Starting phenix.real_space_refine on Mon Jul 6 23:58:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vdv_31926/07_2026/7vdv_31926.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 976 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 274 5.49 5 Mg 1 5.21 5 S 173 5.16 5 Be 1 3.05 5 C 24443 2.51 5 N 7154 2.21 5 O 7979 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 227 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40028 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2752 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "J" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2827 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6652 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 26, 'TRANS': 782} Chain breaks: 5 Chain: "N" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "P" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2482 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Chain: "Q" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3981 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 4 Chain: "R" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 771 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 8, 'TRANS': 83} Chain: "T" Number of atoms: 2166 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain breaks: 2 bond proxies already assigned to first conformer: 2164 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1910 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "W" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2056 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain breaks: 2 Chain: "X" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2072 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Chain: "Y" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2057 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 2 Chain: "Z" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "a" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER T 239 " occ=0.35 ... (10 atoms not shown) pdb=" OG BSER T 239 " occ=0.65 residue: pdb=" N ASER T 243 " occ=0.43 ... (10 atoms not shown) pdb=" OG BSER T 243 " occ=0.57 Time building chain proxies: 7.96, per 1000 atoms: 0.20 Number of scatterers: 40028 At special positions: 0 Unit cell: (238.15, 184.025, 227.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 173 16.00 P 274 15.00 Mg 1 11.99 F 3 9.00 O 7979 8.00 N 7154 7.00 C 24443 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 28 sheets defined 62.9% alpha, 4.3% beta 109 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.712A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.438A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.026A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.750A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.677A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.524A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.468A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.548A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.547A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.573A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.780A pdb=" N HIS A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 removed outlier: 4.046A pdb=" N GLN A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 387 Processing helix chain 'A' and resid 394 through 423 removed outlier: 3.609A pdb=" N THR A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 450 through 516 removed outlier: 4.289A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 511 " --> pdb=" O TYR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.528A pdb=" N ALA A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 755 through 772 removed outlier: 3.509A pdb=" N LEU A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 799 Processing helix chain 'A' and resid 811 through 825 removed outlier: 4.256A pdb=" N SER A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 removed outlier: 3.508A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.748A pdb=" N ARG A 885 " --> pdb=" O GLU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 901 Processing helix chain 'A' and resid 917 through 929 removed outlier: 4.028A pdb=" N LEU A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.926A pdb=" N LYS A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 973 through 976 removed outlier: 4.073A pdb=" N LEU A 976 " --> pdb=" O ARG A 973 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 973 through 976' Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 1001 through 1014 removed outlier: 3.567A pdb=" N VAL A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1048 Processing helix chain 'A' and resid 1049 through 1052 removed outlier: 3.704A pdb=" N PHE A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 3.627A pdb=" N SER A1058 " --> pdb=" O HIS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1079 removed outlier: 4.005A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1096 removed outlier: 3.564A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1105 through 1119 removed outlier: 3.531A pdb=" N MET A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1117 " --> pdb=" O GLU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1144 removed outlier: 3.966A pdb=" N GLY A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A1140 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1179 through 1188 removed outlier: 4.255A pdb=" N ASP A1183 " --> pdb=" O ASN A1179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1229 removed outlier: 3.907A pdb=" N LYS A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A1225 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1252 removed outlier: 3.619A pdb=" N ALA A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A1251 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1267 through 1274 removed outlier: 3.592A pdb=" N GLN A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1292 removed outlier: 3.669A pdb=" N ARG A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A1288 " --> pdb=" O MET A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.695A pdb=" N ARG A1296 " --> pdb=" O GLU A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1309 removed outlier: 3.501A pdb=" N GLU A1309 " --> pdb=" O GLU A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1306 through 1309' Processing helix chain 'A' and resid 1310 through 1315 removed outlier: 4.026A pdb=" N ILE A1315 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 77 removed outlier: 3.927A pdb=" N VAL N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 110 removed outlier: 3.562A pdb=" N ALA N 101 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS N 108 " --> pdb=" O ASP N 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS N 110 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 143 removed outlier: 3.614A pdb=" N MET N 140 " --> pdb=" O LEU N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 162 removed outlier: 3.850A pdb=" N LEU N 157 " --> pdb=" O LYS N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 213 removed outlier: 3.665A pdb=" N MET N 213 " --> pdb=" O LEU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 266 removed outlier: 3.767A pdb=" N HIS N 251 " --> pdb=" O THR N 247 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET N 254 " --> pdb=" O TRP N 250 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS N 255 " --> pdb=" O HIS N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 310 removed outlier: 4.013A pdb=" N LEU N 302 " --> pdb=" O ALA N 299 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE N 304 " --> pdb=" O ARG N 301 " (cutoff:3.500A) Proline residue: N 305 - end of helix Processing helix chain 'N' and resid 324 through 335 Processing helix chain 'N' and resid 340 through 347 Processing helix chain 'N' and resid 352 through 357 Processing helix chain 'N' and resid 360 through 371 removed outlier: 3.556A pdb=" N ARG N 366 " --> pdb=" O ASP N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 390 removed outlier: 3.845A pdb=" N ARG N 389 " --> pdb=" O THR N 386 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG N 390 " --> pdb=" O VAL N 