Starting phenix.real_space_refine on Sat Mar 7 08:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.map" model { file = "/net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z87_14545/03_2026/7z87_14545.cif" } resolution = 2.91 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 52 5.49 5 S 235 5.16 5 Cl 1 4.86 5 C 25160 2.51 5 N 6701 2.21 5 O 7558 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39708 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 29194 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3689, 29184 Classifications: {'peptide': 3689} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 3531} Chain breaks: 18 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 31, 'GLN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 5, 'ARG:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 286 Conformer: "B" Number of residues, atoms: 3689, 29184 Classifications: {'peptide': 3689} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 3531} Chain breaks: 18 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 31, 'GLN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 5, 'ARG:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 286 bond proxies already assigned to first conformer: 29758 Chain: "B" Number of atoms: 3953 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3996 Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5267 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 188 Unusual residues: {'1IX': 1} Classifications: {'undetermined': 1, 'water': 154} Link IDs: {None: 154} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A3122 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A3122 " occ=0.50 Time building chain proxies: 14.53, per 1000 atoms: 0.37 Number of scatterers: 39708 At special positions: 0 Unit cell: (126.488, 169.52, 236.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 235 16.00 P 52 15.00 F 1 9.00 O 7558 8.00 N 6701 7.00 C 25160 6.00 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=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 2.6 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 12 sheets defined 63.8% alpha, 4.8% beta 21 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.970A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 removed outlier: 3.680A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 97 through 102 Proline residue: A 102 - end of helix Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 120 through 138 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.015A pdb=" N GLU A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.520A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.654A pdb=" N GLU A 188 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.501A pdb=" N GLU A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.508A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 355 through 377 removed outlier: 4.336A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.867A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.760A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.807A pdb=" N CYS A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.301A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 559 through 578 Processing helix chain 'A' and resid 616 through 634 removed outlier: 4.131A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.683A pdb=" N LEU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 736 Processing helix chain 'A' and resid 744 through 747 Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.606A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.616A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 827 through 839 removed outlier: 4.350A pdb=" N ASN A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 865 through 870 removed outlier: 3.646A pdb=" N LYS A 868 " --> pdb=" O GLN A 865 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 870 " --> pdb=" O ASN A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 removed outlier: 3.640A pdb=" N MET A 880 " --> pdb=" O SER A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.514A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.551A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.804A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1018 Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 3.974A pdb=" N ARG A1026 " --> pdb=" O ASP A1022 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 Processing helix chain 'A' and resid 1095 through 1116 removed outlier: 3.508A pdb=" N PHE A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1139 removed outlier: 3.620A pdb=" N GLN A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.638A pdb=" N VAL A1169 " --> pdb=" O LEU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1242 through 1246 Processing helix chain 'A' and resid 1250 through 1267 removed outlier: 3.765A pdb=" N LEU A1254 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.502A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1301 removed outlier: 4.096A pdb=" N SER A1300 " --> pdb=" O PHE A1296 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A1301 " --> pdb=" O PHE A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1350 removed outlier: 3.835A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1360 removed outlier: 3.641A pdb=" N LYS A1360 " --> pdb=" O LYS A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1377 removed outlier: 3.546A pdb=" N MET A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1407 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1412 through 1423 removed outlier: 4.080A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1446 through 1462 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.692A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1490 Processing helix chain 'A' and resid 1504 through 1522 removed outlier: 3.857A pdb=" N GLN A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY A1522 " --> pdb=" O ALA A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1556 through 1563 Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.728A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1584 removed outlier: 3.533A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 Processing helix chain 'A' and resid 1612 through 1625 removed outlier: 3.542A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1629 Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 4.598A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 Processing helix chain 'A' and resid 1685 through 1694 Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 3.736A pdb=" N PHE A1698 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1719 Processing helix chain 'A' and resid 1733 through 1753 Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.818A pdb=" N LEU A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1831 removed outlier: 3.792A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS A1831 " --> pdb=" O LEU A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1852 removed outlier: 3.705A pdb=" N PHE A1840 " --> pdb=" O LEU A1836 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1908 through 1924 removed outlier: 4.531A pdb=" N THR A1912 " --> pdb=" O GLY A1908 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A1913 " --> pdb=" O ASN A1909 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1953 removed outlier: 3.548A pdb=" N ARG A1937 " --> pdb=" O LEU A1933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1966 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 Processing helix chain 'A' and resid 2035 through 2048 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2124 through 2134 Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.603A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 Processing helix chain 'A' and resid 2159 through 2164 removed outlier: 5.758A pdb=" N LYS A2162 " --> pdb=" O PRO A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 Processing helix chain 'A' and resid 2184 through 2196 removed outlier: 3.678A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2255 through 2261 Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.687A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2306 removed outlier: 3.895A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.444A pdb=" N ALA A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2354 removed outlier: 3.559A pdb=" N GLN A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2371 removed outlier: 4.172A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2374 through 2386 removed outlier: 4.214A pdb=" N PHE A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN A2380 " --> pdb=" O ASP A2376 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA A2381 " --> pdb=" O ARG A2377 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.604A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.573A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 3.866A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2466 through 2482 removed outlier: 3.526A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.592A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A2500 " --> pdb=" O GLN A2496 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2516 through 2527 Processing helix chain 'A' and resid 2534 through 2544 removed outlier: 3.949A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2546 No H-bonds generated for 'chain 'A' and resid 2545 through 2546' Processing helix chain 'A' and resid 2547 through 2549 No H-bonds generated for 'chain 'A' and resid 2547 through 2549' Processing helix chain 'A' and resid 2550 through 2564 removed outlier: 4.316A pdb=" N LEU A2555 " --> pdb=" O GLU A2551 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N SER A2556 " --> pdb=" O VAL A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2767 removed outlier: 4.128A pdb=" N LYS A2762 " --> pdb=" O LYS A2758 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET A2763 " --> pdb=" O SER A2759 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2864 Processing helix chain 'A' and resid 2865 through 2869 removed outlier: 3.518A pdb=" N LEU A2869 " --> pdb=" O ALA A2866 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2898 removed outlier: 3.580A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2934 Processing helix chain 'A' and resid 2944 through 2948 Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.939A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.603A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3017 Processing helix chain 'A' and resid 3033 through 3037 Processing helix chain 'A' and resid 3040 through 3054 removed outlier: 3.792A pdb=" N GLN A3054 " --> pdb=" O LYS A3050 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3069 Processing helix chain 'A' and resid 3072 through 3082 removed outlier: 3.758A pdb=" N TYR A3082 " --> pdb=" O LEU A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3084 through 3093 Processing helix chain 'A' and resid 3095 through 3116 removed outlier: 3.583A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3130 Processing helix chain 'A' and resid 3131 through 3147 Processing helix chain 'A' and resid 3154 through 3166 Processing helix chain 'A' and resid 3175 through 3196 Processing