Starting phenix.real_space_refine on Thu Nov 20 06:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dlz_7959/11_2025/6dlz_7959.map" } resolution = 3.9 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 19996 2.51 5 N 5129 2.21 5 O 5769 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31070 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.44, per 1000 atoms: 0.24 Number of scatterers: 31070 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 5769 8.00 N 5129 7.00 C 19996 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=2.03 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=2.03 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: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.21 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: 4.034A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.605A 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: 3.836A 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: 4.324A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.655A 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: 3.803A 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: 3.850A 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: 3.804A 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: 3.523A 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: 3.564A 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: 3.585A 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: 3.702A 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: 3.713A 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: 3.584A 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: 3.615A 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: 3.703A 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: 3.575A 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: 3.596A 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: 4.484A 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: 6.262A 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: 3.548A 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: 3.710A 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: 3.672A 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: 3.741A 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: 4.028A 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: 3.943A 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: 3.977A 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: 3.673A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.839A 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: 3.648A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.860A 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: 3.792A 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: 3.699A 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: 3.584A 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: 3.600A 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: 4.485A 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: 3.591A 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: 3.604A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 4.111A 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: 3.614A 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: 3.741A 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: 6.002A 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: 6.573A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.338A 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: 4.721A 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: 3.968A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.426A 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: 5.074A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.084A 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: 5.074A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.084A 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: 7.762A 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: 9.252A 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: 7.950A 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: 5.250A 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: 5.817A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.654A 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: 5.879A 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: 8.045A 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: 4.715A 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: 5.570A 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: 6.095A 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: 6.095A 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: 3.576A 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: 6.329A 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: 6.119A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.286A 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: 6.996A 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: 7.14 Time building geometry restraints manager: 3.40 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: 550 1.23 - 1.38: 11838 1.38 - 1.53: 18308 1.53 - 1.69: 766 1.69 - 1.84: 280 Bond restraints: 31742 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 A1302 " pdb=" C5 CYZ A1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.63e+02 ... (remaining 31737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.20: 42756 6.20 - 12.41: 121 12.41 - 18.61: 14 18.61 - 24.81: 0 24.81 - 