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 386 through 390' Processing helix chain 'N' and resid 391 through 401 Processing helix chain 'N' and resid 404 through 409 removed outlier: 3.546A pdb=" N GLN N 408 " --> pdb=" O GLY N 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 7 Processing helix chain 'P' and resid 80 through 89 removed outlier: 3.610A pdb=" N THR P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 125 removed outlier: 3.601A pdb=" N THR P 120 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN P 121 " --> pdb=" O GLU P 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET P 123 " --> pdb=" O MET P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 removed outlier: 3.524A pdb=" N ALA P 144 " --> pdb=" O LEU P 140 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY P 146 " --> pdb=" O LEU P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 194 removed outlier: 3.509A pdb=" N LEU P 193 " --> pdb=" O LEU P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 216 removed outlier: 3.659A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP P 211 " --> pdb=" O GLU P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 231 Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 258 through 262 Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 284 removed outlier: 3.615A pdb=" N MET P 283 " --> pdb=" O PHE P 279 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 284 " --> pdb=" O ASN P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 301 through 305 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 337 through 347 removed outlier: 3.524A pdb=" N GLY P 343 " --> pdb=" O VAL P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 356 removed outlier: 3.741A pdb=" N TRP P 356 " --> pdb=" O GLN P 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 366 removed outlier: 3.692A pdb=" N ASP P 363 " --> pdb=" O LYS P 359 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 371 Processing helix chain 'Q' and resid 19 through 30 Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'Q' and resid 59 through 67 removed outlier: 3.819A pdb=" N VAL Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 removed outlier: 3.570A pdb=" N ILE Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU Q 74 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE Q 76 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 104 removed outlier: 3.626A pdb=" N TYR Q 96 " --> pdb=" O TYR Q 92 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS Q 99 " --> pdb=" O ARG Q 95 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR Q 100 " --> pdb=" O TYR Q 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 137 removed outlier: 3.704A pdb=" N HIS Q 136 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 147 Processing helix chain 'Q' and resid 158 through 168 removed outlier: 3.775A pdb=" N GLY Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 185 Processing helix chain 'Q' and resid 198 through 208 removed outlier: 3.590A pdb=" N LEU Q 202 " --> pdb=" O LYS Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 230 Processing helix chain 'Q' and resid 232 through 241 removed outlier: 3.570A pdb=" N PHE Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 251 removed outlier: 4.260A pdb=" N LEU Q 249 " --> pdb=" O GLU Q 245 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE Q 250 " --> pdb=" O VAL Q 246 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Q 251 " --> pdb=" O ARG Q 247 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 298 removed outlier: 3.566A pdb=" N VAL Q 291 " --> pdb=" O LEU Q 287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 292 " --> pdb=" O GLN Q 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Q 293 " --> pdb=" O ILE Q 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 309 removed outlier: 3.929A pdb=" N LYS Q 304 " --> pdb=" O GLU Q 300 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN Q 309 " --> pdb=" O LEU Q 305 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 321 Processing helix chain 'Q' and resid 324 through 339 removed outlier: 4.096A pdb=" N ARG Q 328 " --> pdb=" O PHE Q 324 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU Q 330 " --> pdb=" O SER Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 361 Processing helix chain 'Q' and resid 367 through 382 removed outlier: 3.637A pdb=" N ILE Q 377 " --> pdb=" O ARG Q 373 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU Q 378 " --> pdb=" O GLY Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 389 through 393 Processing helix chain 'Q' and resid 399 through 406 Processing helix chain 'Q' and resid 411 through 429 removed outlier: 3.781A pdb=" N VAL Q 421 " --> pdb=" O SER Q 417 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY Q 429 " --> pdb=" O LEU Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 429 through 439 removed outlier: 4.703A pdb=" N ALA Q 437 " --> pdb=" O CYS Q 433 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS Q 438 " --> pdb=" O THR Q 434 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL Q 439 " --> pdb=" O LYS Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 452 removed outlier: 4.163A pdb=" N MET Q 452 " --> pdb=" O CYS Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 465 removed outlier: 3.914A pdb=" N ALA Q 464 " --> pdb=" O ALA Q 461 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL Q 465 " --> pdb=" O LEU Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1762 through 1782 removed outlier: 3.861A pdb=" N LEU Q1776 " --> pdb=" O ALA Q1772 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1783 through 1791 removed outlier: 3.868A pdb=" N ARG Q1788 " --> pdb=" O GLU Q1784 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Q1789 " --> pdb=" O CYS Q1785 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1793 through 1804 removed outlier: 3.941A pdb=" N LEU Q1800 " --> pdb=" O ASN Q1796 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN Q1804 " --> pdb=" O LEU Q1800 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1807 through 1821 removed outlier: 3.871A pdb=" N LYS Q1813 " --> pdb=" O SER Q1809 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q1815 " --> pdb=" O LEU Q1811 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR Q1816 " --> pdb=" O ALA Q1812 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU Q1817 " --> pdb=" O LYS Q1813 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 219 removed outlier: 3.592A pdb=" N GLU R 217 " --> pdb=" O ASN R 213 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET R 219 " --> pdb=" O ASN R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 240 No H-bonds generated for 'chain 'R' and resid 238 through 240' Processing helix chain 'R' and resid 270 through 277 removed outlier: 3.649A pdb=" N TYR R 276 " --> pdb=" O ASP R 272 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 151 removed outlier: 3.557A pdb=" N LEU T 143 " --> pdb=" O ALA T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 172 removed outlier: 3.786A pdb=" N ILE T 171 " --> pdb=" O GLY T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 177 through 188 removed outlier: 4.122A pdb=" N MET T 181 " --> pdb=" O ASP T 177 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU T 183 " --> pdb=" O SER T 179 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 211 removed outlier: 3.513A pdb=" N CYS T 204 " --> pdb=" O PHE T 200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN T 206 " --> pdb=" O LEU T 202 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA T 207 " --> pdb=" O MET T 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET T 208 " --> pdb=" O CYS T 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE T 209 " --> pdb=" O THR T 205 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 220 removed outlier: 3.547A pdb=" N ALA T 220 " --> pdb=" O TYR T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 232 Processing helix chain 'T' and resid 233 through 248 removed outlier: 3.712A pdb=" N ASER T 243 " --> pdb=" O ASER T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 369 through 373 Processing helix chain 'T' and resid 422 through 432 removed outlier: 3.919A