helix chain 'A' and resid 3227 through 3249 removed outlier: 3.620A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3261 Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 3.721A pdb=" N ARG A3289 " --> pdb=" O HIS A3285 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3308 removed outlier: 4.062A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A3304 " --> pdb=" O VAL A3300 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A3306 " --> pdb=" O LYS A3302 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3344 Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 3.860A pdb=" N ILE A3351 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3355 through 3361 Processing helix chain 'A' and resid 3371 through 3394 removed outlier: 3.537A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.739A pdb=" N PHE A3419 " --> pdb=" O THR A3415 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3433 through 3440 Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.715A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3466 through 3474 removed outlier: 3.848A pdb=" N ILE A3472 " --> pdb=" O LEU A3468 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3489 removed outlier: 3.990A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3490 through 3497 removed outlier: 5.922A pdb=" N TRP A3493 " --> pdb=" O VAL A3490 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A3495 " --> pdb=" O CYS A3492 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3529 through 3539 removed outlier: 3.813A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3562 removed outlier: 3.560A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A3555 " --> pdb=" O ASN A3551 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.138A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A3614 " --> pdb=" O TYR A3610 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3627 removed outlier: 3.749A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3640 Processing helix chain 'A' and resid 3641 through 3650 removed outlier: 4.054A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3651 through 3654 removed outlier: 3.514A pdb=" N MET A3654 " --> pdb=" O LEU A3651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3651 through 3654' Processing helix chain 'A' and resid 3660 through 3673 removed outlier: 3.503A pdb=" N ASN A3671 " --> pdb=" O LEU A3667 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A3673 " --> pdb=" O LYS A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3684 removed outlier: 3.551A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3775 Processing helix chain 'A' and resid 3778 through 3784 removed outlier: 3.562A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 3.833A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3861 removed outlier: 4.005A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 Processing helix chain 'A' and resid 3881 through 3890 Processing helix chain 'A' and resid 3893 through 3918 Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.851A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3993 Processing helix chain 'A' and resid 3995 through 4002 Processing helix chain 'A' and resid 4003 through 4008 Processing helix chain 'A' and resid 4039 through 4050 removed outlier: 3.601A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4088 through 4093 removed outlier: 4.125A pdb=" N GLU A4093 " --> pdb=" O ARG A4090 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.244A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.839A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 377 through 393 removed outlier: 3.736A pdb=" N LEU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.749A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'C' and resid 29 through 49 Processing helix chain 'C' and resid 87 through 96 removed outlier: 3.873A pdb=" N ILE C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.757A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 371 through 386 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.727A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 Processing helix chain 'C' and resid 519 through 537 removed outlier: 3.912A pdb=" N THR C 523 " --> pdb=" O PRO C 519 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.837A pdb=" N LYS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 626 Processing helix chain 'C' and resid 628 through 649 removed outlier: 3.640A pdb=" N PHE C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 669 Processing helix chain 'C' and resid 672 through 682 Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 725 through 731 removed outlier: 3.632A pdb=" N LEU C 729 " --> pdb=" O VAL C 725 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 6.945A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.705A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.422A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 88 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 removed outlier: 7.804A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 395 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE B 350 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 397 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 346 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 347 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.273A pdb=" N ARG C 130 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 225 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 253 removed outlier: 3.739A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 361 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLN C 360 " --> pdb=" O GLN C 423 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN C 423 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE C 340 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG C 250 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 342 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 252 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY C 344 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 464 through 466 removed outlier: 3.691A pdb=" N LYS C 465 " --> pdb=" O GLU C 474 " (cutoff:3.500A) 2081 hydrogen bonds defined for protein. 6113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 15.20 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12476 1.34 - 1.46: 9104 1.46 - 1.59: 18360 1.59 - 1.71: 100 1.71 - 1.83: 374 Bond restraints: 40414 Sorted by residual: bond pdb=" C11 1IX A4201 " pdb="CL1 1IX A4201 " ideal model delta sigma weight residual 1.728 1.835 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C24 1IX A4201 " pdb=" N26 1IX A4201 " ideal model delta sigma weight residual 1.371 1.472 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C12 1IX A4201 " pdb=" C13 1IX A4201 " ideal model delta sigma weight residual 1.379 1.466 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C14 1IX A4201 " pdb=" C16 1IX A4201 " ideal model delta sigma weight residual 1.480 1.562 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C ASP B 341 " pdb=" N ASP B 342 " ideal model delta sigma weight residual 1.329 1.253 0.076 1.86e-02 2.89e+03 1.67e+01 ... (remaining 40409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 54274 3.30 - 6.59: 518 6.59 - 9.89: 42 9.89 - 13.18: 6 13.18 - 16.48: 1 Bond angle restraints: 54841 Sorted by residual: angle pdb=" N THR A 169 " pdb=" CA THR A 169 " pdb=" C THR A 169 " ideal model delta sigma weight residual 113.72 97.24 16.48 1.30e+00 5.92e-01 1.61e+02 angle pdb=" C MET A 948 " pdb=" N PRO A 949 " pdb=" CA PRO A 949 " ideal model delta sigma weight residual 119.84 128.86 -9.02 1.25e+00 6.40e-01 5.21e+01 angle pdb=" N ILE A2137 " pdb=" CA ILE A2137 " pdb=" C ILE A2137 " ideal model delta sigma weight residual 113.71 107.53 6.18 9.50e-01 1.11e+00 4.23e+01 angle pdb=" N LYS A 165 " pdb=" CA LYS A 165 " pdb=" C LYS A 165 " ideal model delta sigma weight residual 111.28 119.80 -8.52 1.35e+00 5.49e-01 3.98e+01 angle pdb=" C SER A2547 " pdb=" N PRO A2548 " pdb=" CA PRO A2548 " ideal model delta sigma weight residual 119.84 127.04 -7.20 1.25e+00 6.40e-01 3.32e+01 ... (remaining 54836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 23855 34.15 - 68.29: 668 68.29 - 102.44: 48 102.44 - 136.59: 1 136.59 - 170.73: 1 Dihedral angle restraints: 24573 sinusoidal: 10325 harmonic: 14248 Sorted by residual: dihedral pdb=" CA LEU A2122 " pdb=" C LEU A2122 " pdb=" N PRO A2123 " pdb=" CA PRO A2123 " ideal model delta harmonic sigma weight residual -180.00 -143.46 -36.54 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA LYS A1960 " pdb=" C LYS A1960 " pdb=" N PHE A1961 " pdb=" CA PHE A1961 " ideal model delta harmonic sigma weight residual 180.00 149.04 30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA PRO A1020 " pdb=" C PRO A1020 " pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta harmonic sigma weight residual -180.00 -149.19 -30.81 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 24570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5767 0.084 - 0.168: 458 0.168 - 0.252: 15 0.252 - 0.336: 1 0.336 - 0.420: 2 Chirality restraints: 6243 Sorted by residual: chirality pdb=" CA HIS C 411 " pdb=" N HIS C 411 " pdb=" C HIS C 411 " pdb=" CB HIS C 411 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ASP A 168 " pdb=" N ASP A 168 " pdb=" C ASP A 168 " pdb=" CB ASP A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA LYS A 165 " pdb=" N LYS A 165 " pdb=" C LYS A 165 " pdb=" CB LYS A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 6240 not shown) Planarity restraints: 6791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 165 " 0.027 2.00e-02 2.50e+03 5.36e-02 2.88e+01 pdb=" C LYS A 165 " -0.093 2.00e-02 2.50e+03 pdb=" O LYS A 165 " 0.035 2.00e-02 2.50e+03 pdb=" N ILE A 166 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 499 " -0.063 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO B 500 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 166 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ILE A 166 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE A 166 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 167 " 0.019 2.00e-02 2.50e+03 ... (remaining 6788 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4668 2.74 - 3.28: 43167 3.28 - 3.82: 67966 3.82 - 4.36: 82526 4.36 - 4.90: 134520 Nonbonded interactions: 332847 Sorted by model distance: nonbonded pdb=" O PRO A3960 " pdb=" O HOH A4301 " model vdw 2.199 3.040 nonbonded pdb=" O GLY A1964 " pdb=" OG SER A1968 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 887 " pdb=" NH1 ARG A 891 " model vdw 2.199 3.120 nonbonded pdb=" O VAL A2938 " pdb=" O HOH A4302 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG B 399 " pdb=" O LEU C 516 " model vdw 2.204 3.120 ... (remaining 332842 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 56.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.120 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 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 : 0.006 0.127 40414 Z= 0.290 Angle : 0.852 16.481 54841 Z= 0.481 Chirality : 0.047 0.420 6243 Planarity : 0.005 0.091 6791 Dihedral : 15.493 170.731 15285 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.48 % Favored : 89.39 % Rotamer: Outliers : 0.38 % Allowed : 0.54 % Favored : 99.