D 36 TRP 0.026 0.001 TRP C 578 HIS 0.004 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00284 (31770) covalent geometry : angle 0.58331 (42932) SS BOND : bond 0.00458 ( 16) SS BOND : angle 0.74128 ( 32) hydrogen bonds : bond 0.03487 ( 1434) hydrogen bonds : angle 4.33945 ( 4152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.159 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: 0.8621 (mmt) cc_final: 0.8167 (mmm) REVERT: A 292 MET cc_start: 0.9019 (mmp) cc_final: 0.8342 (ttp) REVERT: A 380 MET cc_start: 0.8836 (tmm) cc_final: 0.8618 (tmm) REVERT: A 517 PHE cc_start: 0.8859 (p90) cc_final: 0.8439 (p90) REVERT: A 577 LEU cc_start: 0.9448 (mm) cc_final: 0.9077 (mm) REVERT: A 1141 PHE cc_start: 0.9430 (m-80) cc_final: 0.9012 (m-80) REVERT: A 1190 GLU cc_start: 0.9488 (mm-30) cc_final: 0.8989 (mm-30) REVERT: A 1199 MET cc_start: 0.8943 (ptp) cc_final: 0.8670 (ppp) REVERT: A 1205 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8212 (tptt) REVERT: B 25 GLU cc_start: 0.9045 (mp0) cc_final: 0.8667 (mp0) REVERT: B 113 MET cc_start: 0.8974 (mmp) cc_final: 0.8652 (mmm) REVERT: B 138 ASP cc_start: 0.8384 (t0) cc_final: 0.8057 (t0) REVERT: B 496 MET cc_start: 0.8395 (tmm) cc_final: 0.7994 (tmm) REVERT: B 503 MET cc_start: 0.8876 (tmm) cc_final: 0.8310 (tmm) REVERT: B 670 MET cc_start: 0.9366 (mtp) cc_final: 0.9033 (mtp) REVERT: B 808 LEU cc_start: 0.8925 (tt) cc_final: 0.8557 (mp) REVERT: C 113 MET cc_start: 0.8637 (mmt) cc_final: 0.8177 (mmm) REVERT: C 292 MET cc_start: 0.9023 (mmp) cc_final: 0.8330 (ttp) REVERT: C 380 MET cc_start: 0.8762 (tmm) cc_final: 0.8328 (tmm) REVERT: C 517 PHE cc_start: 0.8784 (p90) cc_final: 0.8362 (p90) REVERT: C 527 MET cc_start: 0.9096 (ppp) cc_final: 0.8705 (ppp) REVERT: C 577 LEU cc_start: 0.9417 (mm) cc_final: 0.9075 (mm) REVERT: C 674 MET cc_start: 0.8445 (mmm) cc_final: 0.8057 (mmm) REVERT: C 797 TYR cc_start: 0.9037 (m-80) cc_final: 0.8658 (m-80) REVERT: C 1141 PHE cc_start: 0.9421 (m-80) cc_final: 0.9065 (m-80) REVERT: C 1190 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8961 (mm-30) REVERT: C 1199 MET cc_start: 0.9100 (ppp) cc_final: 0.8373 (ppp) REVERT: C 1205 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8270 (tptt) REVERT: D 25 GLU cc_start: 0.9033 (mp0) cc_final: 0.8636 (mp0) REVERT: D 113 MET cc_start: 0.9005 (mmp) cc_final: 0.8681 (mmm) REVERT: D 138 ASP cc_start: 0.8410 (t0) cc_final: 0.8076 (t0) REVERT: D 463 MET cc_start: 0.8854 (ptp) cc_final: 0.8490 (ptt) REVERT: D 496 MET cc_start: 0.8402 (tmm) cc_final: 0.7946 (tmm) REVERT: D 503 MET cc_start: 0.8870 (tmm) cc_final: 0.8300 (tmm) REVERT: D 670 MET cc_start: 0.9354 (mtp) cc_final: 0.9009 (mtp) REVERT: D 808 LEU cc_start: 0.8858 (tt) cc_final: 0.8528 (mp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1647 time to fit residues: 88.4238 Evaluate side-chains 233 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 341 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 355 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.073514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055997 restraints weight = 148316.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057486 restraints weight = 93099.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058512 restraints weight = 68050.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059187 restraints weight = 55275.