pdb=" N TYR T 430 " --> pdb=" O SER T 426 " (cutoff:3.500A) Processing helix chain 'T' and resid 537 through 566 removed outlier: 3.503A pdb=" N SER T 565 " --> pdb=" O ASN T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 579 through 597 Processing helix chain 'V' and resid 137 through 142 Processing helix chain 'V' and resid 159 through 163 removed outlier: 3.622A pdb=" N THR V 163 " --> pdb=" O LYS V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 167 through 171 Processing helix chain 'V' and resid 172 through 182 Processing helix chain 'V' and resid 214 through 227 Processing helix chain 'V' and resid 229 through 248 Proline residue: V 235 - end of helix removed outlier: 3.776A pdb=" N GLU V 246 " --> pdb=" O ARG V 242 " (cutoff:3.500A) Processing helix chain 'V' and resid 289 through 302 Processing helix chain 'V' and resid 305 through 326 removed outlier: 4.238A pdb=" N THR V 309 " --> pdb=" O GLY V 305 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG V 316 " --> pdb=" O ALA V 312 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP V 321 " --> pdb=" O GLY V 317 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 357 through 381 removed outlier: 4.038A pdb=" N ASP V 369 " --> pdb=" O ILE V 365 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG V 370 " --> pdb=" O ARG V 366 " (cutoff:3.500A) Processing helix chain 'W' and resid 439 through 446 Processing helix chain 'W' and resid 447 through 451 removed outlier: 3.622A pdb=" N ASN W 451 " --> pdb=" O GLU W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 458 through 476 removed outlier: 4.058A pdb=" N LEU W 463 " --> pdb=" O PRO W 459 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA W 464 " --> pdb=" O GLU W 460 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN W 476 " --> pdb=" O THR W 472 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 488 removed outlier: 3.550A pdb=" N CYS W 486 " --> pdb=" O THR W 482 " (cutoff:3.500A) Processing helix chain 'W' and resid 493 through 507 removed outlier: 3.577A pdb=" N ILE W 497 " --> pdb=" O ASP W 493 " (cutoff:3.500A) Processing helix chain 'W' and resid 602 through 617 removed outlier: 4.411A pdb=" N MET W 615 " --> pdb=" O GLU W 611 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR W 616 " --> pdb=" O ALA W 612 " (cutoff:3.500A) Processing helix chain 'W' and resid 619 through 628 Processing helix chain 'W' and resid 631 through 642 Processing helix chain 'W' and resid 645 through 649 Processing helix chain 'W' and resid 859 through 949 removed outlier: 3.567A pdb=" N GLU W 881 " --> pdb=" O ALA W 877 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL W 892 " --> pdb=" O VAL W 888 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU W 893 " --> pdb=" O ALA W 889 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS W 905 " --> pdb=" O ILE W 901 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG W 915 " --> pdb=" O THR W 911 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG W 917 " --> pdb=" O MET W 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU W 918 " --> pdb=" O ASP W 914 " (cutoff:3.500A) Processing helix chain 'X' and resid 439 through 446 Processing helix chain 'X' and resid 446 through 452 removed outlier: 3.795A pdb=" N PHE X 450 " --> pdb=" O LEU X 446 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY X 452 " --> pdb=" O GLU X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 458 through 474 removed outlier: 3.542A pdb=" N ARG X 466 " --> pdb=" O TYR X 462 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN X 467 " --> pdb=" O LEU X 463 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 488 removed outlier: 3.604A pdb=" N CYS X 486 " --> pdb=" O THR X 482 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG X 488 " --> pdb=" O THR X 484 " (cutoff:3.500A) Processing helix chain 'X' and resid 493 through 507 Processing helix chain 'X' and resid 602 through 614 removed outlier: 3.669A pdb=" N THR X 606 " --> pdb=" O THR X 602 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU X 613 " --> pdb=" O LEU X 609 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU X 614 " --> pdb=" O LEU X 610 " (cutoff:3.500A) Processing helix chain 'X' and resid 623 through 627 Processing helix chain 'X' and resid 631 through 642 Processing helix chain 'X' and resid 869 through 914 removed outlier: 3.636A pdb=" N ALA X 878 " --> pdb=" O LYS X 874 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL X 879 " --> pdb=" O HIS X 875 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU X 880 " --> pdb=" O LEU X 876 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG X 882 " --> pdb=" O ALA X 878 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS X 883 " --> pdb=" O VAL X 879 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE X 884 " --> pdb=" O GLU X 880 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE X 906 " --> pdb=" O LYS X 902 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU X 907 " --> pdb=" O LEU X 903 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU X 908 " --> pdb=" O ARG X 904 " (cutoff:3.500A) Processing helix chain 'X' and resid 914 through 947 removed outlier: 4.121A pdb=" N GLU X 918 " --> pdb=" O ASP X 914 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS X 935 " --> pdb=" O ARG X 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET X 936 " --> pdb=" O GLN X 932 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU X 937 " --> pdb=" O ALA X 933 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 141 removed outlier: 3.796A pdb=" N LEU Y 140 " --> pdb=" O ARG Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 172 removed outlier: 3.866A pdb=" N TYR Y 147 " --> pdb=" O GLU Y 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET Y 148 " --> pdb=" O SER Y 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET Y 162 " --> pdb=" O ASP Y 158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Y 163 " --> pdb=" O GLN Y 159 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU Y 170 " --> pdb=" O LEU Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 306 removed outlier: 3.646A pdb=" N LEU Y 304 " --> pdb=" O ARG Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 311 through 327 removed outlier: 4.070A pdb=" N ILE Y 315 " --> pdb=" O THR Y 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Y 316 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 363 removed outlier: 3.751A pdb=" N ARG Y 360 " --> pdb=" O GLU Y 356 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA Y 363 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 400 through 413 removed outlier: 4.137A pdb=" N MET Y 404 " --> pdb=" O LEU Y 400 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN Y 405 " --> pdb=" O LYS Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 415 through 447 removed outlier: 3.607A pdb=" N GLN Y 437 " --> pdb=" O GLN Y 433 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG Y 438 " --> pdb=" O LEU Y 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Y 439 " --> pdb=" O LYS Y 435 " (cutoff:3.500A) Processing helix chain 'Y' and resid 447 through 466 removed outlier: 3.679A pdb=" N PHE Y 451 " --> pdb=" O ASP Y 447 " (cutoff:3.500A) Processing helix chain 'Y' and resid 478 through 484 removed outlier: 3.635A pdb=" N GLN Y 484 " --> pdb=" O PHE Y 481 " (cutoff:3.500A) Processing helix chain 'Y' and resid 485 through 511 removed outlier: 4.177A pdb=" N GLU Y 489 " --> pdb=" O PRO Y 485 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS Y 492 " --> pdb=" O GLN Y 488 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG Y 502 " --> pdb=" O LYS Y 498 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG Y 503 " --> pdb=" O VAL Y 499 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN Y 504 " --> pdb=" O GLN Y 500 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 197 removed outlier: 3.504A pdb=" N ARG Z 195 " --> pdb=" O THR Z 191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 198 through 200 No H-bonds generated for 'chain 'Z' and resid 198 through 200' Processing helix chain 'Z' and resid 220 through 276 removed outlier: 3.589A pdb=" N MET Z 235 " --> pdb=" O VAL Z 231 