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % 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: -1.73 (0.12), residues: 4795 helix: -0.04 (0.10), residues: 2839 sheet: -1.56 (0.35), residues: 210 loop : -2.99 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A2530 TYR 0.023 0.002 TYR B 71 PHE 0.022 0.002 PHE A 531 TRP 0.030 0.002 TRP A2196 HIS 0.012 0.001 HIS A2787 Details of bonding type rmsd covalent geometry : bond 0.00640 (40414) covalent geometry : angle 0.85243 (54841) hydrogen bonds : bond 0.15106 ( 2131) hydrogen bonds : angle 6.59719 ( 6209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 917 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6520 (mpt-90) REVERT: A 80 GLU cc_start: 0.6275 (mp0) cc_final: 0.5794 (mp0) REVERT: A 165 LYS cc_start: 0.3880 (OUTLIER) cc_final: 0.3166 (tttt) REVERT: A 172 GLU cc_start: 0.7713 (tt0) cc_final: 0.7001 (tm-30) REVERT: A 210 SER cc_start: 0.7594 (t) cc_final: 0.7105 (m) REVERT: A 214 GLU cc_start: 0.6814 (tt0) cc_final: 0.6593 (tt0) REVERT: A 239 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6315 (mp0) REVERT: A 263 LYS cc_start: 0.7495 (mptt) cc_final: 0.6873 (mppt) REVERT: A 303 HIS cc_start: 0.5763 (t-90) cc_final: 0.5501 (t-90) REVERT: A 309 LYS cc_start: 0.6558 (ttmt) cc_final: 0.6221 (ttmm) REVERT: A 340 TYR cc_start: 0.6818 (t80) cc_final: 0.6342 (t80) REVERT: A 342 MET cc_start: 0.6828 (mmp) cc_final: 0.6479 (mmt) REVERT: A 351 ASN cc_start: 0.6831 (t0) cc_final: 0.6545 (t0) REVERT: A 373 CYS cc_start: 0.6544 (m) cc_final: 0.6106 (m) REVERT: A 438 LEU cc_start: 0.7766 (mp) cc_final: 0.7506 (mm) REVERT: A 466 LEU cc_start: 0.6011 (tt) cc_final: 0.5777 (mt) REVERT: A 534 LEU cc_start: 0.6399 (mt) cc_final: 0.6174 (mt) REVERT: A 578 LYS cc_start: 0.6680 (ptpt) cc_final: 0.6296 (ptpp) REVERT: A 633 ILE cc_start: 0.7376 (mm) cc_final: 0.7126 (mm) REVERT: A 672 ILE cc_start: 0.7737 (mt) cc_final: 0.7380 (mp) REVERT: A 701 TYR cc_start: 0.6183 (m-80) cc_final: 0.5930 (m-80) REVERT: A 720 GLN cc_start: 0.6151 (mm-40) cc_final: 0.5935 (mm110) REVERT: A 775 GLU cc_start: 0.7008 (tt0) cc_final: 0.6019 (mt-10) REVERT: A 781 ASP cc_start: 0.6787 (m-30) cc_final: 0.6307 (m-30) REVERT: A 823 GLN cc_start: 0.6053 (tt0) cc_final: 0.5630 (mm-40) REVERT: A 849 GLU cc_start: 0.5301 (pm20) cc_final: 0.5015 (pt0) REVERT: A 857 GLN cc_start: 0.6391 (mt0) cc_final: 0.5738 (mm110) REVERT: A 865 GLN cc_start: 0.6754 (mt0) cc_final: 0.6205 (mt0) REVERT: A 881 LYS cc_start: 0.5972 (mttp) cc_final: 0.5417 (mmmt) REVERT: A 889 GLU cc_start: 0.6280 (tm-30) cc_final: 0.5437 (tp30) REVERT: A 916 GLU cc_start: 0.6463 (mp0) cc_final: 0.6107 (tt0) REVERT: A 989 MET cc_start: 0.5867 (mmt) cc_final: 0.5651 (mmm) REVERT: A 1015 ASP cc_start: 0.5591 (m-30) cc_final: 0.5178 (m-30) REVERT: A 1084 ASN cc_start: 0.6108 (m-40) cc_final: 0.5887 (m110) REVERT: A 1087 ARG cc_start: 0.4839 (ttm170) cc_final: 0.4232 (mtp85) REVERT: A 1136 ARG cc_start: 0.5004 (ptp90) cc_final: 0.4080 (ptp90) REVERT: A 1185 HIS cc_start: 0.4774 (t-90) cc_final: 0.4517 (t-170) REVERT: A 1489 LYS cc_start: 0.5212 (ttmm) cc_final: 0.4943 (mttp) REVERT: A 1509 GLN cc_start: 0.5593 (tt0) cc_final: 0.4810 (tp-100) REVERT: A 1576 ASP cc_start: 0.6025 (p0) cc_final: 0.5645 (m-30) REVERT: A 1592 MET cc_start: 0.6600 (tpt) cc_final: 0.5937 (tpt) REVERT: A 1607 GLU cc_start: 0.5757 (mm-30) cc_final: 0.5412 (tp30) REVERT: A 1614 GLN cc_start: 0.5572 (tt0) cc_final: 0.5233 (tt0) REVERT: A 1740 VAL cc_start: 0.4954 (t) cc_final: 0.4753 (t) REVERT: A 1762 MET cc_start: 0.4582 (mmp) cc_final: 0.4159 (mmp) REVERT: A 1795 VAL cc_start: 0.6179 (t) cc_final: 0.5766 (t) REVERT: A 1799 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5366 (mt-10) REVERT: A 1804 MET cc_start: 0.5614 (mtp) cc_final: 0.5194 (mtp) REVERT: A 1849 ASP cc_start: 0.6440 (t0) cc_final: 0.5223 (m-30) REVERT: A 1869 LYS cc_start: 0.5807 (mmmm) cc_final: 0.5527 (mmtm) REVERT: A 1936 ARG cc_start: 0.5904 (mmm160) cc_final: 0.5634 (mmm160) REVERT: A 1949 ILE cc_start: 0.6261 (mt) cc_final: 0.5853 (mt) REVERT: A 1971 PRO cc_start: 0.3950 (Cg_endo) cc_final: 0.3635 (Cg_exo) REVERT: A 2085 MET cc_start: 0.6027 (pmm) cc_final: 0.5566 (pmm) REVERT: A 2162 LYS cc_start: 0.7362 (mttp) cc_final: 0.7075 (mmtm) REVERT: A 2163 HIS cc_start: 0.6394 (m-70) cc_final: 0.5691 (m-70) REVERT: A 2170 GLN cc_start: 0.6504 (tt0) cc_final: 0.6288 (tt0) REVERT: A 2220 MET cc_start: 0.6461 (mtm) cc_final: 0.6205 (mtt) REVERT: A 2221 LYS cc_start: 0.5166 (tttm) cc_final: 0.4852 (tppp) REVERT: A 2230 VAL cc_start: 0.6051 (m) cc_final: 0.5679 (p) REVERT: A 2232 ARG cc_start: 0.6508 (ttm170) cc_final: 0.6129 (mtp85) REVERT: A 2239 LYS cc_start: 0.6287 (tmmt) cc_final: 0.5941 (ttpt) REVERT: A 2243 GLU cc_start: 0.6285 (tm-30) cc_final: 0.6001 (pt0) REVERT: A 2309 PHE cc_start: 0.7918 (m-80) cc_final: 0.7601 (m-80) REVERT: A 2356 MET cc_start: 0.5481 (mtm) cc_final: 0.5267 (mtp) REVERT: A 2357 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5446 (mp0) REVERT: A 2369 LYS cc_start: 0.7436 (mttt) cc_final: 0.6329 (mmpt) REVERT: A 2379 MET cc_start: 0.7635 (tpp) cc_final: 0.7199 (tpt) REVERT: A 2414 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7163 (mm-40) REVERT: A 2430 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6451 (tt0) REVERT: A 2434 VAL cc_start: 0.6981 (t) cc_final: 0.6780 (p) REVERT: A 2437 ASP cc_start: 0.5945 (m-30) cc_final: 0.5551 (m-30) REVERT: A 2445 LYS cc_start: 0.7568 (mmtp) cc_final: 0.7244 (ttmt) REVERT: A 2447 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7507 (mmpt) REVERT: A 2498 ILE cc_start: 0.7337 (pt) cc_final: 0.7126 (pp) REVERT: A 2519 LEU cc_start: 0.6631 (tp) cc_final: 0.6425 (tp) REVERT: A 2522 ARG cc_start: 0.5786 (tmt170) cc_final: 0.5176 (ttm-80) REVERT: A 2568 MET cc_start: 0.5317 (ptm) cc_final: 0.4951 (ptt) REVERT: A 2571 ASP cc_start: 0.6078 (m-30) cc_final: 0.5722 (m-30) REVERT: A 2806 LYS cc_start: 0.6877 (tmtt) cc_final: 0.6633 (tttm) REVERT: A 2818 LYS cc_start: 0.7593 (tttt) cc_final: 0.6573 (tmmt) REVERT: A 2824 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5874 (tttt) REVERT: A 2856 SER cc_start: 0.8273 (p) cc_final: 0.7342 (t) REVERT: A 2864 GLN cc_start: 0.6857 (mm-40) cc_final: 0.5877 (tm-30) REVERT: A 2951 GLN cc_start: 0.6047 (tp40) cc_final: 0.5382 (pm20) REVERT: A 2990 GLU cc_start: 0.6957 (tt0) cc_final: 0.6447 (tt0) REVERT: A 2995 GLU cc_start: 0.7338 (tt0) cc_final: 0.6975 (tt0) REVERT: A 3067 LYS cc_start: 0.6843 (ptmm) cc_final: 0.6311 (pttp) REVERT: A 3090 TYR cc_start: 0.7675 (m-80) cc_final: 0.6545 (m-80) REVERT: A 3238 MET cc_start: 0.7470 (mtm) cc_final: 0.6813 (mtp) REVERT: A 3289 ARG cc_start: 0.6892 (mpt90) cc_final: 0.6201 (mpt-90) REVERT: A 3414 MET cc_start: 0.5556 (mmm) cc_final: 0.5309 (mmm) REVERT: A 3442 TYR cc_start: 0.5436 (m-10) cc_final: 0.5117 (m-80) REVERT: A 3460 GLU cc_start: 0.5819 (pm20) cc_final: 0.5224 (tm-30) REVERT: A 3582 GLU cc_start: 0.5563 (mp0) cc_final: 0.5291 (mt-10) REVERT: A 3712 LEU cc_start: 0.5991 (mp) cc_final: 0.5390 (tp) REVERT: A 3718 ARG cc_start: 0.4891 (mpp80) cc_final: 0.4570 (mpp80) REVERT: A 3729 MET cc_start: 0.4595 (mtp) cc_final: 0.4362 (ttm) REVERT: A 3750 PHE cc_start: 0.7292 (m-80) cc_final: 0.7088 (m-80) REVERT: A 3796 MET cc_start: 0.6659 (mmp) cc_final: 0.6248 (mmm) REVERT: A 3813 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6813 (tttt) REVERT: A 3814 ASP cc_start: 0.6008 (m-30) cc_final: 0.5539 (m-30) REVERT: A 3818 ASN cc_start: 0.5985 (p0) cc_final: 0.5651 (p0) REVERT: A 3858 MET cc_start: 0.6917 (tmm) cc_final: 0.6672 (tmm) REVERT: A 3932 MET cc_start: 0.7762 (mmm) cc_final: 0.7345 (tpt) REVERT: A 3941 ASP cc_start: 0.6882 (t0) cc_final: 0.6619 (t0) REVERT: A 3951 GLN cc_start: 0.5330 (tt0) cc_final: 0.4358 (tm-30) REVERT: A 4007 LYS cc_start: 0.5310 (mmmt) cc_final: 0.4551 (mtpt) REVERT: A 4062 ASP cc_start: 0.5494 (m-30) cc_final: 0.5038 (m-30) REVERT: A 4082 ARG cc_start: 0.4658 (ttm110) cc_final: 0.4391 (ttm-80) REVERT: B 61 ASP cc_start: 0.6872 (t0) cc_final: 0.6535 (t70) REVERT: B 78 SER cc_start: 0.7516 (m) cc_final: 0.7285 (m) REVERT: B 99 PHE cc_start: 0.7615 (m-80) cc_final: 0.7052 (m-80) REVERT: B 109 ASP cc_start: 0.6968 (t70) cc_final: 0.6667 (t0) REVERT: B 128 GLN cc_start: 0.5664 (tm-30) cc_final: 0.5456 (tm-30) REVERT: B 130 ARG cc_start: 0.5722 (mtp85) cc_final: 0.5479 (mtp180) REVERT: B 160 LYS cc_start: 0.6948 (tppp) cc_final: 0.6427 (tmtt) REVERT: B 165 ARG cc_start: 0.6480 (ttp-110) cc_final: 0.5987 (mtp85) REVERT: B 182 LYS cc_start: 0.4909 (OUTLIER) cc_final: 0.4103 (ttpp) REVERT: B 192 ASP cc_start: 0.5558 (t70) cc_final: 0.5245 (t70) REVERT: B 294 GLU cc_start: 0.6226 (mm-30) cc_final: 0.5709 (mt-10) REVERT: B 317 LYS cc_start: 0.4922 (mttt) cc_final: 0.4632 (mtmt) REVERT: B 336 GLU cc_start: 0.6329 (pp20) cc_final: 0.5920 (pt0) REVERT: B 346 MET cc_start: 0.5915 (mtm) cc_final: 0.5616 (mtm) REVERT: B 393 GLU cc_start: 0.5770 (mp0) cc_final: 0.5396 (tt0) REVERT: B 445 LYS cc_start: 0.5421 (mttm) cc_final: 0.5072 (mttp) REVERT: B 479 GLU cc_start: 0.7112 (pm20) cc_final: 0.6843 (pt0) REVERT: B 499 GLU cc_start: 0.6738 (pm20) cc_final: 0.6521 (pm20) REVERT: C 90 LEU cc_start: 0.3937 (mm) cc_final: 0.3698 (mp) REVERT: C 210 MET cc_start: 0.5628 (ppp) cc_final: 0.4893 (tpt) REVERT: C 233 LYS cc_start: 0.3907 (mttt) cc_final: 0.3126 (mmtt) REVERT: C 271 ARG cc_start: 0.6458 (mtt-85) cc_final: 0.6148 (ptp-110) REVERT: C 275 THR cc_start: 0.7275 (p) cc_final: 0.6997 (t) REVERT: C 287 GLU cc_start: 0.7055 (mp0) cc_final: 0.6805 (mm-30) REVERT: C 302 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: C 304 GLU cc_start: 0.6381 (tt0) cc_final: 0.6137 (tt0) REVERT: C 309 ASP cc_start: 0.6492 (t0) cc_final: 0.6142 (t0) REVERT: C 315 ARG cc_start: 0.6540 (tpp-160) cc_final: 0.6229 (tpp80) REVERT: C 336 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6081 (pp20) REVERT: C 731 MET cc_start: 0.4021 (ptt) cc_final: 0.3728 (ptp) outliers start: 14 outliers final: 5 residues processed: 926 average time/residue: 0.7224 time to fit residues: 817.7341 Evaluate side-chains 700 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 692 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 947 GLN Chi-restraints excluded: chain A residue 1880 MET Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain C residue 302 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN A 484 HIS A 539 GLN A 561 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 GLN A 947 GLN A1043 GLN A1069 HIS ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1691 GLN A1941 HIS A1980 ASN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2213 ASN A2380 ASN A3037 GLN A3154 GLN A3296 GLN A3516 HIS A3524 ASN A3551 ASN ** A3577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN A3951 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 320 GLN B 359 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 452 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.224420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.198623 restraints weight = 71290.551| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.03 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 