31.02: 8 Bond angle restraints: 42899 Sorted by residual: angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.94 -31.02 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.80 -30.88 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 106.92 137.65 -30.73 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 42894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.06: 18332 24.06 - 48.12: 443 48.12 - 72.18: 16 72.18 - 96.23: 16 96.23 - 120.29: 8 Dihedral angle restraints: 18815 sinusoidal: 7494 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 -124.91 -55.09 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 -125.16 -54.84 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 -135.62 -44.38 0 5.00e+00 4.00e-02 7.88e+01 ... (remaining 18812 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 - 2.179: 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: 5383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.061 5.00e-02 4.00e+02 9.29e-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 9.27e-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 8.07e-02 1.04e+01 pdb=" N PRO B 99 " 0.140 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 5380 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1662 2.72 - 3.26: 30538 3.26 - 3.81: 49666 3.81 - 4.35: 57005 4.35 - 4.90: 96417 Nonbonded interactions: 235288 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 2.228 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 235283 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.540 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 31758 Z= 0.648 Angle : 1.190 31.018 42931 Z= 0.641 Chirality : 0.104 2.179 4762 Planarity : 0.007 0.093 5383 Dihedral : 10.995 120.293 11539 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.47 % Favored : 91.12 % 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 are not related in a simple way. whole: -3.78 (0.11), residues: 3897 helix: -1.98 (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 0.008 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 0.01320 (31742) covalent geometry : angle 1.18994 (42899) SS BOND : bond 0.00447 ( 16) SS BOND : angle 1.17473 ( 32) hydrogen bonds : bond 0.14508 ( 1434) hydrogen bonds : angle 6.14755 ( 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 530 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 510 time to evaluate : 1.275 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 369 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7391 (ttm-80) REVERT: A 408 MET cc_start: 0.8965 (mmm) cc_final: 0.8195 (tpp) REVERT: A 427 ASP cc_start: 0.8453 (m-30) cc_final: 0.8140 (m-30) REVERT: A 670 MET cc_start: 0.9215 (mtp) cc_final: 0.8937 (mtt) REVERT: A 728 ASP cc_start: 0.8165 (p0) cc_final: 0.7934 (m-30) REVERT: A 1104 SER cc_start: 0.8331 (p) cc_final: 0.7459 (t) REVERT: A 1113 LEU cc_start: 0.9072 (mt) cc_final: 0.8806 (mt) REVERT: A 1127 TYR cc_start: 0.8354 (t80) cc_final: 0.8000 (t80) REVERT: A 1140 PHE cc_start: 0.9027 (m-80) cc_final: 0.8566 (m-80) REVERT: A 1170 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8308 (pttp) REVERT: A 1188 ILE cc_start: 0.9365 (mm) cc_final: 0.9088 (tp) REVERT: B 113 MET cc_start: 0.8793 (mmp) cc_final: 0.8046 (mpp) REVERT: B 504 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 710 GLU cc_start: 0.8665 (pt0) cc_final: 0.8044 (pp20) REVERT: B 748 LEU cc_start: 0.9450 (mt) cc_final: 0.9246 (mm) REVERT: B 1009 MET cc_start: 0.8527 (tpt) cc_final: 0.8258 (tpp) REVERT: B 1116 MET cc_start: 0.9036 (tpp) cc_final: 0.8813 (tpp) REVERT: B 1180 TYR cc_start: 0.9290 (m-10) cc_final: 0.8997 (m-80) REVERT: B 1191 MET cc_start: 0.9065 (ttm) cc_final: 0.8752 (tpp) REVERT: B 1199 MET cc_start: 0.9234 (mmm) cc_final: 0.8806 (mmm) REVERT: C 369 ARG cc_start: 0.7646 (ptm160) cc_final: 0.7314 (ttm-80) REVERT: C 408 MET cc_start: 0.8968 (mmm) cc_final: 0.8172 (tpp) REVERT: C 427 ASP cc_start: 0.8443 (m-30) cc_final: 0.8140 (m-30) REVERT: C 670 MET cc_start: 0.9223 (mtp) cc_final: 0.8972 (mtt) REVERT: C 728 ASP cc_start: 0.8153 (p0) cc_final: 0.7903 (m-30) REVERT: C 1104 SER cc_start: 0.8373 (p) cc_final: 0.7447 (t) REVERT: C 1113 LEU cc_start: 0.9076 (mt) cc_final: 0.8804 (mt) REVERT: C 1140 PHE cc_start: 0.9014 (m-80) cc_final: 0.8536 (m-80) REVERT: C 1170 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8207 (pttp) REVERT: C 1188 ILE cc_start: 0.9363 (mm) cc_final: 0.9027 (tt) REVERT: D 113 MET cc_start: 0.8792 (mmp) cc_final: 0.8007 (mpp) REVERT: D 504 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7792 (tt) REVERT: D 519 ASP cc_start: 0.8918 (t70) cc_final: 0.7939 (t70) REVERT: D 623 PHE cc_start: 0.8970 (m-80) cc_final: 0.8427 (m-80) REVERT: D 710 GLU cc_start: 0.8671 (pt0) cc_final: 0.8044 (pp20) REVERT: D 748 LEU cc_start: 0.9457 (mt) cc_final: 0.9247 (mm) REVERT: D 1023 MET cc_start: 0.8989 (tpt) cc_final: 0.8730 (tpp) REVERT: D 1116 MET cc_start: 0.9019 (tpp) cc_final: 0.8809 (tpp) REVERT: D 1180 TYR cc_start: 0.9259 (m-10) cc_final: 0.8931 (m-80) REVERT: D 1191 MET cc_start: 0.9063 (ttm) cc_final: 0.8757 (tpp) outliers start: 20 outliers final: 2 residues processed: 526 average time/residue: 0.2080 time to fit residues: 171.7404 Evaluate side-chains 257 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 253 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain D residue 504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 355 ASN A 587 GLN B 46 HIS B 147 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 586 GLN B 642 GLN B 747 ASN B 791 ASN C 147 GLN C 214 HIS C 355 ASN C 587 GLN D 46 HIS D 147 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 586 GLN D 642 GLN D 747 ASN D 791 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057701 restraints weight = 130636.