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA Z 243 " --> pdb=" O ARG Z 239 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU Z 244 " --> pdb=" O LYS Z 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Z 253 " --> pdb=" O GLU Z 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY Z 275 " --> pdb=" O LYS Z 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 1601 through 1616 Processing helix chain 'a' and resid 1626 through 1633 Processing helix chain 'a' and resid 1642 through 1647 removed outlier: 3.933A pdb=" N SER a1646 " --> pdb=" O LYS a1642 " (cutoff:3.500A) Processing helix chain 'a' and resid 1649 through 1653 removed outlier: 3.630A pdb=" N TRP a1652 " --> pdb=" O PRO a1649 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU a1653 " --> pdb=" O SER a1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1649 through 1653' Processing helix chain 'a' and resid 1662 through 1679 removed outlier: 4.013A pdb=" N ASP a1671 " --> pdb=" O TRP a1667 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU a1672 " --> pdb=" O ARG a1668 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR a1677 " --> pdb=" O MET a1673 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 removed outlier: 4.237A pdb=" N GLU K 50 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG K 53 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 4.279A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.877A pdb=" N ASP K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 326 removed outlier: 3.691A pdb=" N UNK M 325 " --> pdb=" O UNK M 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.391A pdb=" N ARG B 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.970A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.933A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.744A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.034A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AB2, first strand: chain 'A' and resid 776 through 777 Processing sheet with id=AB3, first strand: chain 'A' and resid 992 through 996 removed outlier: 6.956A pdb=" N VAL A 992 " --> pdb=" O VAL A1201 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ARG A1203 " --> pdb=" O VAL A 992 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 994 " --> pdb=" O ARG A1203 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A1171 " --> pdb=" O LEU A1202 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A1204 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A1173 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1100 " --> pdb=" O ILE A1172 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A1152 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A1124 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N SER A1155 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU A1126 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id=AB5, first strand: chain 'N' and resid 35 through 38 removed outlier: 3.655A pdb=" N PHE N 37 " --> pdb=" O VAL N 23 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU N 14 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 41 through 43 Processing sheet with id=AB7, first strand: chain 'N' and resid 88 through 89 Processing sheet with id=AB8, first strand: chain 'N' and resid 186 through 187 removed outlier: 3.763A pdb=" N THR N 177 " --> pdb=" O SER N 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 186 through 187 Processing sheet with id=AC1, first strand: chain 'P' and resid 18 through 21 removed outlier: 7.133A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL P 103 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA P 135 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU P 105 " --> pdb=" O ALA P 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 176 through 178 removed outlier: 3.577A pdb=" N THR P 160 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL P 298 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR P 297 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 238 through 239 Processing sheet with id=AC4, first strand: chain 'Q' and resid 39 through 40 Processing sheet with id=AC5, first strand: chain 'R' and resid 225 through 226 Processing sheet with id=AC6, first strand: chain 'V' and resid 186 through 191 Processing sheet with id=AC7, first strand: chain 'V' and resid 194 through 195 Processing sheet with id=AC8, first strand: chain 'V' and resid 262 through 270 Processing sheet with id=AC9, first strand: chain 'Y' and resid 296 through 297 Processing sheet with id=AD1, first strand: chain 'Y' and resid 336 through 338 1750 hydrogen bonds defined for protein. 5032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 470 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8412 1.33 - 1.45: 10550 1.45 - 1.57: 21532 1.57 - 1.70: 546 1.70 - 1.82: 298 Bond restraints: 41338 Sorted by residual: bond pdb=" F2 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.710 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" F1 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" F3 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C3' DT I 88 " pdb=" O3' DT I 88 " ideal model delta sigma weight residual 1.435 1.364 0.071 1.30e-02 5.92e+03 3.01e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.364 0.071 1.30e-02 5.92e+03 3.00e+01 ... (remaining 41333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 56735 4.46 - 8.92: 233 8.92 - 13.38: 12 13.38 - 17.84: 1 17.84 - 22.30: 1 Bond angle restraints: 56982 Sorted by residual: angle pdb=" F1 BEF A1701 " pdb="BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 120.12 97.82 22.30 3.00e+00 1.11e-01 5.52e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.12 119.04 -8.92 1.47e+00 4.63e-01 3.68e+01 angle pdb=" C GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.79 101.78 9.01 1.66e+00 3.63e-01 2.94e+01 angle pdb=" F2 BEF A1701 " pdb="BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 119.96 104.93 15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" O4' DT J 96 " pdb=" C4' DT J 96 " pdb=" C3' DT J 96 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 ... (remaining 56977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 22874 35.59 - 71.19: 1556 71.19 - 106.78: 60 106.78 - 142.37: 3 142.37 - 177.96: 2 Dihedral angle restraints: 24495 sinusoidal: 11929 harmonic: 12566 Sorted by residual: dihedral pdb=" O2A ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PA ADP A1703 " pdb=" PB ADP A1703 " ideal model delta sinusoidal sigma weight residual 300.00 133.13 166.87 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PB ADP A1703 " pdb=" PA ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 70.10 -130.10 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" CA GLY Q 49 " pdb=" C GLY Q 49 " pdb=" N LEU Q 50 " pdb=" CA LEU Q 50 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 24492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5725 0.087 - 0.174: 634 0.174 - 0.261: 25 0.261 - 0.348: 0 0.348 - 0.436: 1 Chirality restraints: 6385 Sorted by residual: chirality pdb=" CA ARG A1300 " pdb=" N ARG A1300 " pdb=" C ARG A1300 " pdb=" CB ARG A1300 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C3' DG I 101 " pdb=" C4' DG I 101 " pdb=" O3' DG I 101 " pdb=" C2' DG I 101 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE Q 454 " pdb=" CA ILE Q 454 " pdb=" CG1 ILE Q 454 " pdb=" CG2 ILE Q 454 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 6382 not shown) Planarity restraints: 6351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a1648 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO a1649 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO a1649 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO a1649 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 458 " -0.049 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO Q 459 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO Q 459 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO Q 459 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 164 " 0.019 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE V 164 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE V 164 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE V 164 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE V 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE V 164 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE V 164 " -0.003 2.00e-02 2.50e+03 ... (remaining 6348 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 380 2.47 - 3.07: 30472 3.07 - 3.68: 66553 3.68 - 4.29: 94688 4.29 - 4.90: 145087 Nonbonded interactions: 337180 Sorted by model distance: nonbonded pdb=" OG1 THR V 357 " pdb=" OE1 GLU V 360 " model vdw 1.858 3.040 nonbonded pdb="MG MG A1702 " pdb=" O2B ADP A1703 " model vdw 1.891 2.170 nonbonded pdb="MG MG A1702 " pdb=" O1A ADP A1703 " model vdw 1.899 2.170 nonbonded pdb=" O ARG T 377 " pdb=" CD2 LEU T 378 " model vdw 1.959 3.460 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 1.991 3.040 ... (remaining 337175 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } ncs_group { reference = (chain 'W' and (resid 423 through 598 or resid 600 through 647 or resid 868 thro \ ugh 947)) selection = (chain 'X' and (resid 423 through 515 or resid 537 or resid 600 through 947)) } 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=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.140 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.234 41339 Z= 0.656 Angle : 0.947 22.298 56982 Z= 0.600 Chirality : 0.054 0.436 6385 Planarity : 0.005 0.090 6351 Dihedral : 20.103 177.963 16317 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.78 (0.12), residues: 4170 helix: -0.72 (0.10), residues: 2231 sheet: -1.56 (0.37), residues: 183 loop : -1.64 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG V 366 TYR 0.033 0.003 TYR T 414 PHE 0.045 0.003 PHE V 164 TRP 0.040 0.003 TRP a1667 HIS 0.018 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.66 (41338) covalent geometry : angle 0.94666 / 0.60 (56982) hydrogen bonds : bond 0.29936 / 20.58 ( 2005) hydrogen bonds : angle 9.38016 / 6.84 ( 5502) Misc. bond : bond 0.00307 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.8926 (mpp) cc_final: 0.8598 (mpp) REVERT: N 282 MET cc_start: 0.0140 (ptm) cc_final: -0.0395 (ptp) REVERT: N 295 CYS cc_start: 0.5716 (m) cc_final: 0.4572 (t) REVERT: N 327 HIS cc_start: 0.5622 (m90) cc_final: 0.5312 (t-90) REVERT: N 335 MET cc_start: 0.1317 (tpp) cc_final: 0.0757 (ptm) REVERT: P 269 MET cc_start: 0.2252 (ttm) cc_final: 0.1916 (mtp) REVERT: Q 375 MET cc_start: 0.9577 (mtm) cc_final: 0.9326 (mtp) REVERT: Q 456 MET cc_start: 0.8229 (tmm) cc_final: 0.7935 (tmm) REVERT: Y 162 MET cc_start: 0.8013 (mmp) cc_final: 0.7466 (mmm) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.2254 time to fit residues: 112.3710 Evaluate side-chains 215 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 0.0870 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 6.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 HIS A1185 GLN A1236 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 209 ASN W 895 GLN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 253 GLN a1606 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068221 restraints weight = 315145.715| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 7.79 r_work: 0.2937 rms_B_bonded: 6.81 restraints_weight: 2.0000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41339 Z= 0.182 Angle : 0.808 13.039 56982 Z= 0.430 Chirality : 0.050 0.427 6385 Planarity : 0.005 0.054 6351 Dihedral : 22.832 177.765 7658 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 0.73 % Allowed : 6.34 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4170 helix: 0.06 (0.10), residues: 2404 sheet: -1.33 (0.36), residues: 187 loop : -1.62 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 71 TYR 0.034 0.002 TYR X 465 PHE 0.027 0.002 PHE V 164 TRP 0.052 0.003 TRP N 394 HIS 0.009 0.002 HIS X 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (41338) covalent geometry : angle 0.80815 / 0.43 (56982) hydrogen bonds : bond 0.07781 / 5.25 ( 2005) hydrogen bonds : angle 5.58371 / 4.05 ( 5502) Misc. bond : bond 0.00754 / 0.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.9002 (t0) cc_final: 0.8768 (p0) REVERT: G 24 GLN cc_start: 0.9049 (mp10) cc_final: 0.8395 (mp10) REVERT: A 886 MET cc_start: 0.9018 (mpp) cc_final: 0.8327 (mmm) REVERT: A 1284 MET cc_start: 0.7783 (mmm) cc_final: 0.7413 (mmm) REVERT: N 282 MET cc_start: -0.0115 (ptm) cc_final: -0.0383 (ptp) REVERT: N 295 CYS cc_start: 0.3027 (m) cc_final: 0.2434 (t) REVERT: N 376 MET cc_start: -0.1769 (mtt) cc_final: -0.2031 (mtm) REVERT: Q 45 LEU cc_start: 0.8569 (tp) cc_final: 0.8229 (tt) REVERT: Q 372 MET cc_start: 0.9602 (pmm) cc_final: 0.9019 (pmm) REVERT: Q 375 MET cc_start: 0.9636 (mtm) cc_final: 0.9071 (mtp) REVERT: V 279 PHE cc_start: 0.8865 (p90) cc_final: 0.8558 (p90) REVERT: W 645 GLU cc_start: 0.7018 (tp30) cc_final: 0.6511 (tp30) REVERT: X 498 MET cc_start: 0.8832 (mmp) cc_final: 0.8618 (mmp) outliers start: 27 outliers final: 11 residues processed: 297 average time/residue: 0.2156 time to fit residues: 108.2363 Evaluate side-chains 244 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 233 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 1814 CYS Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1681 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 409 optimal weight: 6.9990 chunk 431 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 159 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 508 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A1164 ASN N 354 ASN ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 500 GLN ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1606 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.067818 restraints weight = 269915.676| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 6.88 r_work: 0.2928 rms_B_bonded: 6.46 restraints_weight: 2.0000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41339 Z= 0.186 Angle : 0.706 11.114 56982 Z= 0.378 Chirality : 0.045 0.384 6385 Planarity : 0.005 0.049 6351 Dihedral : 22.675 177.334 7658 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.86 % Allowed : 9.34 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.67 (0.13), residues: 4170 helix: 0.39 (0.10), residues: 2406 sheet: -1.27 (0.36), residues: 192 loop : -1.59 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a1636 TYR 0.027 0.002 TYR X 465 PHE 0.030 0.002 PHE T 178 TRP 0.063 0.002 TRP N 394 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (41338) covalent geometry : angle 0.70582 / 0.38 (56982) hydrogen bonds : bond 0.06878 / 4.67 ( 2005) hydrogen bonds : angle 5.13958 / 3.72 ( 5502) Misc. bond : bond 0.00634 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 1.174 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: E 81 ASP cc_start: 0.8984 (t0) cc_final: 0.8774 (t0) REVERT: F 52 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8613 (mm-30) REVERT: F 63 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: G 24 GLN cc_start: 0.9065 (mp10) cc_final: 0.8403 (mp10) REVERT: A 201 GLN cc_start: 0.3496 (OUTLIER) cc_final: 0.2932 (mm-40) REVERT: A 886 MET cc_start: 0.9084 (mpp) cc_final: 0.8606 (mmm) REVERT: A 1000 MET cc_start: 0.7154 (tmm) cc_final: 0.6664 (tmm) REVERT: A 1233 MET cc_start: 0.6862 (mpp) cc_final: 0.6217 (mpp) REVERT: A 1272 MET cc_start: 0.8932 (mmt) cc_final: 0.8725 (mmt) REVERT: A 1277 GLU cc_start: 0.9555 (mp0) cc_final: 0.9182 (tp30) REVERT: A 1284 MET cc_start: 0.8134 (mmm) cc_final: 0.7834 (mmm) REVERT: N 335 MET cc_start: 0.4288 (OUTLIER) cc_final: 0.3985 (tpp) REVERT: N 376 MET cc_start: -0.1978 (mtt) cc_final: -0.2200 (mtt) REVERT: P 325 MET cc_start: 0.3956 (ptt) cc_final: 0.3748 (ptt) REVERT: Q 375 MET cc_start: 0.9633 (mtm) cc_final: 0.9154 (mtp) REVERT: T 178 PHE cc_start: 0.5737 (m-80) cc_final: 0.5447 (m-80) REVERT: T 203 MET cc_start: 0.4330 (tpt) cc_final: 0.4104 (tpt) REVERT: V 279 PHE cc_start: 0.9011 (p90) cc_final: 0.8636 (p90) REVERT: X 913 MET cc_start: 0.6234 (ppp) cc_final: 0.5607 (ppp) REVERT: Y 162 MET cc_start: 0.6995 (mmm) cc_final: 0.6554 (mmm) REVERT: Y 404 MET cc_start: 0.7385 (mpp) cc_final: 0.6990 (mmt) outliers start: 32 outliers final: 14 residues processed: 269 average time/residue: 0.2133 time to fit residues: 