40414 Z= 0.196 Angle : 0.796 11.791 54841 Z= 0.405 Chirality : 0.047 0.226 6243 Planarity : 0.006 0.068 6791 Dihedral : 12.637 167.439 5786 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.10 % Favored : 89.85 % Rotamer: Outliers : 2.41 % Allowed : 11.26 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.30 (0.12), residues: 4795 helix: 0.28 (0.10), residues: 2884 sheet: -1.26 (0.36), residues: 197 loop : -2.85 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A3282 TYR 0.023 0.002 TYR A1881 PHE 0.042 0.002 PHE A2260 TRP 0.024 0.002 TRP A2196 HIS 0.007 0.001 HIS C 511 Details of bonding type rmsd covalent geometry : bond 0.00455 (40414) covalent geometry : angle 0.79559 (54841) hydrogen bonds : bond 0.04858 ( 2131) hydrogen bonds : angle 4.95784 ( 6209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 773 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7349 (pt0) cc_final: 0.7123 (pt0) REVERT: A 172 GLU cc_start: 0.8450 (tt0) cc_final: 0.7917 (tm-30) REVERT: A 359 LEU cc_start: 0.7464 (tp) cc_final: 0.7159 (tp) REVERT: A 785 MET cc_start: 0.7577 (mmm) cc_final: 0.7270 (mmm) REVERT: A 851 ILE cc_start: 0.8507 (mm) cc_final: 0.8221 (mm) REVERT: A 865 GLN cc_start: 0.7444 (mt0) cc_final: 0.7234 (mt0) REVERT: A 889 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6731 (tp30) REVERT: A 983 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7586 (mm) REVERT: A 1031 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7050 (ttp-170) REVERT: A 1332 TYR cc_start: 0.7286 (t80) cc_final: 0.6602 (t80) REVERT: A 1386 ILE cc_start: 0.8309 (tp) cc_final: 0.8039 (tt) REVERT: A 1557 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: A 1586 SER cc_start: 0.8047 (m) cc_final: 0.7833 (m) REVERT: A 1592 MET cc_start: 0.8157 (tpt) cc_final: 0.7603 (tpt) REVERT: A 1740 VAL cc_start: 0.8349 (t) cc_final: 0.8113 (t) REVERT: A 1762 MET cc_start: 0.6750 (mmp) cc_final: 0.6449 (mmp) REVERT: A 1775 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6890 (mt-10) REVERT: A 1829 TRP cc_start: 0.7474 (m100) cc_final: 0.7107 (m100) REVERT: A 1971 PRO cc_start: 0.6677 (Cg_endo) cc_final: 0.6388 (Cg_exo) REVERT: A 2170 GLN cc_start: 0.8180 (tt0) cc_final: 0.7890 (tt0) REVERT: A 2281 MET cc_start: 0.8706 (tpt) cc_final: 0.8505 (tpp) REVERT: A 2369 LYS cc_start: 0.8150 (mttt) cc_final: 0.7820 (mmpt) REVERT: A 2414 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7987 (mm-40) REVERT: A 2795 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7394 (tp40) REVERT: A 2856 SER cc_start: 0.9005 (p) cc_final: 0.8529 (m) REVERT: A 2864 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7271 (tm-30) REVERT: A 2990 GLU cc_start: 0.7503 (tt0) cc_final: 0.7270 (tt0) REVERT: A 3067 LYS cc_start: 0.7315 (ptmm) cc_final: 0.7044 (pttp) REVERT: A 3090 TYR cc_start: 0.8591 (m-80) cc_final: 0.7846 (m-80) REVERT: A 3140 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 3172 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7582 (ttmt) REVERT: A 3176 MET cc_start: 0.8670 (mmm) cc_final: 0.8311 (mmm) REVERT: A 3237 SER cc_start: 0.8646 (t) cc_final: 0.8293 (m) REVERT: A 3238 MET cc_start: 0.8609 (mtm) cc_final: 0.8211 (mtp) REVERT: A 3289 ARG cc_start: 0.7248 (mpt90) cc_final: 0.6993 (mpt-90) REVERT: A 3339 ASN cc_start: 0.7376 (m-40) cc_final: 0.6920 (m-40) REVERT: A 3425 ARG cc_start: 0.6173 (mtt-85) cc_final: 0.5671 (ttm-80) REVERT: A 3442 TYR cc_start: 0.6759 (m-10) cc_final: 0.6320 (m-10) REVERT: A 3450 MET cc_start: 0.7135 (ttm) cc_final: 0.6764 (ttm) REVERT: A 3456 LEU cc_start: 0.7464 (mt) cc_final: 0.7241 (mp) REVERT: A 3772 ASN cc_start: 0.7561 (p0) cc_final: 0.7017 (p0) REVERT: A 3858 MET cc_start: 0.8049 (tmm) cc_final: 0.7706 (tmm) REVERT: A 3997 LEU cc_start: 0.7501 (mm) cc_final: 0.7288 (mt) REVERT: A 4007 LYS cc_start: 0.6145 (mmmt) cc_final: 0.5622 (mtpt) REVERT: A 4046 TYR cc_start: 0.6785 (m-10) cc_final: 0.5943 (m-80) REVERT: A 4062 ASP cc_start: 0.6399 (m-30) cc_final: 0.6031 (m-30) REVERT: A 4089 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8159 (pt) REVERT: B 258 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6894 (mtp85) REVERT: B 310 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6907 (mt) REVERT: B 335 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6733 (tt0) REVERT: C 233 LYS cc_start: 0.5331 (mttt) cc_final: 0.4902 (mmtt) REVERT: C 246 HIS cc_start: 0.6209 (p90) cc_final: 0.5612 (p-80) REVERT: C 301 ASP cc_start: 0.5504 (p0) cc_final: 0.5108 (p0) REVERT: C 371 GLU cc_start: 0.4612 (OUTLIER) cc_final: 0.4370 (pp20) outliers start: 99 outliers final: 29 residues processed: 817 average time/residue: 0.7235 time to fit residues: 724.9723 Evaluate side-chains 689 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 653 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1452 VAL Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1561 SER Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2340 SER Chi-restraints excluded: chain A residue 2780 LEU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 3227 ILE Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 211 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 205 optimal weight: 0.3980 chunk 177 optimal weight: 0.0470 chunk 233 optimal weight: 0.1980 chunk 256 optimal weight: 0.1980 chunk 399 optimal weight: 0.0970 chunk 203 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 259 GLN A 377 ASN A 415 GLN A 533 HIS A 561 ASN A 613 HIS A 925 GLN A1613 HIS ** A1898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 ASN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2266 ASN A2275 GLN A2523 ASN A3059 GLN A3093 GLN A3154 GLN A3166 ASN A3339 ASN A3516 HIS A3524 ASN ** A3577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3808 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 415 ASN C 432 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.226886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.199696 restraints weight = 64124.409| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.94 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4064 r_free = 0.4064 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40414 Z= 0.142 Angle : 0.710 11.973 54841 Z= 0.360 Chirality : 0.043 0.195 6243 Planarity : 0.005 0.071 6791 Dihedral : 12.275 176.808 5769 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.62 % Allowed : 15.58 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.97 (0.12), residues: 4795 helix: 0.59 (0.10), residues: 2884 sheet: -1.18 (0.36), residues: 201 loop : -2.79 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 476 TYR 0.021 0.002 TYR A 290 PHE 0.039 0.002 PHE A3382 TRP 0.019 0.001 TRP A2196 HIS 0.009 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00316 (40414) covalent geometry : angle 0.70957 (54841) hydrogen bonds : bond 0.04131 ( 2131) hydrogen bonds : angle 4.69400 ( 6209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 693 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 99 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7218 (ptpt) REVERT: A 172 GLU cc_start: 0.8535 (tt0) cc_final: 0.7834 (tm-30) REVERT: A 338 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 359 LEU cc_start: 0.7301 (tp) cc_final: 0.7083 (tp) REVERT: A 453 MET cc_start: 0.6075 (tpp) cc_final: 0.5874 (tpp) REVERT: A 786 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7293 (tm130) REVERT: A 865 GLN cc_start: 0.7432 (mt0) cc_final: 0.7136 (mt0) REVERT: A 889 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6897 (tp30) REVERT: A 983 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7572 (mm) REVERT: A 1332 TYR cc_start: 0.7294 (t80) cc_final: 0.6741 (t80) REVERT: A 1386 ILE cc_start: 0.8202 (tp) cc_final: 0.7904 (tt) REVERT: A 1592 MET cc_start: 0.8172 (tpt) cc_final: 0.7661 (tpt) REVERT: A 1607 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6381 (tp30) REVERT: A 1643 MET cc_start: 0.6683 (mtt) cc_final: 0.6407 (mtt) REVERT: A 1762 MET cc_start: 0.6754 (mmp) cc_final: 0.6516 (mmp) REVERT: A 1775 GLU cc_start: 0.7250 (tt0) cc_final: 0.6975 (mt-10) REVERT: A 1829 TRP cc_start: 0.7219 (m100) cc_final: 0.6896 (m100) REVERT: A 1971 PRO cc_start: 0.6850 (Cg_endo) cc_final: 0.6491 (Cg_exo) REVERT: A 2165 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6023 (tm) REVERT: A 2170 GLN cc_start: 0.8024 (tt0) cc_final: 0.7755 (tt0) REVERT: A 2369 LYS cc_start: 0.8074 (mttt) cc_final: 0.7787 (mmpt) REVERT: A 2414 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 2504 ASP cc_start: 0.6782 (m-30) cc_final: 0.6034 (m-30) REVERT: A 2551 GLU cc_start: 0.8306 (tt0) cc_final: 0.7772 (tt0) REVERT: A 2565 MET cc_start: 0.7666 (mmp) cc_final: 0.7453 (mmp) REVERT: A 2795 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7457 (tp40) REVERT: A 2864 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7368 (tm-30) REVERT: A 3067 LYS cc_start: 0.7253 (ptmm) cc_final: 0.6979 (pttp) REVERT: A 3090 TYR cc_start: 0.8619 (m-80) cc_final: 0.8022 (m-80) REVERT: A 3140 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 3147 LYS cc_start: 0.6415 (ttmt) cc_final: 0.6200 (tttp) REVERT: A 3237 SER cc_start: 0.8658 (t) cc_final: 0.8269 (m) REVERT: A 3238 MET cc_start: 0.8590 (mtm) cc_final: 0.8169 (mtp) REVERT: A 3516 HIS cc_start: 0.4920 (t-170) cc_final: 0.4678 (t-90) REVERT: A 3772 ASN cc_start: 0.7205 (p0) cc_final: 0.6981 (p0) REVERT: A 3858 MET cc_start: 0.8145 (tmm) cc_final: 0.7803 (tmm) REVERT: A 3869 THR cc_start: 0.7472 (m) cc_final: 0.7213 (p) REVERT: A 3932 MET cc_start: 0.6722 (mmm) cc_final: 0.6426 (mmm) REVERT: A 4002 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6706 (mtm) REVERT: A 4007 LYS cc_start: 0.6096 (mmmt) cc_final: 0.5799 (mtpt) REVERT: A 4089 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 310 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6804 (mt) REVERT: C 14 MET cc_start: 0.6800 (ptm) cc_final: 0.6267 (ptm) REVERT: C 84 MET cc_start: 0.4038 (OUTLIER) cc_final: 0.3785 (pmm) REVERT: C 246 HIS cc_start: 0.6027 (p90) cc_final: 0.5761 (p90) REVERT: C 352 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6329 (pt0) REVERT: C 371 GLU cc_start: 0.4537 (OUTLIER) cc_final: 0.4303 (pp20) REVERT: C 427 MET cc_start: 0.7326 (ppp) cc_final: 0.6778 (pp-130) outliers start: 108 outliers final: 29 residues processed: 742 average time/residue: 0.7242 time to fit residues: 658.2434 Evaluate side-chains 673 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 633 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2195 SER Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2417 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3270 ASP Chi-restraints excluded: chain A residue 3302 LYS Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 493 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 300 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 304 optimal weight: 0.4980 chunk 446 optimal weight: 0.6980 chunk 255 optimal weight: 0.5980 chunk 370 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 126 optimal weight: 0.0270 chunk 239 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN A 415 GLN A 561 ASN A 720 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS A1509 GLN ** A2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN A2885 GLN A3059 GLN A3093 GLN A3166 ASN A3501 HIS A3524 ASN ** A3577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3704 GLN A3748 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS C 415 ASN C 432 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.222719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.189597 restraints weight = 57987.007| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.16 r_work: 0.3618 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40414 Z= 0.163 Angle : 0.731 14.461 54841 Z= 0.368 Chirality : 0.044 0.229 6243 Planarity : 0.005 0.076 6791 Dihedral : 12.225 175.972 5769 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.33 % Favored : 90.65 % Rotamer: Outliers : 3.07 % Allowed : 17.39 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.92 (0.12), residues: 4795 helix: 0.61 (0.10), residues: 2877 sheet: -1.00 (0.35), residues: 209 loop : -2.75 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3159 TYR 0.019 0.002 TYR B 71 PHE 0.044 0.002 PHE A3382 TRP 0.020 0.001 TRP A2196 HIS 0.008 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00379 (40414) covalent geometry : angle 0.73064 (54841) hydrogen bonds : bond 0.04142 ( 2131) hydrogen bonds : angle 4.63609 ( 6209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 678 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 172 GLU cc_start: 0.8819 (tt0) cc_final: 0.8203 (tm-30) REVERT: A 326 MET cc_start: 0.8132 (mtp) cc_final: 0.7759 (mtp) REVERT: A 351 ASN cc_start: 0.7448 (t0) cc_final: 0.7246 (t0) REVERT: A 359 LEU cc_start: 0.7434 (tp) cc_final: 0.7194 (tp) REVERT: A 379 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6532 (mtpm) REVERT: A 453 MET cc_start: 0.6383 (tpp) cc_final: 0.6102 (tpp) REVERT: A 524 TYR cc_start: 0.7405 (p90) cc_final: 0.7118 (p90) REVERT: A 535 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6498 (pp) REVERT: A 767 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: A 786 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7721 (tm130) REVERT: A 823 GLN cc_start: 0.6111 (mm-40) cc_final: 0.5897 (mm110) REVERT: A 889 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7342 (tp30) REVERT: A 983 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7662 (mm) REVERT: A 1061 LYS cc_start: 0.7938 (mtpm) cc_final: 0.7698 (mtpp) REVERT: A 1332 TYR cc_start: 0.7307 (t80) cc_final: 0.6694 (t80) REVERT: A 1592 MET cc_start: 0.8443 (tpt) cc_final: 0.7752 (tpt) REVERT: A 1762 MET cc_start: 0.7095 (mmp) cc_final: 0.6791 (mmp) REVERT: A 1775 GLU cc_start: 0.7861 (tt0) cc_final: 0.7463 (mt-10) REVERT: A 1829 TRP cc_start: 0.7297 (m100) cc_final: 0.6955 (m100) REVERT: A 1971 PRO cc_start: 0.6528 (Cg_endo) cc_final: 0.6187 (Cg_exo) REVERT: A 2100 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6696 (pt) REVERT: A 2170 GLN cc_start: 0.8239 (tt0) cc_final: 0.7946 (tt0) REVERT: A 2369 LYS cc_start: 0.8592 (mttt) cc_final: 0.8120 (mmpt) REVERT: A 2504 ASP cc_start: 0.7695 (m-30) cc_final: 0.7068 (m-30) REVERT: A 2551 GLU cc_start: 0.8198 (tt0) cc_final: 0.7723 (tt0) REVERT: A 2733 MET cc_start: 0.6137 (mtt) cc_final: 0.5735 (mtt) REVERT: A 2795 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7489 (tp40) REVERT: A 2839 ASP cc_start: 0.7227 (m-30) cc_final: 0.6980 (m-30) REVERT: A 2864 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7899 (tm-30) REVERT: A 3007 GLU cc_start: 0.7469 (mp0) cc_final: 0.7150 (mm-30) REVERT: A 3090 TYR cc_start: 0.8913 (m-80) cc_final: 0.8422 (m-80) REVERT: A 3140 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 3237 SER cc_start: 0.9030 (t) cc_final: 0.8712 (m) REVERT: A 3238 MET cc_start: 0.8925 (mtm) cc_final: 0.8464 (mtp) REVERT: A 3335 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: A 3339 ASN cc_start: 0.7774 (m110) cc_final: 0.7505 (m-40) REVERT: A 3516 HIS cc_start: 0.5673 (t-170) cc_final: 0.5397 (t-90) REVERT: A 3734 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7340 (tpp-160) REVERT: A 3772 ASN cc_start: 0.8074 (p0) cc_final: 0.7727 (p0) REVERT: A 3858 MET cc_start: 0.8588 (tmm) cc_final: 0.8373 (tmm) REVERT: A 3892 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6639 (t) REVERT: A 3932 MET cc_start: 0.8046 (mmm) cc_final: 0.7821 (mmm) REVERT: A 3997 LEU cc_start: 0.7693 (mm) cc_final: 0.7340 (mt) REVERT: A 4089 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8251 (pt) REVERT: B 160 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (tmtt) REVERT: B 203 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6790 (mtm) REVERT: B 258 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7235 (mtp85) REVERT: B 310 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7092 (mt) REVERT: B 333 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6906 (mt-10) REVERT: C 14 MET cc_start: 0.6926 (ptm) cc_final: 0.6617 (ptm) REVERT: C 84 MET cc_start: 0.3885 (OUTLIER) cc_final: 0.3582 (pmm) REVERT: C 371 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.4859 (pp20) REVERT: C 427 MET cc_start: 0.7843 (ppp) cc_final: 0.7244 (pp-130) REVERT: C 731 MET cc_start: 0.4336 (ptp) cc_final: 0.3980 (ptp) outliers start: 127 outliers final: 47 residues processed: 746 average time/residue: 0.7337 time to fit residues: 672.9770 Evaluate side-chains 691 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 629 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3270 ASP Chi-restraints excluded: chain A residue 3335 ARG Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 493 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 134 optimal weight: 0.6980 chunk 419 optimal weight: 3.9990 chunk 440 optimal weight: 0.6980 chunk 461 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 389 optimal weight: 0.6980 chunk 441 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 406 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 390 GLN A 415 GLN A 720 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN A 925 GLN A2089 ASN ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN A2348 GLN A2432 GLN A3093 GLN A3166 ASN A3524 ASN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 152 ASN C 66 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 298 ASN C 411 HIS C 415 ASN C 432 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.220351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.184221 restraints weight = 56832.350| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.41 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 40414 Z= 0.179 Angle : 0.742 11.608 54841 Z= 0.375 Chirality : 0.045 0.227 6243 Planarity : 0.005 0.062 6791 Dihedral : 12.264 176.171 5766 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.16 % Favored : 90.81 % Rotamer: Outliers : 3.30 % Allowed : 18.86 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -0.93 (0.12), residues: 4795 helix: 0.60 (0.10), residues: 2868 sheet: -0.96 (0.35), residues: 204 loop : -2.74 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A3159 TYR 0.024 0.002 TYR B 71 PHE 0.034 0.002 PHE A2260 TRP 0.017 0.002 TRP A3498 HIS 0.010 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00420 (40414) covalent geometry : angle 0.74164 (54841) hydrogen bonds : bond 0.04200 ( 2131) hydrogen bonds : angle 4.61119 ( 6209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 682 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8559 (tt0) cc_final: 0.7618 (tm-30) REVERT: A 287 LEU cc_start: 0.8491 (mt) cc_final: 0.8221 (mp) REVERT: A 326 MET cc_start: 0.7948 (mtp) cc_final: 0.7534 (mtp) REVERT: A 359 LEU cc_start: 0.7223 (tp) cc_final: 0.7006 (tp) REVERT: A 379 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6712 (mtpm) REVERT: A 410 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7410 (ttp) REVERT: A 423 TYR cc_start: 0.7396 (m-80) cc_final: 0.6660 (m-80) REVERT: A 453 MET cc_start: 0.6153 (tpp) cc_final: 0.5660 (tpp) REVERT: A 524 TYR cc_start: 0.7447 (p90) cc_final: 0.7182 (p90) REVERT: A 540 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.4567 (ptp) REVERT: A 723 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7246 (p0) REVERT: A 786 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 889 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7183 (tp30) REVERT: A 925 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6424 (tp40) REVERT: A 939 MET cc_start: 0.8277 (mmm) cc_final: 0.7940 (mmp) REVERT: A 983 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7608 (mt) REVERT: A 990 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: A 1061 LYS cc_start: 0.7877 (mtpm) cc_final: 0.7664 (mtpp) REVERT: A 1332 TYR cc_start: 0.7379 (t80) cc_final: 0.6765 (t80) REVERT: A 1509 GLN cc_start: 0.7420 (tp40) cc_final: 0.6951 (tp-100) REVERT: A 1592 MET cc_start: 0.8345 (tpt) cc_final: 0.7715 (tpt) REVERT: A 1762 MET cc_start: 0.6973 (mmp) cc_final: 0.6674 (mmp) REVERT: A 1784 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5675 (mtm110) REVERT: A 1971 PRO cc_start: 0.6128 (Cg_endo) cc_final: 0.5837 (Cg_exo) REVERT: A 2100 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6451 (pt) REVERT: A 2127 LYS cc_start: 0.7377 (mptt) cc_final: 0.6896 (mptt) REVERT: A 2170 GLN cc_start: 0.8004 (tt0) cc_final: 0.7761 (tt0) REVERT: A 2369 LYS cc_start: 0.8051 (mttt) cc_final: 0.7786 (mmpt) REVERT: A 2504 ASP cc_start: 0.6830 (m-30) cc_final: 0.6267 (m-30) REVERT: A 2551 GLU cc_start: 0.8368 (tt0) cc_final: 0.7845 (tt0) REVERT: A 2733 MET cc_start: 0.6251 (mtt) cc_final: 0.5815 (mtt) REVERT: A 2795 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7305 (tp40) REVERT: A 2864 GLN cc_start: 0.7470 (mm-40) cc_final: 0.6977 (tm-30) REVERT: A 2951 GLN cc_start: 0.7213 (tp40) cc_final: 0.6954 (pm20) REVERT: A 2958 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7682 (pp) REVERT: A 3007 GLU cc_start: 0.7013 (mp0) cc_final: 0.6780 (mm-30) REVERT: A 3090 TYR cc_start: 0.8710 (m-80) cc_final: 0.8303 (m-80) REVERT: A 3140 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 3159 ARG cc_start: 0.6716 (ttp-110) cc_final: 0.6442 (ttp-110) REVERT: A 3237 SER cc_start: 0.8710 (t) cc_final: 0.8321 (m) REVERT: A 3238 MET cc_start: 0.8781 (mtm) cc_final: 0.8417 (mtp) REVERT: A 3500 SER cc_start: 0.8546 (t) cc_final: 0.7908 (m) REVERT: A 3734 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7431 (tpp-160) REVERT: A 3772 ASN cc_start: 0.8087 (p0) cc_final: 0.7595 (p0) REVERT: A 3858 MET cc_start: 0.8230 (tmm) cc_final: 0.7960 (tmm) REVERT: A 3869 THR cc_start: 0.7733 (m) cc_final: 0.7393 (p) REVERT: A 3892 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6303 (t) REVERT: A 3941 ASP cc_start: 0.7908 (t0) cc_final: 0.7231 (t70) REVERT: A 4089 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8168 (pt) REVERT: A 4098 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7117 (mp) REVERT: B 100 LYS cc_start: 0.7303 (mptp) cc_final: 0.7003 (tppp) REVERT: B 160 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (tmtt) REVERT: B 203 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7017 (mtm) REVERT: B 258 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6850 (mtp85) REVERT: B 310 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6900 (mt) REVERT: C 14 MET cc_start: 0.6772 (ptm) cc_final: 0.6422 (ptm) REVERT: C 20 MET cc_start: 