Starting phenix.real_space_refine on Mon Jul 6 18:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zvw_14989/07_2026/7zvw_14989.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 141 5.16 5 C 24175 2.51 5 N 6550 2.21 5 O 7031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37905 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 24052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3226, 24052 Classifications: {'peptide': 3226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 608} Link IDs: {'PTRANS': 127, 'TRANS': 3098} Chain breaks: 38 Unresolved non-hydrogen bonds: 2187 Unresolved non-hydrogen angles: 2792 Unresolved non-hydrogen dihedrals: 1764 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 34, 'PHE:plan': 30, 'ARG:plan': 28, 'TYR:plan': 24, 'HIS:plan': 11, 'GLU:plan': 60, 'ASN:plan1': 40, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 1177 Chain: "B" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2735 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "G" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3310 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3952 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 34, 'TRANS': 453} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1877 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1805 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 16, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.19, per 1000 atoms: 0.19 Number of scatterers: 37905 At special positions: 0 Unit cell: (138.782, 180.158, 233.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 141 16.00 P 6 15.00 Mg 2 11.99 O 7031 8.00 N 6550 7.00 C 24175 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: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... Secondary structure from input PDB file: 258 helices and 25 sheets defined 69.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.534A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 135 through 158 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 188 through 203 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 264 through 289 removed outlier: 3.805A pdb=" N GLN A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.503A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.511A pdb=" N GLY A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 379 removed outlier: 4.817A pdb=" N ARG A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 404 through 425 removed outlier: 3.986A pdb=" N GLU A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.611A pdb=" N GLN A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.119A pdb=" N TYR A 544 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 545 " --> pdb=" O GLN A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 556 through 581 removed outlier: 3.714A pdb=" N THR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 622 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 654 through 669 removed outlier: 3.907A pdb=" N HIS A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 691 Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 693 through 696 removed outlier: 3.646A pdb=" N LEU A 696 " --> pdb=" O PHE A 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 693 through 696' Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.659A pdb=" N GLN A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 725 removed outlier: 4.226A pdb=" N SER A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 732 through 753 removed outlier: 3.701A pdb=" N VAL A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 762 removed outlier: 5.144A pdb=" N SER A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 777 removed outlier: 4.510A pdb=" N GLU A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 removed outlier: 3.548A pdb=" N PHE A 786 " --> pdb=" O PRO A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 822 removed outlier: 4.339A pdb=" N GLU A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 829 through 841 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 852 through 865 removed outlier: 3.693A pdb=" N LEU A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Proline residue: A 859 - end of helix removed outlier: 4.155A pdb=" N TYR A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 885 removed outlier: 3.789A pdb=" N ASP A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 895 Proline residue: A 892 - end of helix Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 915 through 930 removed outlier: 4.077A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 983 removed outlier: 3.672A pdb=" N SER A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1007 Processing helix chain 