97.0668 Evaluate side-chains 241 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 1814 CYS Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 208 MET Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 120 optimal weight: 0.4980 chunk 422 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 405 optimal weight: 8.9990 chunk 424 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 287 optimal weight: 0.0070 chunk 307 optimal weight: 0.5980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A1164 ASN N 105 HIS ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 599 GLN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.103934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.069011 restraints weight = 341470.196| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 7.66 r_work: 0.2954 rms_B_bonded: 6.88 restraints_weight: 2.0000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41339 Z= 0.136 Angle : 0.648 10.930 56982 Z= 0.348 Chirality : 0.043 0.374 6385 Planarity : 0.004 0.045 6351 Dihedral : 22.475 173.531 7658 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.15 % Allowed : 10.58 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.29 (0.13), residues: 4170 helix: 0.72 (0.10), residues: 2415 sheet: -1.10 (0.37), residues: 192 loop : -1.48 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1285 TYR 0.028 0.001 TYR a1613 PHE 0.022 0.002 PHE Q 221 TRP 0.067 0.002 TRP N 394 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (41338) covalent geometry : angle 0.64825 / 0.35 (56982) hydrogen bonds : bond 0.05788 / 3.89 ( 2005) hydrogen bonds : angle 4.73298 / 3.42 ( 5502) Misc. bond : bond 0.00552 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 1.352 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: E 81 ASP cc_start: 0.8968 (t0) cc_final: 0.8751 (t0) REVERT: E 133 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8633 (mp0) REVERT: F 59 LYS cc_start: 0.9477 (tptm) cc_final: 0.9213 (tptm) REVERT: F 63 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: G 24 GLN cc_start: 0.9045 (mp10) cc_final: 0.8702 (mp10) REVERT: A 185 MET cc_start: 0.6491 (mmm) cc_final: 0.6268 (mmm) REVERT: A 886 MET cc_start: 0.9088 (mpp) cc_final: 0.8619 (mmm) REVERT: A 942 TRP cc_start: 0.8436 (m-90) cc_final: 0.7965 (m-90) REVERT: A 1040 MET cc_start: 0.8712 (tpp) cc_final: 0.8410 (tpp) REVERT: A 1233 MET cc_start: 0.6684 (mpp) cc_final: 0.6361 (mpp) REVERT: A 1277 GLU cc_start: 0.9558 (mp0) cc_final: 0.9191 (tp30) REVERT: A 1284 MET cc_start: 0.8411 (mmm) cc_final: 0.8200 (mmm) REVERT: N 335 MET cc_start: 0.4503 (ptm) cc_final: 0.4268 (tpp) REVERT: Q 45 LEU cc_start: 0.8610 (tp) cc_final: 0.8334 (tt) REVERT: Q 372 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9098 (pmm) REVERT: Q 375 MET cc_start: 0.9595 (mtm) cc_final: 0.9072 (mtp) REVERT: V 279 PHE cc_start: 0.8942 (p90) cc_final: 0.8552 (p90) REVERT: V 360 GLU cc_start: 0.9401 (mp0) cc_final: 0.9153 (mp0) REVERT: W 645 GLU cc_start: 0.6998 (tp30) cc_final: 0.6708 (tp30) REVERT: X 908 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: Y 162 MET cc_start: 0.6875 (mmm) cc_final: 0.6453 (mmm) REVERT: Y 486 TRP cc_start: 0.7252 (p-90) cc_final: 0.7036 (p-90) REVERT: a 1675 ARG cc_start: 0.8028 (tpm170) cc_final: 0.7794 (tpm170) outliers start: 43 outliers final: 19 residues processed: 294 average time/residue: 0.2063 time to fit residues: 102.8274 Evaluate side-chains 256 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 908 GLU Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain K residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 427 optimal weight: 7.9990 chunk 180 optimal weight: 30.0000 chunk 270 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 367 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 47 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 89 ASN H 47 GLN H 67 ASN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 GLN P 121 GLN Q 27 HIS ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 148 GLN T 599 GLN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 476 ASN W 478 GLN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 344 GLN ** a1606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.101428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067721 restraints weight = 361617.577| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 8.49 r_work: 0.2839 rms_B_bonded: 7.44 restraints_weight: 2.0000 r_work: 0.2951 rms_B_bonded: 5.20 restraints_weight: 4.0000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 41339 Z= 0.306 Angle : 0.749 10.575 56982 Z= 0.395 Chirality : 0.047 0.369 6385 Planarity : 0.005 0.085 6351 Dihedral : 22.686 175.996 7658 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.48 % Allowed : 12.54 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.44 (0.13), residues: 4170 helix: 0.62 (0.10), residues: 2424 sheet: -1.11 (0.38), residues: 185 loop : -1.61 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a1635 TYR 0.026 0.002 TYR a1613 PHE 0.022 0.002 PHE A1150 TRP 0.065 0.002 TRP N 394 HIS 0.015 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.31 (41338) covalent geometry : angle 0.74924 / 0.40 (56982) hydrogen bonds : bond 0.06811 / 4.65 ( 2005) hydrogen bonds : angle 4.92393 / 3.56 ( 5502) Misc. bond : bond 0.00601 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.8803 (t0) cc_final: 0.8577 (t0) REVERT: F 63 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: A 201 GLN cc_start: 0.3683 (OUTLIER) cc_final: 0.3233 (mm-40) REVERT: A 886 MET cc_start: 0.9095 (mpp) cc_final: 0.8651 (mmm) REVERT: A 942 TRP cc_start: 0.8512 (m-90) cc_final: 0.8100 (m-90) REVERT: A 1233 MET cc_start: 0.6643 (mpp) cc_final: 0.6442 (mpp) REVERT: N 335 MET cc_start: 0.4242 (ptm) cc_final: 0.4030 (tpp) REVERT: P 132 MET cc_start: -0.1101 (mtp) cc_final: -0.1311 (ttp) REVERT: Q 375 MET cc_start: 0.9574 (mtm) cc_final: 0.9016 (mtp) REVERT: T 203 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5185 (tpt) REVERT: V 246 GLU cc_start: 0.9463 (OUTLIER) cc_final: 0.8998 (pm20) REVERT: X 913 MET cc_start: 0.6017 (ppp) cc_final: 0.5557 (ppp) REVERT: Y 404 MET cc_start: 0.7035 (mpp) cc_final: 0.6523 (mmt) REVERT: a 1634 ARG cc_start: 0.3499 (OUTLIER) cc_final: 0.3266 (ptt-90) outliers start: 55 outliers final: 28 residues processed: 269 average time/residue: 0.2020 time to fit residues: 92.6909 Evaluate side-chains 254 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 467 LEU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 208 MET Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 478 GLN Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1634 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 327 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN Q 27 HIS ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1606 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 = 0.4272 r_free = 0.4272 target = 0.102348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.068958 restraints weight = 295543.140| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 7.49 r_work: 0.2886 rms_B_bonded: 7.04 restraints_weight: 2.0000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 41339 Z= 0.200 Angle : 0.674 11.462 56982 Z= 0.360 Chirality : 0.044 0.369 6385 Planarity : 0.004 0.046 6351 Dihedral : 22.635 174.757 7658 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.29 % Allowed : 13.83 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.24 (0.13), residues: 4170 helix: 0.78 (0.10), residues: 2414 sheet: -1.11 (0.38), residues: 186 loop : -1.51 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 80 TYR 0.018 0.002 TYR A1220 PHE 0.057 0.002 PHE Z 259 TRP 0.060 0.002 TRP N 394 HIS 0.011 0.001 HIS a1651 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (41338) covalent geometry : angle 0.67387 / 0.36 (56982) hydrogen bonds : bond 0.05934 / 4.05 ( 2005) hydrogen bonds : angle 4.74070 / 3.43 ( 5502) Misc. bond : bond 0.00536 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 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: C 90 ASP cc_start: 0.8945 (t0) cc_final: 0.8663 (t0) REVERT: E 81 ASP cc_start: 0.9029 (t0) cc_final: 0.8809 (t0) REVERT: F 63 