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059632 restraints weight = 70513.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060861 restraints weight = 48071.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061634 restraints weight = 37996.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062114 restraints weight = 32896.010| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31758 Z= 0.157 Angle : 0.647 9.932 42931 Z= 0.341 Chirality : 0.043 0.296 4762 Planarity : 0.005 0.070 5383 Dihedral : 7.697 93.874 4385 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.62 % Favored : 93.12 % Rotamer: Outliers : 1.98 % Allowed : 9.67 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.12), residues: 3897 helix: 0.30 (0.12), residues: 1774 sheet: -1.76 (0.25), residues: 406 loop : -2.82 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 303 TYR 0.018 0.001 TYR A 523 PHE 0.020 0.001 PHE C 541 TRP 0.017 0.001 TRP A1177 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00337 (31742) covalent geometry : angle 0.64607 (42899) SS BOND : bond 0.00570 ( 16) SS BOND : angle 1.17293 ( 32) hydrogen bonds : bond 0.04065 ( 1434) hydrogen bonds : angle 4.70841 ( 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 371 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 305 time to evaluate : 1.248 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 369 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7420 (ttm-80) REVERT: A 408 MET cc_start: 0.8879 (mmm) cc_final: 0.8417 (tpp) REVERT: A 414 MET cc_start: 0.8561 (mpp) cc_final: 0.7975 (tpp) REVERT: A 577 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9150 (mm) REVERT: A 670 MET cc_start: 0.9238 (mtp) cc_final: 0.8975 (mtp) REVERT: A 728 ASP cc_start: 0.8173 (p0) cc_final: 0.7954 (m-30) REVERT: A 1113 LEU cc_start: 0.8998 (mt) cc_final: 0.8707 (mt) REVERT: A 1127 TYR cc_start: 0.8268 (t80) cc_final: 0.8049 (t80) REVERT: A 1140 PHE cc_start: 0.9035 (m-80) cc_final: 0.8534 (m-80) REVERT: A 1188 ILE cc_start: 0.9543 (mm) cc_final: 0.9226 (tp) REVERT: B 113 MET cc_start: 0.8762 (mmp) cc_final: 0.8347 (mpp) REVERT: B 463 MET cc_start: 0.8998 (mtp) cc_final: 0.8657 (mmt) REVERT: B 503 MET cc_start: 0.8219 (tmm) cc_final: 0.8009 (tmm) REVERT: B 527 MET cc_start: 0.8257 (tpt) cc_final: 0.7904 (tpp) REVERT: B 710 GLU cc_start: 0.8645 (pt0) cc_final: 0.8096 (pp20) REVERT: B 721 MET cc_start: 0.7801 (ttm) cc_final: 0.7520 (mtp) REVERT: B 1180 TYR cc_start: 0.9193 (m-10) cc_final: 0.8920 (m-80) REVERT: B 1191 MET cc_start: 0.9155 (ttm) cc_final: 0.8872 (tpp) REVERT: C 369 ARG cc_start: 0.7635 (ptm160) cc_final: 0.7418 (ttm-80) REVERT: C 408 MET cc_start: 0.8866 (mmm) cc_final: 0.8395 (tpp) REVERT: C 414 MET cc_start: 0.8657 (mpp) cc_final: 0.8006 (tpp) REVERT: C 670 MET cc_start: 0.9211 (mtp) cc_final: 0.8999 (mtp) REVERT: C 728 ASP cc_start: 0.8200 (p0) cc_final: 0.7923 (m-30) REVERT: C 1113 LEU cc_start: 0.9002 (mt) cc_final: 0.8712 (mt) REVERT: C 1140 PHE cc_start: 0.9026 (m-80) cc_final: 0.8337 (m-80) REVERT: C 1188 ILE cc_start: 0.9543 (mm) cc_final: 0.9240 (tp) REVERT: D 113 MET cc_start: 0.8754 (mmp) cc_final: 0.8307 (mpp) REVERT: D 463 MET cc_start: 0.8964 (mtp) cc_final: 0.8646 (mmt) REVERT: D 527 MET cc_start: 0.8253 (tpt) cc_final: 0.7894 (tpp) REVERT: D 710 GLU cc_start: 0.8627 (pt0) cc_final: 0.8120 (pp20) REVERT: D 1023 MET cc_start: 0.8927 (tpt) cc_final: 0.8671 (tpp) REVERT: D 1180 TYR cc_start: 0.9207 (m-10) cc_final: 0.8936 (m-80) REVERT: D 1191 MET cc_start: 0.9155 (ttm) cc_final: 0.8880 (tpp) outliers start: 66 outliers final: 34 residues processed: 348 average time/residue: 0.1995 time to fit residues: 111.6683 Evaluate side-chains 282 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1192 VAL Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 291 optimal weight: 3.9990 chunk 383 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 359 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057106 restraints weight = 131012.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058974 restraints weight = 70781.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060181 restraints weight = 48372.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060940 restraints weight = 38282.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061420 restraints weight = 33194.738| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31758 Z= 0.159 Angle : 0.627 12.332 42931 Z= 0.326 Chirality : 0.042 0.264 4762 Planarity : 0.004 0.064 5383 Dihedral : 6.812 76.838 4381 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.34 % Favored : 92.40 % Rotamer: Outliers : 2.61 % Allowed : 10.39 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3897 helix: 1.24 (0.12), residues: 1774 sheet: -1.32 (0.25), residues: 420 loop : -2.67 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 308 TYR 0.016 0.001 TYR C 711 PHE 0.022 0.001 PHE B1096 TRP 0.016 0.001 TRP A1177 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00350 (31742) covalent geometry : angle 0.62690 (42899) SS BOND : bond 0.00404 ( 16) SS BOND : angle 1.17986 ( 32) hydrogen bonds : bond 0.03666 ( 1434) hydrogen bonds : angle 