'A' and resid 1014 through 1029 removed outlier: 3.614A pdb=" N ARG A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1035 removed outlier: 3.771A pdb=" N ASP A1034 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1035 " --> pdb=" O ILE A1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1030 through 1035' Processing helix chain 'A' and resid 1047 through 1068 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1074 through 1099 removed outlier: 3.519A pdb=" N ILE A1099 " --> pdb=" O ASN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1134 removed outlier: 3.644A pdb=" N ALA A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1159 Processing helix chain 'A' and resid 1160 through 1167 removed outlier: 4.018A pdb=" N LYS A1166 " --> pdb=" O ASP A1162 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1167 " --> pdb=" O CYS A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1181 Processing helix chain 'A' and resid 1185 through 1202 Processing helix chain 'A' and resid 1206 through 1213 Processing helix chain 'A' and resid 1213 through 1228 removed outlier: 3.636A pdb=" N THR A1228 " --> pdb=" O VAL A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1251 removed outlier: 4.199A pdb=" N LYS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1263 through 1276 Processing helix chain 'A' and resid 1280 through 1298 removed outlier: 3.535A pdb=" N THR A1298 " --> pdb=" O LEU A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1307 Processing helix chain 'A' and resid 1310 through 1319 Proline residue: A1316 - end of helix removed outlier: 3.893A pdb=" N GLY A1319 " --> pdb=" O ALA A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1342 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.800A pdb=" N LEU A1364 " --> pdb=" O GLU A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1404 Processing helix chain 'A' and resid 1404 through 1412 removed outlier: 3.546A pdb=" N ALA A1410 " --> pdb=" O GLU A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1429 removed outlier: 4.249A pdb=" N LYS A1419 " --> pdb=" O ASN A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1448 removed outlier: 3.811A pdb=" N ASP A1448 " --> pdb=" O LYS A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1471 Proline residue: A1464 - end of helix removed outlier: 3.554A pdb=" N ASP A1471 " --> pdb=" O MET A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1488 Processing helix chain 'A' and resid 1496 through 1511 removed outlier: 3.674A pdb=" N SER A1500 " --> pdb=" O VAL A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1518 Processing helix chain 'A' and resid 1526 through 1538 Processing helix chain 'A' and resid 1549 through 1564 Processing helix chain 'A' and resid 1572 through 1583 removed outlier: 3.768A pdb=" N LEU A1576 " --> pdb=" O PHE A1572 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A1579 " --> pdb=" O PRO A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1593 removed outlier: 4.120A pdb=" N SER A1587 " --> pdb=" O PHE A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1610 removed outlier: 3.761A pdb=" N THR A1601 " --> pdb=" O LYS A1597 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1623 Processing helix chain 'A' and resid 1623 through 1633 removed outlier: 4.088A pdb=" N ARG A1628 " --> pdb=" O LEU A1624 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A1629 " --> pdb=" O PRO A1625 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A1630 " --> pdb=" O ARG A1626 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A1631 " --> pdb=" O VAL A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1658 removed outlier: 3.732A pdb=" N LEU A1647 " --> pdb=" O ARG A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1664 removed outlier: 3.899A pdb=" N ILE A1662 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1663 " --> pdb=" O GLU A1660 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A1664 " --> pdb=" O TRP A1661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1659 through 1664' Processing helix chain 'A' and resid 1665 through 1684 Processing helix chain 'A' and resid 1693 through 1714 removed outlier: 4.163A pdb=" N ASP A1697 " --> pdb=" O TYR A1693 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A1714 " --> pdb=" O TYR A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1727 removed outlier: 3.797A pdb=" N VAL A1721 " --> pdb=" O GLY A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1748 removed outlier: 3.753A pdb=" N ASP A1740 " --> pdb=" O VAL A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1766 Processing helix chain 'A' and resid 1773 through 1795 Proline residue: A1786 - end of helix removed outlier: 