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059633 restraints weight = 48273.804| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31786 Z= 0.220 Angle : 0.678 11.093 42964 Z= 0.355 Chirality : 0.044 0.218 4762 Planarity : 0.005 0.070 5385 Dihedral : 5.325 52.387 4391 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.34 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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 aren not related in a simple way. whole: -0.49 (0.14), residues: 3897 helix: 1.40 (0.12), residues: 1815 sheet: -0.91 (0.25), residues: 421 loop : -2.21 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1064 TYR 0.026 0.002 TYR B 647 PHE 0.024 0.002 PHE C1115 TRP 0.035 0.002 TRP A 578 HIS 0.005 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00478 (31770) covalent geometry : angle 0.67796 (42932) SS BOND : bond 0.00620 ( 16) SS BOND : angle 0.81428 ( 32) hydrogen bonds : bond 0.04208 ( 1434) hydrogen bonds : angle 4.66590 ( 4152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.308 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: 0.8683 (mmt) cc_final: 0.8360 (mmm) REVERT: A 292 MET cc_start: 0.9079 (mmp) cc_final: 0.8345 (ttt) REVERT: A 380 MET cc_start: 0.8884 (tmm) cc_final: 0.8381 (tmm) REVERT: A 517 PHE cc_start: 0.8840 (p90) cc_final: 0.8419 (p90) REVERT: A 577 LEU cc_start: 0.9487 (mm) cc_final: 0.9111 (mm) REVERT: A 586 GLN cc_start: 0.9101 (mp10) cc_final: 0.8775 (mp10) REVERT: A 1141 PHE cc_start: 0.9469 (m-80) cc_final: 0.9123 (m-80) REVERT: A 1190 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8906 (mm-30) REVERT: A 1199 MET cc_start: 0.8951 (ptp) cc_final: 0.8742 (ppp) REVERT: A 1205 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8204 (tptt) REVERT: B 25 GLU cc_start: 0.9046 (mp0) cc_final: 0.8593 (mp0) REVERT: B 113 MET cc_start: 0.9028 (mmp) cc_final: 0.8699 (mmm) REVERT: B 138 ASP cc_start: 0.8421 (t0) cc_final: 0.8028 (t0) REVERT: B 407 MET cc_start: 0.8989 (mmm) cc_final: 0.8752 (mmm) REVERT: B 496 MET cc_start: 0.8451 (tmm) cc_final: 0.7942 (tmm) REVERT: B 503 MET cc_start: 0.8843 (tmm) cc_final: 0.8508 (tmm) REVERT: B 670 MET cc_start: 0.9351 (mtp) cc_final: 0.9007 (mtp) REVERT: B 808 LEU cc_start: 0.8955 (tt) cc_final: 0.8533 (mt) REVERT: C 113 MET cc_start: 0.8703 (mmt) cc_final: 0.8429 (mmm) REVERT: C 292 MET cc_start: 0.9065 (mmp) cc_final: 0.8291 (ttt) REVERT: C 380 MET cc_start: 0.8871 (tmm) cc_final: 0.8358 (tmm) REVERT: C 517 PHE cc_start: 0.8806 (p90) cc_final: 0.8394 (p90) REVERT: C 527 MET cc_start: 0.9118 (ppp) cc_final: 0.8861 (ppp) REVERT: C 577 LEU cc_start: 0.9505 (mm) cc_final: 0.9102 (mm) REVERT: C 674 MET cc_start: 0.8562 (mmm) cc_final: 0.8253 (mmm) REVERT: C 1115 PHE cc_start: 0.7946 (p90) cc_final: 0.7420 (p90) REVERT: C 1141 PHE cc_start: 0.9470 (m-80) cc_final: 0.9186 (m-80) REVERT: C 1190 GLU cc_start: 0.9458 (mm-30) cc_final: 0.8938 (mm-30) REVERT: C 1199 MET cc_start: 0.9082 (ppp) cc_final: 0.8543 (ppp) REVERT: C 1205 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8241 (tptt) REVERT: D 25 GLU cc_start: 0.9025 (mp0) cc_final: 0.8570 (mp0) REVERT: D 113 MET cc_start: 0.9073 (mmp) cc_final: 0.8864 (mmm) REVERT: D 138 ASP cc_start: 0.8498 (t0) cc_final: 0.8095 (t0) REVERT: D 463 MET cc_start: 0.8739 (ptp) cc_final: 0.8368 (ptt) REVERT: D 496 MET cc_start: 0.8461 (tmm) cc_final: 0.7916 (tmm) REVERT: D 503 MET cc_start: 0.8864 (tmm) cc_final: 0.8405 (tmm) REVERT: D 670 MET cc_start: 0.9353 (mtp) cc_final: 0.9031 (mtp) REVERT: D 808 LEU cc_start: 0.8903 (tt) cc_final: 0.8560 (mp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1713 time to fit residues: 86.6544 Evaluate side-chains 232 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 363 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 302 GLN A 642 GLN A1059 HIS B 355 ASN C1059 HIS D 355 ASN D 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058124 restraints weight = 146499.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059712 restraints weight = 90432.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060788 restraints weight = 65989.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061487 restraints weight = 53480.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061951 restraints weight = 46654.139| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31786 Z= 0.116 Angle : 0.583 9.283 42964 Z= 0.302 Chirality : 0.042 0.201 4762 Planarity : 0.004 0.052 5385 Dihedral : 4.944 45.788 4391 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.01 % Favored : 92.84 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % 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 aren not related in a simple way. whole: -0.16 (0.14), residues: 3897 helix: 1.67 (0.12), residues: 1821 sheet: -0.57 (0.25), residues: 437 loop : -2.13 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.023 0.001 TYR C1180 PHE 0.022 0.001 PHE C1115 TRP 0.031 0.001 TRP C1032 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00252 (31770) covalent geometry : angle 0.58219 (42932) SS BOND : bond 0.00402 ( 16) SS BOND : angle 0.94812 ( 32) hydrogen bonds : bond 0.03381 ( 1434) hydrogen bonds : angle 4.24519 ( 4152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.148 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: A 25 GLU cc_start: 0.8994 (mp0) cc_final: 0.8676 (mp0) REVERT: A 113 MET cc_start: 0.8705 (mmt) cc_final: 0.8306 (mmm) REVERT: A 292 MET cc_start: 0.9190 (mmp) cc_final: 0.8317 (ttt) REVERT: A 517 PHE cc_start: 0.8837 (p90) cc_final: 0.8392 (p90) REVERT: A 1141 PHE cc_start: 0.9456 (m-80) cc_final: 0.9083 (m-80) REVERT: A 1190 GLU cc_start: 0.9505 (mm-30) cc_final: 0.8971 (mm-30) REVERT: A 1199 MET cc_start: 0.8954 (ptp) cc_final: 0.8677 (ppp) REVERT: A 1205 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8214 (tptt) REVERT: B 25 GLU cc_start: 0.8971 (mp0) cc_final: 0.8531 (mp0) REVERT: B 113 MET cc_start: 0.9061 (mmp) cc_final: 0.8645 (mmm) REVERT: B 138 ASP cc_start: 0.8469 (t0) cc_final: 0.8048 (t0) REVERT: B 503 MET cc_start: 0.8875 (tmm) cc_final: 0.8300 (tmm) REVERT: B 533 TYR cc_start: 0.9130 (t80) cc_final: 0.8671 (t80) REVERT: B 670 MET cc_start: 0.9382 (mtp) cc_final: 0.9035 (mtp) REVERT: B 808 LEU cc_start: 0.8863 (tt) cc_final: 0.8502 (mt) REVERT: C 113 MET cc_start: 0.8747 (mmt) cc_final: 0.8295 (mmm) REVERT: C 292 MET cc_start: 0.9046 (mmp) cc_final: 0.8257 (ttt) REVERT: C 380 MET cc_start: 0.8889 (tmm) cc_final: 0.8496 (tmm) REVERT: C 483 LEU cc_start: 0.9103 (tp) cc_final: 0.8877 (tt) REVERT: C 517 PHE cc_start: 0.8804 (p90) cc_final: 0.8358 (p90) REVERT: C 577 LEU cc_start: 0.9366 (mm) cc_final: 0.9151 (mm) REVERT: C 674 MET cc_start: 0.8541 (mmm) cc_final: 0.8197 (mmm) REVERT: C 1115 PHE cc_start: 