4.46725 ( 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 349 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 1.068 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: 0.9250 (mmt) cc_final: 0.8513 (mmm) REVERT: A 193 ILE cc_start: 0.9421 (mt) cc_final: 0.9209 (mm) REVERT: A 369 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7434 (ttm-80) REVERT: A 407 MET cc_start: 0.8290 (mtm) cc_final: 0.7965 (mpp) REVERT: A 414 MET cc_start: 0.8604 (mpp) cc_final: 0.8046 (tpp) REVERT: A 670 MET cc_start: 0.9195 (mtp) cc_final: 0.8983 (mtp) REVERT: A 728 ASP cc_start: 0.8241 (p0) cc_final: 0.8004 (m-30) REVERT: A 819 ARG cc_start: 0.8720 (mpt-90) cc_final: 0.8379 (mpt-90) REVERT: A 1113 LEU cc_start: 0.9167 (mt) cc_final: 0.8888 (mt) REVERT: A 1140 PHE cc_start: 0.8997 (m-80) cc_final: 0.8499 (m-80) REVERT: B 390 LEU cc_start: 0.4121 (OUTLIER) cc_final: 0.3404 (mm) REVERT: B 463 MET cc_start: 0.8965 (mtp) cc_final: 0.8700 (mmt) REVERT: B 498 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9245 (pp) REVERT: B 503 MET cc_start: 0.8274 (tmm) cc_final: 0.7984 (tmm) REVERT: B 573 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9267 (mt) REVERT: B 670 MET cc_start: 0.9145 (tpp) cc_final: 0.8897 (mmp) REVERT: B 710 GLU cc_start: 0.8682 (pt0) cc_final: 0.8204 (pp20) REVERT: B 721 MET cc_start: 0.7921 (ttm) cc_final: 0.7703 (mtp) REVERT: B 1180 TYR cc_start: 0.9221 (m-10) cc_final: 0.8985 (m-80) REVERT: C 113 MET cc_start: 0.9247 (mmt) cc_final: 0.8517 (mmm) REVERT: C 193 ILE cc_start: 0.9409 (mt) cc_final: 0.9192 (mm) REVERT: C 369 ARG cc_start: 0.7621 (ptm160) cc_final: 0.7406 (ttm-80) REVERT: C 414 MET cc_start: 0.8711 (mpp) cc_final: 0.8113 (tpp) REVERT: C 1113 LEU cc_start: 0.9181 (mt) cc_final: 0.8828 (mt) REVERT: C 1140 PHE cc_start: 0.9028 (m-80) cc_final: 0.8363 (m-80) REVERT: C 1191 MET cc_start: 0.9241 (mtm) cc_final: 0.9025 (mtm) REVERT: D 390 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3414 (mm) REVERT: D 463 MET cc_start: 0.8963 (mtp) cc_final: 0.8698 (mmt) REVERT: D 573 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9274 (mt) REVERT: D 710 GLU cc_start: 0.8589 (pt0) cc_final: 0.8153 (pp20) REVERT: D 1180 TYR cc_start: 0.9206 (m-10) cc_final: 0.8974 (m-80) outliers start: 87 outliers final: 42 residues processed: 324 average time/residue: 0.1865 time to fit residues: 100.2429 Evaluate side-chains 275 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1192 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1142 VAL Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 322 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 377 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 273 optimal weight: 0.5980 chunk 348 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN B 224 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058375 restraints weight = 131068.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.059973 restraints weight = 80087.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061020 restraints weight = 58931.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061642 restraints weight = 48600.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062074 restraints weight = 43343.661| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31758 Z= 0.181 Angle : 0.623 10.915 42931 Z= 0.324 Chirality : 0.042 0.267 4762 Planarity : 0.004 0.059 5383 Dihedral : 6.009 61.005 4381 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.85 % Favored : 91.97 % Rotamer: Outliers : 3.03 % Allowed : 10.75 % Favored : 86.22 % 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 are not related in a simple way. whole: -0.68 (0.14), residues: 3897 helix: 1.54 (0.13), residues: 1784 sheet: -1.27 (0.25), residues: 410 loop : -2.55 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 308 TYR 0.018 0.002 TYR A 711 PHE 0.018 0.001 PHE C 541 TRP 0.018 0.001 TRP A1177 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00396 (31742) covalent geometry : angle 0.62244 (42899) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.93864 ( 32) hydrogen bonds : bond 0.03657 ( 1434) hydrogen bonds : angle 4.45785 ( 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 344 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 243 time to evaluate : 1.053 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: 0.9023 (mmt) cc_final: 0.8565 (mmm) REVERT: A 728 ASP cc_start: 0.8111 (p0) cc_final: 0.7772 (m-30) REVERT: A 789 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9175 (tt) REVERT: A 1126 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8715 (t80) REVERT: B 390 LEU cc_start: 0.3952 (OUTLIER) cc_final: 0.3288 (mm) REVERT: B 490 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8444 (t0) REVERT: B 710 GLU cc_start: 0.8754 (pt0) cc_final: 0.8321 (pp20) REVERT: B 1069 GLU cc_start: 0.8354 (tp30) cc_final: 0.7962 (pt0) REVERT: B 1078 GLN cc_start: 0.7947 (tp40) cc_final: 0.7583 (tp40) REVERT: C 113 MET cc_start: 0.9020 (mmt) cc_final: 0.8571 (mmm) REVERT: C 789 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9185 (tt) REVERT: C 1140 PHE cc_start: 0.8865 (m-80) cc_final: 0.8364 (m-80) REVERT: D 390 LEU cc_start: 0.3948 (OUTLIER) cc_final: 0.3230 (mm) REVERT: D 490 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8444 (t0) REVERT: D 710 GLU cc_start: 0.8643 (pt0) cc_final: 0.8241 (pp20) REVERT: D 721 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7934 (mpp) outliers start: 101 outliers final: 56 residues processed: 316 average time/residue: 0.1867 time to fit residues: 98.0602 Evaluate side-chains 280 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1192 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1142 VAL Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 143 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 chunk 302 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.074769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055436 restraints weight = 135907.