3.678A pdb=" N MET A1794 " --> pdb=" O TYR A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1820 removed outlier: 4.262A pdb=" N SER A1818 " --> pdb=" O LYS A1814 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1820 " --> pdb=" O PHE A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1829 Processing helix chain 'A' and resid 1836 through 1854 Processing helix chain 'A' and resid 1859 through 1874 Processing helix chain 'A' and resid 1877 through 1895 Processing helix chain 'A' and resid 1902 through 1910 Processing helix chain 'A' and resid 1914 through 1933 removed outlier: 3.945A pdb=" N LEU A1920 " --> pdb=" O ASP A1916 " (cutoff:3.500A) Proline residue: A1930 - end of helix removed outlier: 4.159A pdb=" N SER A1933 " --> pdb=" O ALA A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1952 removed outlier: 3.582A pdb=" N GLU A1952 " --> pdb=" O ARG A1948 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1970 Processing helix chain 'A' and resid 1971 through 1975 Processing helix chain 'A' and resid 1980 through 1994 removed outlier: 4.010A pdb=" N ASN A1984 " --> pdb=" O HIS A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2020 Processing helix chain 'A' and resid 2086 through 2102 Processing helix chain 'A' and resid 2111 through 2124 Processing helix chain 'A' and resid 2134 through 2140 Processing helix chain 'A' and resid 2153 through 2168 Processing helix chain 'A' and resid 2174 through 2188 removed outlier: 4.616A pdb=" N GLN A2183 " --> pdb=" O VAL A2179 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS A2184 " --> pdb=" O SER A2180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A2185 " --> pdb=" O TYR A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2214 Processing helix chain 'A' and resid 2222 through 2239 Processing helix chain 'A' and resid 2249 through 2262 Processing helix chain 'A' and resid 2272 through 2286 Processing helix chain 'A' and resid 2304 through 2312 Processing helix chain 'A' and resid 2312 through 2322 removed outlier: 4.034A pdb=" N ILE A2316 " --> pdb=" O LEU A2312 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU A2319 " --> pdb=" O LYS A2315 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N CYS A2320 " --> pdb=" O ILE A2316 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A2322 " --> pdb=" O ASN A2318 " (cutoff:3.500A) Processing helix chain 'A' and resid 2330 through 2344 Processing helix chain 'A' and resid 2347 through 2363 Processing helix chain 'A' and resid 2371 through 2386 removed outlier: 3.554A pdb=" N LEU A2386 " --> pdb=" O MET A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2392 through 2407 Processing helix chain 'A' and resid 2412 through 2428 Processing helix chain 'A' and resid 2430 through 2445 removed outlier: 3.518A pdb=" N ARG A2434 " --> pdb=" O ASP A2430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A2445 " --> pdb=" O LEU A2441 " (cutoff:3.500A) Processing helix chain 'A' and resid 2448 through 2459 Processing helix chain 'A' and resid 2470 through 2480 Processing helix chain 'A' and resid 2522 through 2536 Processing helix chain 'A' and resid 2540 through 2551 Proline residue: A2546 - end of helix Processing helix chain 'A' and resid 2554 through 2572 removed outlier: 4.012A pdb=" N ILE A2558 " --> pdb=" O SER A2554 " (cutoff:3.500A) Proline residue: A2567 - end of helix Processing helix chain 'A' and resid 2574 through 2576 No H-bonds generated for 'chain 'A' and resid 2574 through 2576' Processing helix chain 'A' and resid 2577 through 2591 Processing helix chain 'A' and resid 2592 through 2598 removed outlier: 3.781A pdb=" N ARG A2596 " --> pdb=" O TYR A2593 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN A2598 " --> pdb=" O ILE A2595 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2615 removed outlier: 3.586A pdb=" N SER A2607 " --> pdb=" O ASN A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2621 through 2632 Processing helix chain 'A' and resid 2634 through 2647 removed outlier: 3.944A pdb=" N LEU A2645 " --> pdb=" O LEU A2641 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A2647 " --> pdb=" O GLU A2643 " (cutoff:3.500A) Processing helix chain 'A' and resid 2650 through 2652 No H-bonds generated for 'chain 'A' and resid 2650 through 2652' Processing helix chain 'A' and resid 2653 through 2671 Processing helix chain 'A' and resid 2673 through 2685 Processing helix chain 'A' and resid 2687 through 2700 removed outlier: 3.504A pdb=" N ASN A2691 " --> pdb=" O TYR A2687 " (cutoff:3.500A) Processing helix chain 'A' and resid 2702 through 2718 Processing helix chain 'A' and resid 2727 through 2742 Processing helix chain 'A' and resid 2744 through 