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: G 24 GLN cc_start: 0.9092 (mp10) cc_final: 0.8751 (mp10) REVERT: A 201 GLN cc_start: 0.3740 (OUTLIER) cc_final: 0.3369 (mm-40) REVERT: A 886 MET cc_start: 0.9186 (mpp) cc_final: 0.8755 (mmm) REVERT: A 942 TRP cc_start: 0.8439 (m-90) cc_final: 0.8093 (m-90) REVERT: A 1000 MET cc_start: 0.7258 (tmm) cc_final: 0.6904 (tmm) REVERT: A 1040 MET cc_start: 0.8789 (tpp) cc_final: 0.8567 (tpp) REVERT: A 1233 MET cc_start: 0.6751 (mpp) cc_final: 0.6409 (mpp) REVERT: A 1272 MET cc_start: 0.9021 (tpp) cc_final: 0.8772 (mmt) REVERT: N 335 MET cc_start: 0.4372 (ptm) cc_final: 0.4119 (tpp) REVERT: Q 191 MET cc_start: 0.8696 (tpt) cc_final: 0.8496 (tpt) REVERT: Q 375 MET cc_start: 0.9578 (mtm) cc_final: 0.9005 (mtp) REVERT: T 203 MET cc_start: 0.4518 (OUTLIER) cc_final: 0.4190 (tpt) REVERT: V 246 GLU cc_start: 0.9473 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: V 360 GLU cc_start: 0.9335 (mp0) cc_final: 0.9047 (mp0) REVERT: W 645 GLU cc_start: 0.7125 (tp30) cc_final: 0.6914 (tp30) REVERT: W 913 MET cc_start: 0.5874 (mmm) cc_final: 0.5532 (ttt) REVERT: X 615 MET cc_start: 0.4894 (ttm) cc_final: 0.4530 (tpp) REVERT: Y 162 MET cc_start: 0.6863 (mmm) cc_final: 0.6609 (mmm) REVERT: Y 172 LEU cc_start: 0.0613 (OUTLIER) cc_final: 0.0362 (tp) REVERT: Y 404 MET cc_start: 0.7255 (mpp) cc_final: 0.6812 (mmt) outliers start: 48 outliers final: 29 residues processed: 264 average time/residue: 0.2125 time to fit residues: 96.4769 Evaluate side-chains 257 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 172 LEU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 135 optimal weight: 0.0010 chunk 304 optimal weight: 20.0000 chunk 330 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 351 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 476 ASN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** 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 = 0.4286 r_free = 0.4286 target = 0.103144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.069984 restraints weight = 303524.860| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 6.91 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41339 Z= 0.142 Angle : 0.643 13.202 56982 Z= 0.344 Chirality : 0.043 0.354 6385 Planarity : 0.004 0.050 6351 Dihedral : 22.443 173.287 7658 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.24 % Allowed : 14.42 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.01 (0.13), residues: 4170 helix: 0.97 (0.11), residues: 2413 sheet: -1.04 (0.38), residues: 181 loop : -1.41 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a1635 TYR 0.019 0.001 TYR X 465 PHE 0.017 0.001 PHE T 163 TRP 0.060 0.002 TRP N 394 HIS 0.015 0.001 HIS Z 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (41338) covalent geometry : angle 0.64330 / 0.34 (56982) hydrogen bonds : bond 0.05443 / 3.71 ( 2005) hydrogen bonds : angle 4.56697 / 3.31 ( 5502) Misc. bond : bond 0.00523 / 0.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 63 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: A 201 GLN cc_start: 0.3698 (OUTLIER) cc_final: 0.3250 (mm-40) REVERT: A 886 MET cc_start: 0.9128 (mpp) cc_final: 0.8701 (mmm) REVERT: A 942 TRP cc_start: 0.8413 (m-90) cc_final: 0.7968 (m-90) REVERT: A 1000 MET cc_start: 0.7347 (tmm) cc_final: 0.6979 (tmm) REVERT: A 1040 MET cc_start: 0.8817 (tpp) cc_final: 0.8563 (tpp) REVERT: A 1233 MET cc_start: 0.6725 (mpp) cc_final: 0.6383 (mpp) REVERT: N 335 MET cc_start: 0.4137 (ptm) cc_final: 0.3386 (tpp) REVERT: Q 375 MET cc_start: 0.9361 (mtm) cc_final: 0.8717 (mtp) REVERT: Q 419 LEU cc_start: 0.9526 (mt) cc_final: 0.9297 (pp) REVERT: T 174 HIS cc_start: 0.5950 (m90) cc_final: 0.5149 (p90) REVERT: T 203 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4561 (tpt) REVERT: V 246 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: V 279 PHE cc_start: 0.9238 (p90) cc_final: 0.8693 (p90) REVERT: W 645 GLU cc_start: 0.7013 (tp30) cc_final: 0.6444 (tp30) REVERT: W 913 MET cc_start: 0.5747 (mmm) cc_final: 0.5355 (ttt) REVERT: X 615 MET cc_start: 0.4605 (ttm) cc_final: 0.4105 (tpp) REVERT: Y 162 MET cc_start: 0.7574 (mmm) cc_final: 0.6934 (mmm) REVERT: Y 172 LEU cc_start: 0.0509 (OUTLIER) cc_final: 0.0277 (tp) REVERT: Y 404 MET cc_start: 0.7568 (mpp) cc_final: 0.7078 (mmt) REVERT: Z 256 LYS cc_start: 0.8218 (pptt) cc_final: 0.8008 (pttp) REVERT: a 1675 ARG cc_start: 0.8149 (tpm170) cc_final: 0.7939 (tpm170) outliers start: 46 outliers final: 29 residues processed: 272 average time/residue: 0.2059 time to fit residues: 95.5651 Evaluate side-chains 265 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 172 LEU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain K residue 120 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 248 optimal weight: 0.9980 chunk 433 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 306 optimal weight: 0.0020 chunk 412 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN Q 27 HIS ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 187 ASN T 199 ASN T 599 GLN W 950 HIS ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.103107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.070075 restraints weight = 347961.798| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 7.62 r_work: 0.2911 rms_B_bonded: 7.29 restraints_weight: 2.0000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41339 Z= 0.143 Angle : 0.648 12.666 56982 Z= 0.342 Chirality : 0.042 0.340 6385 Planarity : 0.004 0.051 6351 Dihedral : 22.391 175.091 7658 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.32 % Allowed : 14.88 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4170 helix: 1.08 (0.11), residues: 2413 sheet: -1.21 (0.39), residues: 170 loop : -1.36 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 499 TYR 0.021 0.001 TYR a1613 PHE 0.018 0.001 PHE Y 153 TRP 0.055 0.002 TRP N 394 HIS 0.010 0.001 HIS a1651 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (41338) covalent geometry : angle 0.64835 / 0.34 (56982) hydrogen bonds : bond 0.05337 / 3.65 ( 2005) hydrogen bonds : angle 4.44853 / 3.21 ( 5502) Misc. bond : bond 0.00505 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 1.511 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: F 52 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8654 (mm-30) REVERT: F 63 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: G 90 ASP cc_start: 0.9152 (t0) cc_final: 0.8950 (t0) REVERT: A 886 MET cc_start: 0.9171 (mpp) cc_final: 0.8756 (mmm) REVERT: A 942 TRP cc_start: 0.8483 (m-90) cc_final: 0.8081 (m-90) REVERT: A 1000 MET cc_start: 0.7339 (tmm) cc_final: 0.6870 (tmm) REVERT: A 1040 MET cc_start: 0.8710 (tpp) cc_final: 0.8457 (tpp) REVERT: A 1233 MET cc_start: 0.6738 (mpp) cc_final: 0.6414 (mpp) REVERT: Q 375 MET cc_start: 0.9596 (mtm) cc_final: 0.9117 (mtp) REVERT: Q 419 LEU cc_start: 0.9604 (mt) cc_final: 0.9376 (pp) REVERT: T 174 HIS cc_start: 0.6003 (m90) cc_final: 0.5117 (p90) REVERT: T 203 MET cc_start: 0.4714 (OUTLIER) cc_final: 0.3961 (tpt) REVERT: T 247 MET cc_start: 0.0422 (mmt) cc_final: -0.0549 (ptt) REVERT: V 246 GLU cc_start: 0.9508 (OUTLIER) cc_final: 0.9099 (pm20) REVERT: V 279 PHE cc_start: 0.9119 (p90) cc_final: 0.8617 (p90) REVERT: W 645 GLU cc_start: 0.7011 (tp30) cc_final: 0.6547 (tp30) REVERT: W 913 MET cc_start: 0.5969 (mmm) cc_final: 0.5662 (ttt) REVERT: X 615 MET cc_start: 0.4724 (ttm) cc_final: 0.4487 (tpp) REVERT: X 905 HIS cc_start: 0.9148 (t-90) cc_final: 0.8896 (t-90) REVERT: Y 162 MET cc_start: 0.7116 (mmm) cc_final: 0.6702 (mmm) REVERT: Y 172 LEU cc_start: 0.0651 (OUTLIER) cc_final: 0.0362 (tp) REVERT: Y 404 MET cc_start: 0.7251 (mpp) cc_final: 0.6845 (mmt) REVERT: a 1675 ARG cc_start: 0.7988 (tpm170) cc_final: 0.7775 (tpm170) outliers start: 49 outliers final: 32 residues processed: 271 average time/residue: 0.2160 time to fit residues: 100.2476 Evaluate side-chains 266 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 172 LEU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 137 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 377 optimal weight: 0.5980 chunk 387 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 384 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 