0.7984 (p90) cc_final: 0.7530 (p90) REVERT: C 1141 PHE cc_start: 0.9459 (m-80) cc_final: 0.9129 (m-80) REVERT: C 1190 GLU cc_start: 0.9487 (mm-30) cc_final: 0.8986 (mm-30) REVERT: C 1199 MET cc_start: 0.9147 (ppp) cc_final: 0.8505 (ppp) REVERT: C 1205 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8252 (tptt) REVERT: D 25 GLU cc_start: 0.8965 (mp0) cc_final: 0.8539 (mp0) REVERT: D 113 MET cc_start: 0.9086 (mmp) cc_final: 0.8672 (mmm) REVERT: D 138 ASP cc_start: 0.8494 (t0) cc_final: 0.8079 (t0) REVERT: D 463 MET cc_start: 0.8888 (ptp) cc_final: 0.8589 (ptt) REVERT: D 503 MET cc_start: 0.8886 (tmm) cc_final: 0.8311 (tmm) REVERT: D 533 TYR cc_start: 0.9130 (t80) cc_final: 0.8670 (t80) REVERT: D 670 MET cc_start: 0.9386 (mtp) cc_final: 0.9045 (mtp) REVERT: D 808 LEU cc_start: 0.8827 (tt) cc_final: 0.8506 (mp) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1729 time to fit residues: 92.7552 Evaluate side-chains 242 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 193 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 264 optimal weight: 0.0470 chunk 266 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 250 optimal weight: 0.0010 chunk 294 optimal weight: 9.9990 chunk 209 optimal weight: 0.6980 chunk 256 optimal weight: 10.0000 overall best weight: 1.7488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 642 GLN B 355 ASN D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057817 restraints weight = 146394.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059388 restraints weight = 90135.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060455 restraints weight = 65687.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061142 restraints weight = 53175.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061621 restraints weight = 46345.129| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31786 Z= 0.130 Angle : 0.592 8.823 42964 Z= 0.307 Chirality : 0.041 0.196 4762 Planarity : 0.004 0.061 5385 Dihedral : 4.861 45.537 4391 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.52 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 aren not related in a simple way. whole: -0.12 (0.14), residues: 3897 helix: 1.69 (0.12), residues: 1819 sheet: -0.56 (0.25), residues: 437 loop : -2.10 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 661 TYR 0.023 0.001 TYR A 797 PHE 0.021 0.001 PHE C1115 TRP 0.028 0.001 TRP C 578 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00285 (31770) covalent geometry : angle 0.59133 (42932) SS BOND : bond 0.00528 ( 16) SS BOND : angle 1.02195 ( 32) hydrogen bonds : bond 0.03470 ( 1434) hydrogen bonds : angle 4.26777 ( 4152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.094 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: A 113 MET cc_start: 0.8788 (mmt) cc_final: 0.8341 (mmm) REVERT: A 292 MET cc_start: 0.9092 (mmp) cc_final: 0.8353 (ttt) REVERT: A 517 PHE cc_start: 0.8873 (p90) cc_final: 0.8357 (p90) REVERT: A 586 GLN cc_start: 0.8877 (mp10) cc_final: 0.8525 (mp10) REVERT: A 674 MET cc_start: 0.8553 (mmm) cc_final: 0.8159 (mmm) REVERT: A 1141 PHE cc_start: 0.9439 (m-80) cc_final: 0.9084 (m-80) REVERT: A 1190 GLU cc_start: 0.9511 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 1205 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8206 (tptt) REVERT: B 25 GLU cc_start: 0.8985 (mp0) cc_final: 0.8550 (mp0) REVERT: B 113 