2756 removed outlier: 4.120A pdb=" N GLU A2750 " --> pdb=" O GLU A2746 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2758 through 2765 removed outlier: 4.253A pdb=" N LEU A2762 " --> pdb=" O THR A2758 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A2765 " --> pdb=" O LEU A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2774 through 2786 removed outlier: 4.097A pdb=" N LEU A2778 " --> pdb=" O ASP A2774 " (cutoff:3.500A) Processing helix chain 'A' and resid 2790 through 2807 removed outlier: 3.503A pdb=" N GLN A2807 " --> pdb=" O GLN A2803 " (cutoff:3.500A) Processing helix chain 'A' and resid 2811 through 2833 removed outlier: 3.610A pdb=" N VAL A2815 " --> pdb=" O THR A2811 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2866 removed outlier: 4.145A pdb=" N LEU A2844 " --> pdb=" O ALA A2840 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR A2866 " --> pdb=" O SER A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2871 through 2888 removed outlier: 4.342A pdb=" N LYS A2875 " --> pdb=" O ASN A2871 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A2877 " --> pdb=" O ASP A2873 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A2878 " --> pdb=" O VAL A2874 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A2888 " --> pdb=" O GLN A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2896 through 2918 removed outlier: 3.538A pdb=" N TRP A2900 " --> pdb=" O ASP A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2959 removed outlier: 4.608A pdb=" N ALA A2946 " --> pdb=" O TYR A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2962 through 2974 removed outlier: 4.060A pdb=" N ILE A2966 " --> pdb=" O PRO A2962 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A2974 " --> pdb=" O THR A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2997 Processing helix chain 'A' and resid 2997 through 3004 removed outlier: 3.788A pdb=" N LEU A3001 " --> pdb=" O ASN A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3004 through 3009 Processing helix chain 'A' and resid 3017 through 3035 removed outlier: 3.629A pdb=" N LEU A3035 " --> pdb=" O PHE A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3052 Processing helix chain 'A' and resid 3055 through 3073 removed outlier: 3.949A pdb=" N TRP A3059 " --> pdb=" O LEU A3055 " (cutoff:3.500A) Processing helix chain 'A' and resid 3079 through 3091 removed outlier: 3.585A pdb=" N SER A3085 " --> pdb=" O LYS A3081 " (cutoff:3.500A) Processing helix chain 'A' and resid 3099 through 3112 Processing helix chain 'A' and resid 3117 through 3126 Processing helix chain 'A' and resid 3132 through 3136 Processing helix chain 'A' and resid 3138 through 3147 removed outlier: 3.595A pdb=" N LEU A3142 " --> pdb=" O PHE A3138 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A3147 " --> pdb=" O LEU A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3150 through 3165 removed outlier: 4.528A pdb=" N HIS A3156 " --> pdb=" O LYS A3152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A3157 " --> pdb=" O ILE A3153 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A3164 " --> pdb=" O GLN A3160 " (cutoff:3.500A) Processing helix chain 'A' and resid 3165 through 3176 removed outlier: 4.019A pdb=" N LEU A3169 " --> pdb=" O TYR A3165 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A3171 " --> pdb=" O GLN A3167 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A3172 " --> pdb=" O SER A3168 " (cutoff:3.500A) Processing helix chain 'A' and resid 3282 through 3296 removed outlier: 3.906A pdb=" N VAL A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3315 Processing helix chain 'A' and resid 3318 through 3341 Processing helix chain 'A' and resid 3351 through 3365 removed outlier: 3.791A pdb=" N GLU A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) Processing helix chain 'A' and resid 3368 through 3380 removed outlier: 3.541A pdb=" N ALA A3380 " --> pdb=" O GLN A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3384 through 3406 removed outlier: 4.003A pdb=" N SER A3406 " --> pdb=" O LYS A3402 " (cutoff:3.500A) Processing helix chain 'A' and resid 3412 through 3416 Processing helix chain 'A' and resid 3416 through 3421 removed outlier: 3.972A pdb=" N SER A3420 " --> pdb=" O SER A3416 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3426 Processing helix chain 'A' and resid 3434 through 3438 Processing helix chain 'A' and resid 3490 through 3509 Processing helix chain 'A' and resid 3511 through 3516 Processing helix chain 'A' and resid 3544 through 3557 Processing helix chain 'A' and resid 3561 through 3575 removed outlier: 3.559A pdb=" N PHE A3575 " --> pdb=" O LEU A3571 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3599 