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.056930 restraints weight = 84739.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057913 restraints weight = 63311.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058529 restraints weight = 52745.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058897 restraints weight = 47167.345| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 31758 Z= 0.320 Angle : 0.775 12.130 42931 Z= 0.402 Chirality : 0.045 0.268 4762 Planarity : 0.005 0.060 5383 Dihedral : 6.097 48.495 4381 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.44 % Favored : 90.27 % Rotamer: Outliers : 3.00 % Allowed : 12.64 % Favored : 84.35 % 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 are not related in a simple way. whole: -1.00 (0.13), residues: 3897 helix: 1.13 (0.12), residues: 1794 sheet: -1.43 (0.25), residues: 430 loop : -2.56 (0.13), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 594 TYR 0.026 0.002 TYR A 711 PHE 0.021 0.002 PHE A 541 TRP 0.028 0.002 TRP A1177 HIS 0.007 0.002 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00700 (31742) covalent geometry : angle 0.77495 (42899) SS BOND : bond 0.00697 ( 16) SS BOND : angle 1.24151 ( 32) hydrogen bonds : bond 0.04598 ( 1434) hydrogen bonds : angle 5.01349 ( 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 311 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 211 time to evaluate : 1.113 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 1126 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 1175 TYR cc_start: 0.8216 (m-80) cc_final: 0.8003 (m-80) REVERT: B 390 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3452 (mm) REVERT: B 490 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (t0) REVERT: B 527 MET cc_start: 0.8220 (tpt) cc_final: 0.7946 (tpt) REVERT: B 710 GLU cc_start: 0.8729 (pt0) cc_final: 0.8299 (pp20) REVERT: B 1069 GLU cc_start: 0.8403 (tp30) cc_final: 0.8082 (pt0) REVERT: C 1101 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8450 (tpt-90) REVERT: C 1175 TYR cc_start: 0.8013 (m-80) cc_final: 0.7705 (m-80) REVERT: D 390 LEU cc_start: 0.3985 (OUTLIER) cc_final: 0.3279 (mm) REVERT: D 490 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8520 (t0) REVERT: D 527 MET cc_start: 0.8175 (tpt) cc_final: 0.7890 (tpt) REVERT: D 710 GLU cc_start: 0.8698 (pt0) cc_final: 0.8290 (pp20) REVERT: D 721 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7990 (mpp) outliers start: 100 outliers final: 60 residues processed: 287 average time/residue: 0.1891 time to fit residues: 89.4565 Evaluate side-chains 272 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1101 ARG Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1192 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1142 VAL Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 213 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 292 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN C 207 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN ** C1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.056681 restraints weight = 130183.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058528 restraints weight = 70559.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059710 restraints weight = 48524.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.060494 restraints weight = 38531.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060969 restraints weight = 33337.791| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31758 Z= 0.122 Angle : 0.620 13.619 42931 Z= 0.314 Chirality : 0.042 0.296 4762 Planarity : 0.004 0.048 5383 Dihedral : 5.412 43.708 4381 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.52 % Favored : 93.30 % Rotamer: Outliers : 1.95 % Allowed : 13.99 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3897 helix: 1.75 (0.13), residues: 1787 sheet: -1.12 (0.25), residues: 408 loop : -2.51 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1064 TYR 0.029 0.001 TYR D1031 PHE 0.020 0.001 PHE C 541 TRP 0.015 0.001 TRP C1177 HIS 0.004 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00270 (31742) covalent geometry : angle 0.61880 (42899) SS BOND : bond 0.01030 ( 16) SS BOND : angle 1.49154 ( 32) hydrogen bonds : bond 0.03411 ( 1434) hydrogen bonds : angle 4.27874 ( 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 308 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 243 time to evaluate : 1.291 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: 0.9219 (mmt) cc_final: 0.8453 (mmm) REVERT: A 670 MET cc_start: 0.9180 (ptp) cc_final: 0.8940 (ptp) REVERT: A 728 ASP cc_start: 0.8286 (p0) cc_final: 0.7991 (m-30) REVERT: A 789 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9215 (tt) REVERT: A 1126 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8774 (t80) REVERT: B 390 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.3951 (mm) REVERT: B 407 MET cc_start: 0.8626 (mtm) cc_final: 0.8384 (mtt) REVERT: B 463 MET cc_start: 0.8855 (mmt) cc_final: 0.8652 (mmt) REVERT: B 527 MET cc_start: 0.8353 (tpt) cc_final: 0.8091 (tpt) REVERT: B 710 GLU cc_start: 0.8709 (pt0) cc_final: 0.8227 (pp20) REVERT: B 1069 GLU cc_start: 0.8406 (tp30) cc_final: 0.8099 (pt0) REVERT: B 1191 MET cc_start: 0.9349 (tpp) cc_final: 0.8946 (tpt) REVERT: B 1199 MET cc_start: 0.9431 (ttm) cc_final: 0.9212 (mmm) REVERT: C 113 MET cc_start: 0.9211 (mmt) cc_final: 0.8422 (mmm) REVERT: C 407 MET cc_start: 0.8142 (mpp) cc_final: 0.7724 (mpp) REVERT: C 767 TRP cc_start: 0.9078 (OUTLIER) cc_final: 0.8717 (m-90) REVERT: C 789 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9178 (tt) REVERT: C 1175 TYR cc_start: 0.7631 (m-80) cc_final: 0.7271 (m-80) REVERT: D 390 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3449 (mm) REVERT: D 463 MET cc_start: 0.8887 (mmt) cc_final: 0.8685 (mmt) REVERT: D 527 MET cc_start: 0.8343 (tpt) cc_final: 0.8081 (tpt) REVERT: D 710 GLU cc_start: 0.8641 (pt0) cc_final: 0.8182 (pp20) REVERT: D 721 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: D 1069 GLU cc_start: 0.8616 (tp30) cc_final: 0.8178 (tt0) outliers start: 65 outliers final: 36 residues processed: 296 average time/residue: 0.1892 time to fit residues: 91.8147 Evaluate side-chains 265 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 262 optimal weight: 9.9990 chunk 364 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 345 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056636 restraints weight = 130399.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058466 restraints weight = 71023.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059676 restraints weight = 49010.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060428 restraints weight = 38867.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060904 restraints weight = 33707.668| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31758 Z= 0.136 Angle : 0.605 11.202 42931 Z= 0.307 Chirality : 0.041 0.205 4762 Planarity : 0.004 0.051 5383 Dihedral : 5.163 37.440 4381 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.39 % Favored : 92.46 % Rotamer: Outliers : 2.10 % Allowed : 14.17 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3897 helix: 1.92 (0.13), residues: 1786 sheet: -0.96 (0.26), residues: 402 loop : -2.41 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.022 0.001 TYR B1031 PHE 0.021 0.001 PHE A 541 TRP 0.018 0.001 TRP C1177 HIS 0.004 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00304 (31742) covalent geometry : angle 0.60440 (42899) SS BOND : bond 0.00780 ( 16) SS BOND : angle 1.43771 ( 32) hydrogen bonds : bond 0.03366 ( 1434) hydrogen bonds : angle 4.23204 ( 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 311 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 1.205 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: 0.9221 (mmt) cc_final: 0.8477 (mmm) REVERT: A 789 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9190 (tt) REVERT: A 1126 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8766 (t80) REVERT: A 1190 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8764 (mp0) REVERT: B 116 ASP cc_start: 0.8640 (m-30) cc_final: 0.7851 (t0) REVERT: B 390 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4202 (mm) REVERT: B 463 MET cc_start: 0.8893 (mmt) cc_final: 0.8690 (mmt) REVERT: B 527 MET cc_start: 0.8397 (tpt) cc_final: 0.8123 (tpt) REVERT: B 710 GLU cc_start: 0.8769 (pt0) cc_final: 0.8287 (pp20) REVERT: B 1064 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8644 (ptm-80) REVERT: B 1069 GLU cc_start: 0.8431 (tp30) cc_final: 0.8184 (pt0) REVERT: B 1191 MET cc_start: 0.9387 (tpp) cc_final: 0.9028 (tpt) REVERT: C 113 MET cc_start: 0.9218 (mmt) cc_final: 0.8459 (mmm) REVERT: C 407 MET cc_start: 0.8131 (mpp) cc_final: 0.7734 (mpp) REVERT: C 728 ASP cc_start: 0.8225 (p0) cc_final: 0.7907 (m-30) REVERT: C 767 TRP cc_start: 0.9112 (OUTLIER) cc_final: 0.8672 (m-90) REVERT: C 789 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9228 (tt) REVERT: C 1126 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8799 (t80) REVERT: C 1175 TYR cc_start: 0.7781 (m-80) cc_final: 0.7448 (m-80) REVERT: C 1190 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: D 116 ASP cc_start: 0.8624 (m-30) cc_final: 0.7789 (t0) REVERT: D 390 LEU cc_start: 0.4173 (OUTLIER) cc_final: 0.3580 (mm) REVERT: D 463 MET cc_start: 0.8860 (mmt) cc_final: 0.8640 (mmt) REVERT: D 527 MET cc_start: 0.8388 (tpt) cc_final: 0.8109 (tpt) REVERT: D 538 VAL cc_start: 0.9411 (t) cc_final: 0.9135 (p) REVERT: D 710 GLU cc_start: 0.8549 (pt0) cc_final: 0.8195 (pp20) REVERT: D 721 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7761 (mpp) REVERT: D 1069 GLU cc_start: 0.8618 (tp30) cc_final: 0.8289 (pt0) outliers start: 70 outliers final: 41 residues processed: 297 average time/residue: 0.1913 time to fit residues: 94.4426 Evaluate side-chains 274 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1190 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 272 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.0470 chunk 189 optimal weight: 6.9990 chunk 366 optimal weight: 0.0670 chunk 172 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055905 restraints weight = 131461.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057722 restraints weight = 71378.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058919 restraints weight = 49205.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059675 restraints weight = 39018.