0.4207 (OUTLIER) cc_final: 0.3783 (tmt) REVERT: C 84 MET cc_start: 0.3981 (pmt) cc_final: 0.3594 (pmm) REVERT: C 311 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7367 (tt) REVERT: C 427 MET cc_start: 0.7704 (ppp) cc_final: 0.7181 (pp-130) outliers start: 137 outliers final: 54 residues processed: 755 average time/residue: 0.7210 time to fit residues: 669.2774 Evaluate side-chains 703 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 630 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1452 VAL Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2100 LEU Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2411 LEU Chi-restraints excluded: chain A residue 2417 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2958 LEU Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3302 LYS Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4059 ILE Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 493 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 381 optimal weight: 2.9990 chunk 430 optimal weight: 20.0000 chunk 266 optimal weight: 0.0970 chunk 156 optimal weight: 0.9990 chunk 419 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 442 optimal weight: 0.7980 chunk 475 optimal weight: 6.9990 chunk 357 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 207 GLN A 561 ASN A 720 GLN A1716 GLN ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN A3037 GLN A3166 ASN A3704 GLN B 65 GLN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.219471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.186734 restraints weight = 51647.675| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.74 r_work: 0.3593 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40414 Z= 0.173 Angle : 0.740 12.151 54841 Z= 0.374 Chirality : 0.045 0.225 6243 Planarity : 0.005 0.066 6791 Dihedral : 12.216 172.427 5766 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.33 % Favored : 90.65 % Rotamer: Outliers : 3.30 % Allowed : 20.44 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -0.90 (0.12), residues: 4795 helix: 0.60 (0.10), residues: 2872 sheet: -0.82 (0.35), residues: 212 loop : -2.70 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 476 TYR 0.028 0.002 TYR A3442 PHE 0.033 0.002 PHE A2260 TRP 0.015 0.002 TRP A2196 HIS 0.012 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00409 (40414) covalent geometry : angle 0.74041 (54841) hydrogen bonds : bond 0.04122 ( 2131) hydrogen bonds : angle 4.60384 ( 6209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 656 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7634 (tt) cc_final: 0.7347 (tt) REVERT: A 143 LEU cc_start: 0.8431 (mt) cc_final: 0.8044 (mt) REVERT: A 172 GLU cc_start: 0.8734 (tt0) cc_final: 0.8146 (tm-30) REVERT: A 243 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6509 (mp10) REVERT: A 287 LEU cc_start: 0.8531 (mt) cc_final: 0.8200 (mp) REVERT: A 326 MET cc_start: 0.8272 (mtp) cc_final: 0.7839 (mtp) REVERT: A 340 TYR cc_start: 0.8210 (t80) cc_final: 0.8002 (t80) REVERT: A 359 LEU cc_start: 0.7259 (tp) cc_final: 0.7048 (tp) REVERT: A 379 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6858 (mtpm) REVERT: A 380 ASP cc_start: 0.5859 (OUTLIER) cc_final: 0.5353 (m-30) REVERT: A 410 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (ttp) REVERT: A 415 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7802 (mm-40) REVERT: A 423 TYR cc_start: 0.7719 (m-80) cc_final: 0.6996 (m-80) REVERT: A 435 LEU cc_start: 0.8195 (tt) cc_final: 0.7972 (tp) REVERT: A 524 TYR cc_start: 0.7493 (p90) cc_final: 0.7226 (p90) REVERT: A 643 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 669 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 786 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7671 (tm130) REVERT: A 828 LYS cc_start: 0.7702 (mmmm) cc_final: 0.7420 (mttp) REVERT: A 847 SER cc_start: 0.8056 (t) cc_final: 0.7790 (p) REVERT: A 889 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7389 (tp30) REVERT: A 983 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 990 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: A 1125 GLN cc_start: 0.7689 (tp40) cc_final: 0.7240 (tp-100) REVERT: A 1129 ASP cc_start: 0.6463 (t70) cc_final: 0.6214 (m-30) REVERT: A 1332 TYR cc_start: 0.7361 (t80) cc_final: 0.6821 (t80) REVERT: A 1509 GLN cc_start: 0.7319 (tp40) cc_final: 0.6790 (tp-100) REVERT: A 1531 LEU cc_start: 0.8157 (pp) cc_final: 0.7915 (pt) REVERT: A 1762 MET cc_start: 0.7301 (mmp) cc_final: 0.6882 (mmp) REVERT: A 1775 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 1784 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.5861 (mtm110) REVERT: A 1874 TYR cc_start: 0.4778 (t80) cc_final: 0.3973 (t80) REVERT: A 1971 PRO cc_start: 0.5967 (Cg_endo) cc_final: 0.5667 (Cg_exo) REVERT: A 2127 LYS cc_start: 0.7549 (mptt) cc_final: 0.7049 (mptt) REVERT: A 2170 GLN cc_start: 0.8257 (tt0) cc_final: 0.7975 (tt0) REVERT: A 2362 VAL cc_start: 0.8966 (t) cc_final: 0.8688 (m) REVERT: A 2369 LYS cc_start: 0.8553 (mttt) cc_final: 0.8076 (mmpt) REVERT: A 2504 ASP cc_start: 0.7423 (m-30) cc_final: 0.6925 (m-30) REVERT: A 2551 GLU cc_start: 0.8191 (tt0) cc_final: 0.7790 (tt0) REVERT: A 2733 MET cc_start: 0.6134 (mtt) cc_final: 0.5800 (mtt) REVERT: A 2795 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7475 (tp40) REVERT: A 2864 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7801 (tm-30) REVERT: A 3007 GLU cc_start: 0.7584 (mp0) cc_final: 0.7327 (mm-30) REVERT: A 3090 TYR cc_start: 0.8865 (m-80) cc_final: 0.8399 (m-80) REVERT: A 3093 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 3140 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 3159 ARG cc_start: 0.7364 (ttp-110) cc_final: 0.7142 (ttp-110) REVERT: A 3237 SER cc_start: 0.9001 (t) cc_final: 0.8745 (m) REVERT: A 3335 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7862 (ttm-80) REVERT: A 3339 ASN cc_start: 0.7719 (m110) cc_final: 0.7367 (m-40) REVERT: A 3500 SER cc_start: 0.8674 (t) cc_final: 0.8263 (m) REVERT: A 3734 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7487 (tpp-160) REVERT: A 3772 ASN cc_start: 0.8228 (p0) cc_final: 0.7730 (p0) REVERT: A 3838 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 3840 LYS cc_start: 0.6882 (mmmm) cc_final: 0.6602 (ttmt) REVERT: A 3869 THR cc_start: 0.8051 (m) cc_final: 0.7665 (p) REVERT: A 3941 ASP cc_start: 0.8144 (t0) cc_final: 0.7568 (t70) REVERT: A 3974 MET cc_start: 0.8443 (mtm) cc_final: 0.8048 (mtm) REVERT: A 4089 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8168 (pt) REVERT: A 4098 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7389 (mp) REVERT: B 161 MET cc_start: 0.8530 (mtm) cc_final: 0.8266 (mtt) REVERT: B 203 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7097 (mtm) REVERT: B 258 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7115 (mtp85) REVERT: C 14 MET cc_start: 0.6858 (ptm) cc_final: 0.6458 (ptm) REVERT: C 20 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.3251 (tmt) REVERT: C 271 ARG cc_start: 0.7997 (ptp-110) cc_final: 0.7716 (ptp-110) REVERT: C 311 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7341 (tt) REVERT: C 328 GLU cc_start: 0.7304 (pt0) cc_final: 0.6893 (tt0) REVERT: C 427 MET cc_start: 0.7823 (ppp) cc_final: 0.7275 (pp-130) outliers start: 137 outliers final: 67 residues processed: 725 average time/residue: 0.7272 time to fit residues: 645.5700 Evaluate side-chains 712 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 630 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2279 ILE Chi-restraints excluded: chain A residue 2454 LEU Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 3030 ILE Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3093 GLN Chi-restraints excluded: chain A residue 3326 GLN Chi-restraints excluded: chain A residue 3335 ARG Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 192 optimal weight: 0.0770 chunk 291 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 410 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 337 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 207 GLN A 250 ASN A 720 GLN A 823 GLN A1043 GLN ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN A3166 ASN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.219877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.193030 restraints weight = 66435.076| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.98 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40414 Z= 0.160 Angle : 0.726 12.156 54841 Z= 0.367 Chirality : 0.044 0.277 6243 Planarity : 0.005 0.065 6791 Dihedral : 12.180 172.233 5766 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.04 % Favored : 90.94 % Rotamer: Outliers : 3.00 % Allowed : 21.74 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -0.80 (0.12), residues: 4795 helix: 0.68 (0.10), residues: 2866 sheet: -0.70 (0.35), residues: 206 loop : -2.66 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 476 TYR 0.028 0.002 TYR A3442 PHE 0.030 0.002 PHE A2260 TRP 0.018 0.001 TRP A3498 HIS 0.012 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00376 (40414) covalent geometry : angle 0.72632 (54841) hydrogen bonds : bond 0.03999 ( 2131) hydrogen bonds : angle 4.56653 ( 6209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 657 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8283 (mt) cc_final: 0.7875 (mt) REVERT: A 172 GLU cc_start: 0.8572 (tt0) cc_final: 0.7787 (tm-30) REVERT: A 287 LEU cc_start: 0.8434 (mt) cc_final: 0.8169 (mp) REVERT: A 326 MET cc_start: 0.7879 (mtp) cc_final: 0.7427 (mtp) REVERT: A 359 LEU cc_start: 0.7341 (tp) cc_final: 0.7110 (tp) REVERT: A 380 ASP cc_start: 0.5542 (OUTLIER) cc_final: 0.5024 (m-30) REVERT: A 410 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7383 (ttp) REVERT: A 423 TYR cc_start: 0.7503 (m-80) cc_final: 0.7037 (m-80) REVERT: A 435 LEU cc_start: 0.8071 (tt) cc_final: 0.7827 (tp) REVERT: A 453 MET cc_start: 0.6475 (tpp) cc_final: 0.6079 (tpp) REVERT: A 643 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 669 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 713 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: A 723 ASP cc_start: 0.7453 (p0) cc_final: 0.7117 (p0) REVERT: A 724 GLU cc_start: 0.6827 (mp0) cc_final: 0.6570 (mp0) REVERT: A 767 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 786 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7213 (tm130) REVERT: A 983 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7688 (mt) REVERT: A 990 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: A 1125 GLN cc_start: 0.7284 (tp40) cc_final: 0.6844 (tp-100) REVERT: A 1332 TYR cc_start: 0.7379 (t80) cc_final: 0.6734 (t80) REVERT: A 1509 GLN cc_start: 0.6981 (tp40) cc_final: 0.6687 (tp-100) REVERT: A 1762 MET cc_start: 0.7190 (mmp) cc_final: 0.6846 (mmp) REVERT: A 1775 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 1784 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5608 (mtm110) REVERT: A 1971 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5847 (Cg_exo) REVERT: A 2127 LYS cc_start: 0.7299 (mptt) cc_final: 0.6956 (mptt) REVERT: A 2170 GLN cc_start: 0.7963 (tt0) cc_final: 0.7709 (tt0) REVERT: A 2362 VAL cc_start: 0.8644 (t) cc_final: 0.8408 (m) REVERT: A 2369 LYS cc_start: 0.8191 (mttt) cc_final: 0.7860 (mmpt) REVERT: A 2504 ASP cc_start: 0.6613 (m-30) cc_final: 0.6090 (m-30) REVERT: A 2551 GLU cc_start: 0.8359 (tt0) cc_final: 0.7858 (tt0) REVERT: A 2733 MET cc_start: 0.6282 (mtt) cc_final: 0.5930 (mtt) REVERT: A 2795 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7515 (tp40) REVERT: A 2839 ASP cc_start: 0.6605 (m-30) cc_final: 0.6259 (m-30) REVERT: A 2864 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7188 (tm-30) REVERT: A 2958 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 3090 TYR cc_start: 0.8493 (m-80) cc_final: 0.8021 (m-80) REVERT: A 3140 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 3237 SER cc_start: 0.8745 (t) cc_final: 0.8481 (m) REVERT: A 3339 ASN cc_start: 0.7382 (m110) cc_final: 0.7078 (m-40) REVERT: A 3456 LEU cc_start: 0.7924 (mt) cc_final: 0.7614 (mp) REVERT: A 3500 SER cc_start: 0.8599 (t) cc_final: 0.8153 (m) REVERT: A 3529 ILE cc_start: 0.7596 (tp) cc_final: 0.7369 (tp) REVERT: A 3772 ASN cc_start: 0.8050 (p0) cc_final: 0.7548 (p0) REVERT: A 3838 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6548 (tm-30) REVERT: A 3840 LYS cc_start: 0.6896 (mmmm) cc_final: 0.6622 (ttmt) REVERT: A 3869 THR cc_start: 0.7926 (m) cc_final: 0.7641 (p) REVERT: A 3974 MET cc_start: 0.8258 (mtm) cc_final: 0.7773 (mtm) REVERT: A 4089 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8184 (pt) REVERT: A 4098 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7237 (mp) REVERT: B 161 MET cc_start: 0.8412 (mtm) cc_final: 0.8183 (mtt) REVERT: B 258 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6774 (mtp85) REVERT: B 409 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.6755 (t80) REVERT: C 14 MET cc_start: 0.6811 (ptm) cc_final: 0.6493 (ptm) REVERT: C 20 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.3228 (tmt) REVERT: C 328 GLU cc_start: 0.7020 (pt0) cc_final: 0.6761 (tt0) REVERT: C 356 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: C 427 MET cc_start: 0.7635 (ppp) cc_final: 0.7135 (pp-130) outliers start: 124 outliers final: 60 residues processed: 720 average time/residue: 0.7033 time to fit residues: 622.8618 Evaluate side-chains 703 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 628 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1023 SER Chi-restraints excluded: chain A residue 1057 LYS Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1137 ILE Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2040 MET Chi-restraints excluded: chain A residue 2193 ILE Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2450 GLU Chi-restraints excluded: chain A residue 2454 LEU Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2807 GLN Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2958 LEU Chi-restraints excluded: chain A residue 3044 MET Chi-restraints excluded: chain A residue 3302 LYS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4059 ILE Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4098 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 266 optimal weight: 0.0970 chunk 429 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 417 optimal weight: 2.9990 chunk 309 optimal weight: 0.0770 chunk 367 optimal weight: 0.5980 chunk 431 optimal weight: 0.0470 chunk 379 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 185 optimal weight: 0.0870 chunk 261 optimal weight: 0.7980 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 243 GLN A 415 GLN A 561 ASN A 720 GLN A1385 ASN ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 ASN A2275 GLN A3166 ASN A3339 ASN A3602 ASN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 360 HIS C 103 GLN C 246 HIS C 411 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.223656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.197266 restraints weight = 72687.007| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.10 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40414 Z= 0.135 Angle : 0.700 12.261 54841 Z= 0.353 Chirality : 0.042 0.285 6243 Planarity : 0.005 0.063 6791 Dihedral : 12.055 172.262 5766 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.22 % Allowed : 22.92 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -0.63 (0.12), residues: 4795 helix: 0.86 (0.10), residues: 2871 sheet: -0.72 (0.34), residues: 210 loop : -2.66 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A3159 TYR 0.025 0.001 TYR A3442 PHE 0.037 0.001 PHE B 131 TRP 0.018 0.001 TRP A3498 HIS 0.015 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00299 (40414) covalent geometry : angle 0.69957 (54841) hydrogen bonds : bond 0.03673 ( 2131) hydrogen bonds : angle 4.46533 ( 6209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 668 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8205 (mt) cc_final: 0.7773 (mt) REVERT: A 172 GLU cc_start: 0.8326 (tt0) cc_final: 0.7772 (pt0) REVERT: A 208 MET cc_start: 0.8464 (mtp) cc_final: 0.8195 (mtp) REVERT: A 287 LEU cc_start: 0.8477 (mt) cc_final: 0.8268 (mp) REVERT: A 359 LEU cc_start: 0.7268 (tp) cc_final: 0.7050 (tp) REVERT: A 380 ASP cc_start: 0.5472 (OUTLIER) cc_final: 0.4916 (m-30) REVERT: A 395 MET cc_start: 0.7074 (ptm) cc_final: 0.6683 (ptm) REVERT: A 410 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7377 (ttp) REVERT: A 423 TYR cc_start: 0.7521 (m-80) cc_final: 0.7058 (m-80) REVERT: A 435 LEU cc_start: 0.8015 (tt) cc_final: 0.7796 (tp) REVERT: A 453 MET cc_start: 0.6529 (tpp) cc_final: 0.6257 (tpp) REVERT: A 491 CYS cc_start: 0.7350 (m) cc_final: 0.6893 (m) REVERT: A 643 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 723 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7465 (p0) REVERT: A 786 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7241 (tm130) REVERT: A 983 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7603 (mt) REVERT: A 989 MET cc_start: 0.7486 (mmm) cc_final: 0.7079 (mmp) REVERT: A 990 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: A 1303 MET cc_start: 0.4667 (mmt) cc_final: 0.4357 (mtt) REVERT: A 1332 TYR cc_start: 0.7498 (t80) cc_final: 0.6963 (t80) REVERT: A 1509 GLN cc_start: 0.6808 (tp40) cc_final: 0.6500 (tp-100) REVERT: A 1653 LEU cc_start: 0.8397 (pp) cc_final: 0.7749 (mp) REVERT: A 1762 MET cc_start: 0.7115 (mmp) cc_final: 0.6878 (mmp) REVERT: A 1768 ARG cc_start: 0.7366 (ptt90) cc_final: 0.7116 (ptt-90) REVERT: A 1775 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 1784 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5782 (ttp-110) REVERT: A 1971 PRO cc_start: 0.6141 (Cg_endo) cc_final: 0.5830 (Cg_exo) REVERT: A 2040 MET cc_start: 0.7768 (ptt) cc_final: 0.7552 (mtt) REVERT: A 2163 HIS cc_start: 0.7478 (m90) cc_final: 0.7219 (m-70) REVERT: A 2347 LYS cc_start: 0.7369 (tttm) cc_final: 0.7161 (ttpp) REVERT: A 2369 LYS cc_start: 0.8101 (mttt) cc_final: 0.7837 (mmpt) REVERT: A 2504 ASP cc_start: 0.6566 (m-30) cc_final: 0.6019 (m-30) REVERT: A 2551 GLU cc_start: 0.8298 (tt0) cc_final: 0.7790 (tt0) REVERT: A 2733 MET cc_start: 0.6321 (mtt) cc_final: 0.5969 (mtt) REVERT: A 2839 ASP cc_start: 0.6424 (m-30) cc_final: 0.6169 (m-30) REVERT: A 3079 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 3090 TYR cc_start: 0.8453 (m-80) cc_final: 0.7851 (m-80) REVERT: A 3140 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 3237 SER cc_start: 0.8741 (t) cc_final: 0.8457 (m) REVERT: A 3238 MET cc_start: 0.8674 (mtm) cc_final: 0.8171 (mtm) REVERT: A 3339 ASN cc_start: 0.7171 (m-40) cc_final: 0.6842 (m-40) REVERT: A 3456 LEU cc_start: 0.7951 (mt) cc_final: 0.7687 (mp) REVERT: A 3500 SER cc_start: 0.8365 (t) cc_final: 0.7950 (m) REVERT: A 3772 ASN cc_start: 0.7881 (p0) cc_final: 0.7386 (p0) REVERT: A 3838 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 3840 LYS cc_start: 0.6598 (mmmm) cc_final: 0.6347 (ttmt) REVERT: A 3841 ASP cc_start: 0.7195 (t70) cc_final: 0.6932 (t70) REVERT: A 3846 MET cc_start: 0.5797 (tmt) cc_final: 0.5351 (tpt) REVERT: A 4089 ILE cc_start: 0.8632 (tt) cc_final: 0.8281 (pt) REVERT: B 409 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6716 (t80) REVERT: C 14 MET cc_start: 0.6681 (ptm) cc_final: 0.6445 (ptm) REVERT: C 20 MET cc_start: 0.4426 (OUTLIER) cc_final: 0.3852 (tmt) REVERT: C 328 GLU cc_start: 0.6822 (pt0) cc_final: 0.6566 (tt0) outliers start: 91 outliers final: 39 residues processed: 721 average time/residue: 0.7068 time to fit residues: 626.4583 Evaluate side-chains 673 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 626 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2450 GLU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 3166 ASN Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 67 optimal weight: 0.1980 chunk 288 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 474 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN A 415 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 GLN A1385 ASN ** A2091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2275 GLN ** A2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3093 GLN A3166 ASN A3326 GLN A3602 ASN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 326 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 411 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.223194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.188067 restraints weight = 57749.013| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.71 r_work: 0.3653 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 40414 Z= 0.187 Angle : 0.778 59.200 54841 Z= 0.413 Chirality : 0.043 0.400 6243 Planarity : 0.005 0.061 6791 Dihedral : 12.054 172.299 5766 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.75 % Favored : 91.23 % Rotamer: Outliers : 1.89 % Allowed : 23.67 % Favored : 74.