MET cc_start: 0.9059 (mmp) cc_final: 0.8651 (mmm) REVERT: B 138 ASP cc_start: 0.8490 (t0) cc_final: 0.8076 (t0) REVERT: B 503 MET cc_start: 0.8875 (tmm) cc_final: 0.8306 (tmm) REVERT: B 533 TYR cc_start: 0.9137 (t80) cc_final: 0.8710 (t80) REVERT: B 670 MET cc_start: 0.9396 (mtp) cc_final: 0.9097 (mtp) REVERT: B 808 LEU cc_start: 0.8869 (tt) cc_final: 0.8504 (mt) REVERT: C 113 MET cc_start: 0.8780 (mmt) cc_final: 0.8340 (mmm) REVERT: C 292 MET cc_start: 0.9050 (mmp) cc_final: 0.8264 (ttt) REVERT: C 380 MET cc_start: 0.8913 (tmm) cc_final: 0.8536 (tmm) REVERT: C 483 LEU cc_start: 0.9128 (tp) cc_final: 0.8892 (tt) REVERT: C 517 PHE cc_start: 0.8820 (p90) cc_final: 0.8366 (p90) REVERT: C 577 LEU cc_start: 0.9375 (mm) cc_final: 0.9146 (mm) REVERT: C 674 MET cc_start: 0.8537 (mmm) cc_final: 0.8169 (mmm) REVERT: C 1115 PHE cc_start: 0.8059 (p90) cc_final: 0.7636 (p90) REVERT: C 1141 PHE cc_start: 0.9495 (m-80) cc_final: 0.9178 (m-80) REVERT: C 1190 GLU cc_start: 0.9482 (mm-30) cc_final: 0.8973 (mm-30) REVERT: C 1199 MET cc_start: 0.9072 (ppp) cc_final: 0.8549 (ppp) REVERT: C 1205 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8249 (tptt) REVERT: D 25 GLU cc_start: 0.9040 (mp0) cc_final: 0.8599 (mp0) REVERT: D 113 MET cc_start: 0.9120 (mmp) cc_final: 0.8700 (mmm) REVERT: D 138 ASP cc_start: 0.8516 (t0) cc_final: 0.8090 (t0) REVERT: D 463 MET cc_start: 0.8897 (ptp) cc_final: 0.8594 (ptt) REVERT: D 503 MET cc_start: 0.8884 (tmm) cc_final: 0.8326 (tmm) REVERT: D 533 TYR cc_start: 0.9136 (t80) cc_final: 0.8695 (t80) REVERT: D 670 MET cc_start: 0.9396 (mtp) cc_final: 0.9124 (mtp) REVERT: D 808 LEU cc_start: 0.8866 (tt) cc_final: 0.8502 (mp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1617 time to fit residues: 84.8171 Evaluate side-chains 242 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 128 optimal weight: 20.0000 chunk 350 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN A 642 GLN B 355 ASN B1081 HIS D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.076031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058167 restraints weight = 146629.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059768 restraints weight = 90256.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060856 restraints weight = 65811.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061559 restraints weight = 53265.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062046 restraints weight = 46442.813| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31786 Z= 0.109 Angle : 0.580 8.551 42964 Z= 0.298 Chirality : 0.041 0.192 4762 Planarity : 0.004 0.052 5385 Dihedral : 4.704 41.857 4391 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 aren not related in a simple way. whole: 0.01 (0.14), residues: 3897 helix: 1.80 (0.12), residues: 1819 sheet: -0.59 (0.25), residues: 461 loop : -2.00 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 297 TYR 0.023 0.001 TYR A 797 PHE 0.021 0.001 PHE C 546 TRP 0.028 0.001 TRP C1032 HIS 0.005 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00238 (31770) covalent geometry : angle 0.57982 (42932) SS BOND : bond 0.00504 ( 16) SS BOND : angle 0.95353 ( 32) hydrogen bonds : bond 0.03201 ( 1434) hydrogen bonds : angle 4.15425 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4555.54 seconds wall clock time: 79 minutes 57.58 seconds (4797.58 seconds total)