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060145 restraints weight = 33791.515| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31758 Z= 0.174 Angle : 0.641 12.553 42931 Z= 0.324 Chirality : 0.041 0.220 4762 Planarity : 0.004 0.050 5383 Dihedral : 5.184 37.286 4381 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.83 % Favored : 92.02 % Rotamer: Outliers : 2.07 % Allowed : 14.80 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3897 helix: 1.88 (0.13), residues: 1786 sheet: -1.03 (0.26), residues: 412 loop : -2.37 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1130 TYR 0.017 0.001 TYR D 673 PHE 0.030 0.001 PHE B 74 TRP 0.022 0.001 TRP C1177 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00389 (31742) covalent geometry : angle 0.64016 (42899) SS BOND : bond 0.00869 ( 16) SS BOND : angle 1.49890 ( 32) hydrogen bonds : bond 0.03560 ( 1434) hydrogen bonds : angle 4.33927 ( 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 290 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 221 time to evaluate : 1.290 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: 0.9209 (mmt) cc_final: 0.8467 (mmm) REVERT: A 521 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9184 (mm) REVERT: A 1126 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8787 (t80) REVERT: A 1190 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: B 390 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4629 (tp) REVERT: B 407 MET cc_start: 0.8635 (mtm) cc_final: 0.8435 (mtt) REVERT: B 527 MET cc_start: 0.8268 (tpt) cc_final: 0.7982 (tpt) REVERT: B 538 VAL cc_start: 0.9432 (t) cc_final: 0.9222 (p) REVERT: B 710 GLU cc_start: 0.8749 (pt0) cc_final: 0.8253 (pp20) REVERT: B 1069 GLU cc_start: 0.8471 (tp30) cc_final: 0.8256 (pt0) REVERT: C 113 MET cc_start: 0.9207 (mmt) cc_final: 0.8457 (mmm) REVERT: C 380 MET cc_start: 0.8152 (ptm) cc_final: 0.7868 (tmm) REVERT: C 407 MET cc_start: 0.8144 (mpp) cc_final: 0.7375 (mpp) REVERT: C 767 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.8675 (m-90) REVERT: C 1126 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8798 (t80) REVERT: C 1175 TYR cc_start: 0.7980 (m-80) cc_final: 0.7681 (m-80) REVERT: C 1190 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: D 116 ASP cc_start: 0.8645 (m-30) cc_final: 0.7980 (t0) REVERT: D 390 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.3888 (mm) REVERT: D 527 MET cc_start: 0.8285 (tpt) cc_final: 0.8005 (tpt) REVERT: D 538 VAL cc_start: 0.9432 (t) cc_final: 0.9219 (p) REVERT: D 710 GLU cc_start: 0.8575 (pt0) cc_final: 0.8235 (pp20) REVERT: D 721 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: D 1069 GLU cc_start: 0.8680 (tp30) cc_final: 0.8309 (tt0) outliers start: 69 outliers final: 44 residues processed: 278 average time/residue: 0.1880 time to fit residues: 87.8844 Evaluate side-chains 272 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1190 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 216 optimal weight: 4.9990 chunk 384 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 132 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 362 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058109 restraints weight = 129236.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060009 restraints weight = 69814.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061249 restraints weight = 47827.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062035 restraints weight = 37753.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062528 restraints weight = 32623.962| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31758 Z= 0.103 Angle : 0.611 12.753 42931 Z= 0.300 Chirality : 0.041 0.255 4762 Planarity : 0.003 0.050 5383 Dihedral : 4.860 33.606 4381 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.93 % Favored : 93.94 % Rotamer: Outliers : 1.53 % Allowed : 15.17 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3897 helix: 2.07 (0.13), residues: 1792 sheet: -0.74 (0.26), residues: 432 loop : -2.29 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1130 TYR 0.043 0.001 TYR D1031 PHE 0.026 0.001 PHE B 74 TRP 0.017 0.001 TRP A 578 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00231 (31742) covalent geometry : angle 0.61029 (42899) SS BOND : bond 0.00682 ( 16) SS BOND : angle 1.27038 ( 32) hydrogen bonds : bond 0.03049 ( 1434) hydrogen bonds : angle 4.02037 ( 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 300 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 1.199 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: 0.9138 (mmt) cc_final: 0.8452 (mmm) REVERT: A 1126 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8763 (t80) REVERT: A 1190 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: B 116 ASP cc_start: 0.8729 (m-30) cc_final: 0.8019 (t0) REVERT: B 225 LEU cc_start: 0.8522 (mt) cc_final: 0.8203 (mt) REVERT: B 390 LEU cc_start: 0.4956 (OUTLIER) cc_final: 0.4667 (tp) REVERT: B 407 MET cc_start: 0.8645 (mtm) cc_final: 0.8394 (mtt) REVERT: B 710 GLU cc_start: 0.8683 (pt0) cc_final: 0.8324 (pp20) REVERT: B 1191 MET cc_start: 0.9323 (tpp) cc_final: 0.8932 (tpt) REVERT: C 113 MET cc_start: 0.9135 (mmt) cc_final: 0.8444 (mmm) REVERT: C 380 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: C 407 MET cc_start: 0.8136 (mpp) cc_final: 0.7717 (mpp) REVERT: C 521 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9113 (mm) REVERT: C 1126 