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.48 % 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: -0.63 (0.12), residues: 4795 helix: 0.85 (0.10), residues: 2871 sheet: -0.71 (0.35), residues: 210 loop : -2.67 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A1136 TYR 0.022 0.002 TYR A3442 PHE 0.033 0.001 PHE B 131 TRP 0.015 0.001 TRP A3498 HIS 0.012 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00425 (40414) covalent geometry : angle 0.77798 (54841) hydrogen bonds : bond 0.03730 ( 2131) hydrogen bonds : angle 4.47662 ( 6209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 625 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.7977 (mt) cc_final: 0.7562 (mt) REVERT: A 172 GLU cc_start: 0.8530 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 208 MET cc_start: 0.8710 (mtp) cc_final: 0.8453 (mtp) REVERT: A 287 LEU cc_start: 0.8455 (mt) cc_final: 0.8204 (mp) REVERT: A 380 ASP cc_start: 0.5736 (OUTLIER) cc_final: 0.5159 (m-30) REVERT: A 395 MET cc_start: 0.7394 (ptm) cc_final: 0.6922 (ptm) REVERT: A 423 TYR cc_start: 0.7726 (m-80) cc_final: 0.7232 (m-80) REVERT: A 435 LEU cc_start: 0.8069 (tt) cc_final: 0.7827 (tp) REVERT: A 453 MET cc_start: 0.6719 (tpp) cc_final: 0.6345 (tpp) REVERT: A 491 CYS cc_start: 0.7720 (m) cc_final: 0.7250 (m) REVERT: A 643 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 718 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6283 (ptt) REVERT: A 723 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7952 (p0) REVERT: A 786 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7624 (tm130) REVERT: A 983 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7554 (mt) REVERT: A 990 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: A 1303 MET cc_start: 0.4802 (mmt) cc_final: 0.4444 (mtt) REVERT: A 1332 TYR cc_start: 0.7026 (t80) cc_final: 0.6479 (t80) REVERT: A 1509 GLN cc_start: 0.7231 (tp40) cc_final: 0.6567 (tp-100) REVERT: A 1653 LEU cc_start: 0.8488 (pp) cc_final: 0.7751 (mp) REVERT: A 1762 MET cc_start: 0.7175 (mmp) cc_final: 0.6834 (mmp) REVERT: A 1768 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7307 (ptt-90) REVERT: A 1775 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 1784 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5982 (ttp-110) REVERT: A 1971 PRO cc_start: 0.5839 (Cg_endo) cc_final: 0.5499 (Cg_exo) REVERT: A 2040 MET cc_start: 0.7966 (ptt) cc_final: 0.7673 (mtt) REVERT: A 2163 HIS cc_start: 0.7505 (m90) cc_final: 0.7100 (m-70) REVERT: A 2347 LYS cc_start: 0.7883 (tttm) cc_final: 0.7633 (ttpp) REVERT: A 2369 LYS cc_start: 0.8346 (mttt) cc_final: 0.7981 (mmpt) REVERT: A 2504 ASP cc_start: 0.7180 (m-30) cc_final: 0.6644 (m-30) REVERT: A 2551 GLU cc_start: 0.8149 (tt0) cc_final: 0.7715 (tt0) REVERT: A 2733 MET cc_start: 0.6174 (mtt) cc_final: 0.5838 (mtt) REVERT: A 2864 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: A 3079 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 3090 TYR cc_start: 0.8699 (m-80) cc_final: 0.8157 (m-80) REVERT: A 3237 SER cc_start: 0.8867 (t) cc_final: 0.8595 (m) REVERT: A 3238 MET cc_start: 0.8953 (mtm) cc_final: 0.8390 (mtm) REVERT: A 3456 LEU cc_start: 0.7994 (mt) cc_final: 0.7687 (mp) REVERT: A 3500 SER cc_start: 0.8302 (t) cc_final: 0.7950 (m) REVERT: A 3772 ASN cc_start: 0.8002 (p0) cc_final: 0.7572 (p0) REVERT: A 3838 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6364 (tm-30) REVERT: A 3840 LYS cc_start: 0.6722 (mmmm) cc_final: 0.6419 (ttmt) REVERT: A 3841 ASP cc_start: 0.7497 (t70) cc_final: 0.7153 (t70) REVERT: A 3846 MET cc_start: 0.6130 (tmt) cc_final: 0.5757 (tpt) REVERT: A 4089 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8203 (pt) REVERT: B 409 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6793 (t80) REVERT: C 14 MET cc_start: 0.6502 (ptm) cc_final: 0.6113 (ptm) REVERT: C 20 MET cc_start: 0.4593 (OUTLIER) cc_final: 0.3246 (tmt) REVERT: C 328 GLU cc_start: 0.7129 (pt0) cc_final: 0.6766 (tt0) REVERT: C 356 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: C 427 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7153 (pp-130) outliers start: 77 outliers final: 48 residues processed: 668 average time/residue: 0.7205 time to fit residues: 595.7241 Evaluate side-chains 679 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 619 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1125 GLN Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2450 GLU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2864 GLN Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 482 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 253 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 378 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 483 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 322 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 332 optimal weight: 0.9990 chunk 454 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 ASN A2275 GLN ** A3166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN A3339 ASN A3602 ASN A3704 GLN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 411 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.222878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.190678 restraints weight = 52424.634| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.73 r_work: 0.3633 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 40414 Z= 0.189 Angle : 0.836 59.183 54841 Z= 0.454 Chirality : 0.045 0.990 6243 Planarity : 0.005 0.060 6791 Dihedral : 12.049 172.309 5766 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.79 % Allowed : 23.96 % Favored : 74.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.48 % 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: -0.64 (0.12), residues: 4795 helix: 0.85 (0.10), residues: 2871 sheet: -0.71 (0.35), residues: 210 loop : -2.67 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A1136 TYR 0.022 0.002 TYR A3442 PHE 0.031 0.001 PHE B 131 TRP 0.015 0.001 TRP A3498 HIS 0.012 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00433 (40414) covalent geometry : angle 0.83600 (54841) hydrogen bonds : bond 0.03746 ( 2131) hydrogen bonds : angle 4.47584 ( 6209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 621 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8100 (mt) cc_final: 0.7680 (mt) REVERT: A 172 GLU cc_start: 0.8528 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 208 MET cc_start: 0.8737 (mtp) cc_final: 0.8496 (mtp) REVERT: A 287 LEU cc_start: 0.8505 (mt) cc_final: 0.8248 (mp) REVERT: A 380 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5283 (m-30) REVERT: A 395 MET cc_start: 0.7562 (ptm) cc_final: 0.7134 (ptm) REVERT: A 423 TYR cc_start: 0.7726 (m-80) cc_final: 0.7229 (m-80) REVERT: A 435 LEU cc_start: 0.8121 (tt) cc_final: 0.7893 (tp) REVERT: A 453 MET cc_start: 0.6814 (tpp) cc_final: 0.6502 (tpp) REVERT: A 491 CYS cc_start: 0.7823 (m) cc_final: 0.7369 (m) REVERT: A 643 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 723 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 786 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7756 (tm130) REVERT: A 983 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7590 (mt) REVERT: A 990 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: A 1303 MET cc_start: 0.4985 (mmt) cc_final: 0.4589 (mtt) REVERT: A 1332 TYR cc_start: 0.7348 (t80) cc_final: 0.6801 (t80) REVERT: A 1509 GLN cc_start: 0.7146 (tp40) cc_final: 0.6589 (tp-100) REVERT: A 1653 LEU cc_start: 0.8506 (pp) cc_final: 0.7794 (mp) REVERT: A 1762 MET cc_start: 0.7295 (mmp) cc_final: 0.6992 (mmp) REVERT: A 1768 ARG cc_start: 0.7684 (ptt90) cc_final: 0.7296 (ptt-90) REVERT: A 1775 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7557 (mt-10) REVERT: A 1784 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.6027 (ttp-110) REVERT: A 1971 PRO cc_start: 0.5991 (Cg_endo) cc_final: 0.5659 (Cg_exo) REVERT: A 2040 MET cc_start: 0.7979 (ptt) cc_final: 0.7692 (mtt) REVERT: A 2163 HIS cc_start: 0.7615 (m90) cc_final: 0.7261 (m-70) REVERT: A 2347 LYS cc_start: 0.7874 (tttm) cc_final: 0.7629 (ttpp) REVERT: A 2369 LYS cc_start: 0.8462 (mttt) cc_final: 0.8070 (mmpt) REVERT: A 2504 ASP cc_start: 0.7310 (m-30) cc_final: 0.6782 (m-30) REVERT: A 2551 GLU cc_start: 0.8133 (tt0) cc_final: 0.7707 (tt0) REVERT: A 2733 MET cc_start: 0.6194 (mtt) cc_final: 0.5863 (mtt) REVERT: A 2864 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: A 3079 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 3085 GLU cc_start: 0.8296 (mp0) cc_final: 0.7541 (mm-30) REVERT: A 3090 TYR cc_start: 0.8776 (m-80) cc_final: 0.8207 (m-80) REVERT: A 3237 SER cc_start: 0.9009 (t) cc_final: 0.8784 (m) REVERT: A 3339 ASN cc_start: 0.7584 (m-40) cc_final: 0.7208 (m-40) REVERT: A 3456 LEU cc_start: 0.8061 (mt) cc_final: 0.7775 (mp) REVERT: A 3500 SER cc_start: 0.8441 (t) cc_final: 0.8107 (m) REVERT: A 3704 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: A 3772 ASN cc_start: 0.8071 (p0) cc_final: 0.7655 (p0) REVERT: A 3838 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6552 (tm-30) REVERT: A 3840 LYS cc_start: 0.6827 (mmmm) cc_final: 0.6526 (ttmt) REVERT: A 3841 ASP cc_start: 0.7492 (t70) cc_final: 0.7171 (t70) REVERT: A 3846 MET cc_start: 0.6403 (tmt) cc_final: 0.6074 (tpt) REVERT: A 4089 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8265 (pt) REVERT: B 409 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6819 (t80) REVERT: C 14 MET cc_start: 0.6760 (ptm) cc_final: 0.6394 (ptm) REVERT: C 20 MET cc_start: 0.4581 (OUTLIER) cc_final: 0.3285 (tmt) REVERT: C 328 GLU cc_start: 0.7207 (pt0) cc_final: 0.6825 (tt0) REVERT: C 356 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7641 (m-10) REVERT: C 427 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7173 (pp-130) outliers start: 73 outliers final: 51 residues processed: 660 average time/residue: 0.7653 time to fit residues: 636.3383 Evaluate side-chains 677 residues out of total 4334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 614 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1125 GLN Chi-restraints excluded: chain A residue 1329 ARG Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1712 ARG Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1774 MET Chi-restraints excluded: chain A residue 1784 ARG Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1953 CYS Chi-restraints excluded: chain A residue 2165 LEU Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2450 GLU Chi-restraints excluded: chain A residue 2811 SER Chi-restraints excluded: chain A residue 2864 GLN Chi-restraints excluded: chain A residue 3326 GLN Chi-restraints excluded: chain A residue 3483 MET Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3665 MET Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3704 GLN Chi-restraints excluded: chain A residue 3727 THR Chi-restraints excluded: chain A residue 3740 ILE Chi-restraints excluded: chain A residue 3892 THR Chi-restraints excluded: chain A residue 4002 MET Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 356 PHE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 482 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 487 random chunks: chunk 271 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 172 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 128 optimal weight: 0.0570 chunk 204 optimal weight: 0.5980 chunk 392 optimal weight: 0.0980 chunk 241 optimal weight: 6.9990 chunk 297 optimal weight: 0.7980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 207 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 GLN A1385 ASN A2275 GLN A3166 ASN A3326 GLN A3602 ASN A3704 GLN B 98 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C 411 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.223233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.196697 restraints weight = 66492.245| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.94 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 40414 Z= 0.175 Angle : 0.928 59.193 54841 Z= 0.528 Chirality : 0.044 0.409 6243 Planarity : 0.005 0.105 6791 Dihedral : 12.046 172.271 5766 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 1.86 % Allowed : 23.86 % Favored : 74.27 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.48 % 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: -0.63 (0.12), residues: 4795 helix: 0.85 (0.10), residues: 2872 sheet: -0.71 (0.35), residues: 210 loop : -2.67 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A1136 TYR 0.023 0.001 TYR A3442 PHE 0.030 0.001 PHE B 131 TRP 0.014 0.001 TRP A3498 HIS 0.011 0.001 HIS A1367 Details of bonding type rmsd covalent geometry : bond 0.00403 (40414) covalent geometry : angle 0.92752 (54841) hydrogen bonds : bond 0.03734 ( 2131) hydrogen bonds : angle 4.47801 ( 6209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14091.28 seconds wall clock time: 241 minutes 17.29 seconds (14477.29 seconds total)