626 HIS ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1606 HIS ** 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 = 0.4278 r_free = 0.4278 target = 0.102540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.069000 restraints weight = 336603.318| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 7.66 r_work: 0.2896 rms_B_bonded: 7.40 restraints_weight: 2.0000 r_work: 0.3008 rms_B_bonded: 5.13 restraints_weight: 4.0000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41339 Z= 0.177 Angle : 0.663 13.499 56982 Z= 0.351 Chirality : 0.043 0.337 6385 Planarity : 0.004 0.051 6351 Dihedral : 22.454 175.893 7658 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.26 % Allowed : 15.17 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4170 helix: 1.05 (0.11), residues: 2419 sheet: -1.34 (0.39), residues: 175 loop : -1.31 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 931 TYR 0.020 0.001 TYR a1613 PHE 0.015 0.002 PHE N 391 TRP 0.042 0.002 TRP Y 486 HIS 0.009 0.001 HIS a1651 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (41338) covalent geometry : angle 0.66330 / 0.35 (56982) hydrogen bonds : bond 0.05505 / 3.79 ( 2005) hydrogen bonds : angle 4.47282 / 3.24 ( 5502) Misc. bond : bond 0.00503 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 1.146 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: F 52 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8369 (mm-30) REVERT: F 63 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: A 886 MET cc_start: 0.9134 (mpp) cc_final: 0.8715 (mmm) REVERT: A 942 TRP cc_start: 0.8373 (m-90) cc_final: 0.7963 (m-90) REVERT: A 1040 MET cc_start: 0.8686 (tpp) cc_final: 0.8439 (tpp) REVERT: A 1233 MET cc_start: 0.6768 (mpp) cc_final: 0.6435 (mpp) REVERT: P 190 MET cc_start: -0.1328 (mtt) cc_final: -0.1603 (mmm) REVERT: Q 375 MET cc_start: 0.9575 (mtm) cc_final: 0.8982 (mtp) REVERT: Q 1805 MET cc_start: 0.1665 (ptt) cc_final: 0.1381 (ppp) REVERT: T 174 HIS cc_start: 0.5975 (m90) cc_final: 0.5115 (p90) REVERT: T 203 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4138 (tpt) REVERT: V 246 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.9071 (pm20) REVERT: V 279 PHE cc_start: 0.9108 (p90) cc_final: 0.8615 (p90) REVERT: W 913 MET cc_start: 0.5998 (mmm) cc_final: 0.5650 (ttt) REVERT: X 615 MET cc_start: 0.4954 (ttm) cc_final: 0.4744 (tpp) REVERT: X 905 HIS cc_start: 0.9112 (t-90) cc_final: 0.8878 (t-90) REVERT: Y 162 MET cc_start: 0.7183 (mmm) cc_final: 0.6859 (mmm) REVERT: Y 172 LEU cc_start: 0.0559 (OUTLIER) cc_final: 0.0281 (tp) REVERT: Y 352 MET cc_start: 0.1777 (tmm) cc_final: 0.1559 (ttp) REVERT: Y 404 MET cc_start: 0.7313 (mpp) cc_final: 0.6924 (mmt) REVERT: Z 256 LYS cc_start: 0.8149 (pttp) cc_final: 0.7949 (mmmt) REVERT: Z 259 PHE cc_start: 0.6656 (m-80) cc_final: 0.6238 (m-80) REVERT: a 1675 ARG cc_start: 0.8014 (tpm170) cc_final: 0.7778 (tpm170) REVERT: K 53 ARG cc_start: 0.7979 (ttt180) cc_final: 0.6774 (mmp-170) outliers start: 47 outliers final: 32 residues processed: 270 average time/residue: 0.1993 time to fit residues: 91.8571 Evaluate side-chains 265 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 282 GLU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 172 LEU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 352 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 203 optimal weight: 40.0000 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 50.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN N 414 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1606 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 = 0.4272 r_free = 0.4272 target = 0.102166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067288 restraints weight = 346428.617| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 8.77 r_work: 0.2888 rms_B_bonded: 7.17 restraints_weight: 2.0000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41339 Z= 0.200 Angle : 0.692 13.177 56982 Z= 0.363 Chirality : 0.044 0.386 6385 Planarity : 0.004 0.062 6351 Dihedral : 22.529 175.482 7658 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.05 % Allowed : 15.76 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4170 helix: 1.03 (0.11), residues: 2427 sheet: -1.22 (0.39), residues: 170 loop : -1.35 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a1635 TYR 0.028 0.002 TYR A1123 PHE 0.015 0.002 PHE Q 324 TRP 0.045 0.002 TRP Y 486 HIS 0.009 0.001 HIS a1651 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (41338) covalent geometry : angle 0.69241 / 0.36 (56982) hydrogen bonds : bond 0.05591 / 3.85 ( 2005) hydrogen bonds : angle 4.50121 / 3.26 ( 5502) Misc. bond : bond 0.00523 / 0.28 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8934 (t0) cc_final: 0.8700 (t0) REVERT: F 63 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: A 201 GLN cc_start: 0.3930 (OUTLIER) cc_final: 0.3560 (mm-40) REVERT: A 886 MET cc_start: 0.9152 (mpp) cc_final: 0.8699 (mmm) REVERT: A 942 TRP cc_start: 0.8362 (m-90) cc_final: 0.7938 (m-90) REVERT: A 1000 MET cc_start: 0.7144 (tmm) cc_final: 0.6743 (tmm) REVERT: N 122 MET cc_start: 0.3928 (pmm) cc_final: 0.3398 (tpt) REVERT: N 414 GLN cc_start: 0.3289 (OUTLIER) cc_final: 0.2428 (pt0) REVERT: P 190 MET cc_start: -0.1282 (mtt) cc_final: -0.1582 (mmm) REVERT: Q 375 MET cc_start: 0.9587 (mtm) cc_final: 0.8987 (mtp) REVERT: Q 1805 MET cc_start: 0.1624 (ptt) cc_final: 0.1149 (ppp) REVERT: R 265 TYR cc_start: 0.8672 (t80) cc_final: 0.8407 (t80) REVERT: T 174 HIS cc_start: 0.5977 (m90) cc_final: 0.5096 (p90) REVERT: T 203 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.4349 (tpt) REVERT: V 246 GLU cc_start: 0.9486 (OUTLIER) cc_final: 0.9098 (pm20) REVERT: V 279 PHE cc_start: 0.9158 (p90) cc_final: 0.8672 (p90) REVERT: W 913 MET cc_start: 0.6116 (mmm) cc_final: 0.5783 (ttt) REVERT: X 615 MET cc_start: 0.4969 (ttm) cc_final: 0.4768 (tpp) REVERT: Y 162 MET cc_start: 0.7167 (mmm) cc_final: 0.6886 (mmm) REVERT: Y 172 LEU cc_start: 0.0768 (OUTLIER) cc_final: 0.0515 (tp) REVERT: Y 352 MET cc_start: 0.1814 (tmm) cc_final: 0.1586 (ttp) REVERT: Y 404 MET cc_start: 0.7280 (mpp) cc_final: 0.6897 (mmt) REVERT: Z 259 PHE cc_start: 0.6666 (m-80) cc_final: 0.6436 (m-80) outliers start: 39 outliers final: 27 residues processed: 261 average time/residue: 0.2033 time to fit residues: 90.5643 Evaluate side-chains 259 residues out of total 3733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 414 GLN Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 203 MET Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 172 LEU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 215 VAL Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 403 optimal weight: 20.0000 chunk 390 optimal weight: 30.0000 chunk 402 optimal weight: 5.9990 chunk 336 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 408 optimal weight: 0.2980 chunk 256 optimal weight: 8.9990 chunk 425 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1606 HIS ** 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 = 0.4275 r_free = 0.4275 target = 0.102365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.069802 restraints weight = 286802.303| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 6.85 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 41339 Z= 0.198 Angle : 0.774 59.152 56982 Z= 0.420 Chirality : 0.044 0.689 6385 Planarity : 0.004 0.083 6351 Dihedral : 22.534 175.499 7658 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.05 % Allowed : 15.60 % Favored : 83.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.09 (0.13), residues: 4170 helix: 1.06 (0.11), residues: 2419 sheet: -1.25 (0.39), residues: 171 loop : -1.34 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a1675 TYR 0.024 0.001 TYR A1123 PHE 0.015 0.001 PHE Q 324 TRP 0.040 0.002 TRP Y 486 HIS 0.088 0.002 HIS X 905 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (41338) covalent geometry : angle 0.77367 / 0.42 (56982) hydrogen bonds : bond 0.05572 / 3.84 ( 2005) hydrogen bonds : angle 4.49923 / 3.25 ( 5502) Misc. bond : bond 0.00523 / 0.28 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18135.83 seconds wall clock time: 307 minutes 55.11 seconds (18475.11 seconds total)