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8775 (t80) REVERT: C 1190 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8782 (mp0) REVERT: D 116 ASP cc_start: 0.8610 (m-30) cc_final: 0.7832 (t0) REVERT: D 361 MET cc_start: 0.8411 (mmm) cc_final: 0.8059 (mmm) REVERT: D 390 LEU cc_start: 0.4228 (OUTLIER) cc_final: 0.3726 (mm) REVERT: D 639 LEU cc_start: 0.7046 (mp) cc_final: 0.6828 (mp) REVERT: D 710 GLU cc_start: 0.8357 (pt0) cc_final: 0.8149 (tm-30) REVERT: D 721 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7701 (mpp) outliers start: 51 outliers final: 33 residues processed: 286 average time/residue: 0.1831 time to fit residues: 88.2602 Evaluate side-chains 273 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1190 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 203 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 363 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054729 restraints weight = 132266.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.056498 restraints weight = 72204.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057648 restraints weight = 49878.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058400 restraints weight = 39653.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058863 restraints weight = 34406.293| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 31758 Z= 0.282 Angle : 0.738 13.117 42931 Z= 0.375 Chirality : 0.044 0.251 4762 Planarity : 0.004 0.054 5383 Dihedral : 5.289 39.993 4381 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.44 % Favored : 91.40 % Rotamer: Outliers : 1.59 % Allowed : 15.44 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3897 helix: 1.71 (0.12), residues: 1785 sheet: -1.11 (0.26), residues: 435 loop : -2.29 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 594 TYR 0.022 0.002 TYR A 711 PHE 0.029 0.002 PHE B 74 TRP 0.017 0.002 TRP A 578 HIS 0.005 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00618 (31742) covalent geometry : angle 0.73793 (42899) SS BOND : bond 0.00689 ( 16) SS BOND : angle 1.25100 ( 32) hydrogen bonds : bond 0.04001 ( 1434) hydrogen bonds : angle 4.64086 ( 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 272 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.270 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 521 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9214 (mm) REVERT: A 1126 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8859 (t80) REVERT: A 1190 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8733 (mp0) REVERT: B 390 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4784 (tp) REVERT: B 407 MET cc_start: 0.8615 (mtm) cc_final: 0.8369 (mtt) REVERT: B 527 MET cc_start: 0.8267 (tpt) cc_final: 0.7998 (tpt) REVERT: B 710 GLU cc_start: 0.8765 (pt0) cc_final: 0.8314 (pp20) REVERT: B 1191 MET cc_start: 0.9357 (tpp) cc_final: 0.8958 (tpt) REVERT: C 380 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7928 (tmm) REVERT: C 407 MET cc_start: 0.8150 (mpp) cc_final: 0.7442 (mpp) REVERT: C 521 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 767 TRP cc_start: 0.9227 (OUTLIER) cc_final: 0.8749 (m-90) REVERT: C 1126 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8829 (t80) REVERT: C 1190 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: D 361 MET cc_start: 0.8359 (mmm) cc_final: 0.8028 (mmm) REVERT: D 407 MET cc_start: 0.8594 (mtm) cc_final: 0.8330 (mtt) REVERT: D 527 MET cc_start: 0.8306 (tpt) cc_final: 0.8012 (tpt) REVERT: D 710 GLU cc_start: 0.8543 (pt0) cc_final: 0.8285 (pp20) REVERT: D 721 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7761 (mpp) REVERT: D 1191 MET cc_start: 0.9369 (tpp) cc_final: 0.8948 (tpt) outliers start: 53 outliers final: 37 residues processed: 261 average time/residue: 0.1930 time to fit residues: 84.2061 Evaluate side-chains 261 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1190 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 355 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 312 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 367 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064780 restraints weight = 114565.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066263 restraints weight = 68747.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067248 restraints weight = 51541.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067893 restraints weight = 43392.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068238 restraints weight = 39191.725| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31758 Z= 0.123 Angle : 0.637 15.387 42931 Z= 0.314 Chirality : 0.041 0.273 4762 Planarity : 0.004 0.050 5383 Dihedral : 5.023 36.446 4381 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.34 % Favored : 93.58 % Rotamer: Outliers : 1.65 % Allowed : 15.29 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3897 helix: 1.96 (0.13), residues: 1792 sheet: -0.86 (0.26), residues: 428 loop : -2.28 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1130 TYR 0.017 0.001 TYR B 673 PHE 0.028 0.001 PHE A 541 TRP 0.024 0.001 TRP A1177 HIS 0.004 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00280 (31742) covalent geometry : angle 0.63675 (42899) SS BOND : bond 0.00621 ( 16) SS BOND : angle 1.15809 ( 32) hydrogen bonds : bond 0.03321 ( 1434) hydrogen bonds : angle 4.19307 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.24 seconds wall clock time: 93 minutes 1.68 seconds (5581.68 seconds total)