Processing helix chain 'A' and resid 3604 through 3613 Processing helix chain 'A' and resid 3615 through 3640 removed outlier: 3.914A pdb=" N MET A3640 " --> pdb=" O MET A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3672 through 3674 No H-bonds generated for 'chain 'A' and resid 3672 through 3674' Processing helix chain 'A' and resid 3677 through 3681 removed outlier: 3.646A pdb=" N ASN A3681 " --> pdb=" O ALA A3678 " (cutoff:3.500A) Processing helix chain 'A' and resid 3706 through 3714 Processing helix chain 'A' and resid 3716 through 3721 Processing helix chain 'A' and resid 3721 through 3733 Processing helix chain 'A' and resid 3739 through 3759 removed outlier: 4.194A pdb=" N TYR A3743 " --> pdb=" O ASP A3739 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A3745 " --> pdb=" O GLU A3741 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU A3746 " --> pdb=" O GLN A3742 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A3747 " --> pdb=" O TYR A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3765 through 3787 removed outlier: 4.075A pdb=" N LEU A3787 " --> pdb=" O ARG A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3798 through 3810 Processing helix chain 'A' and resid 3810 through 3816 removed outlier: 3.529A pdb=" N TYR A3816 " --> pdb=" O ARG A3812 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3822 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.644A pdb=" N LYS B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.566A pdb=" N MET B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 128 removed outlier: 3.561A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 173 through 176 removed outlier: 4.006A pdb=" N ILE B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.638A pdb=" N THR B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.610A pdb=" N ALA B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.520A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.501A pdb=" N ARG B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.647A pdb=" N ARG B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.761A pdb=" N TRP B 357 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.972A pdb=" N LEU G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE G 63 " --> pdb=" O ASN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 96 removed outlier: 3.583A pdb=" N LYS G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 128 Processing helix chain 'G' and resid 139 through 148 Processing helix chain 'G' and resid 174 through 177 removed outlier: 3.654A pdb=" N VAL G 177 " --> pdb=" O ARG G 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 177' Processing helix chain 'G' and resid 183 through 199 Processing helix chain 'G' and resid 232 through 252 removed outlier: 3.647A pdb=" N ARG G 242 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE G 243 " --> pdb=" O HIS G 239 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 270 removed outlier: 4.328A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 296 Processing helix chain 'G' and resid 363 through 375 removed outlier: 3.765A pdb=" N LEU G 375 " --> pdb=" O ALA G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 386 removed outlier: 3.503A pdb=" N ASN G 386 " --> pdb=" O GLN G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 396 Processing helix chain 'G' and resid 398 through 411 Processing helix chain 'G' and resid 423 through 429 Processing helix chain 'G' and resid 429 through 441 Processing helix chain 'G' and resid 442 through 448 removed outlier: 3.889A pdb=" N TRP G 448 " --> pdb=" O HIS G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 458 Processing helix chain 'G' and resid 459 through 467 removed outlier: 3.951A pdb=" N ILE G 463 " --> pdb=" O ALA G 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 219 through 229 Processing helix chain 'E' and resid 231 through 236 removed outlier: 4.078A pdb=" N LEU E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 244 through 270 removed outlier: 3.609A pdb=" N TYR E 248 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.905A pdb=" N ARG E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 288 " --> pdb=" O PRO E 284 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 289 " --> pdb=" O PHE E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 289' Processing helix chain 'E' and resid 291 through 332 Processing helix chain 'E' and resid 333 through 336 Processing helix chain 'E' and resid 346 through 353 removed outlier: 3.607A pdb=" N ILE E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 452 through 458 Processing helix chain 'E' and resid 477 through 482 removed outlier: 3.794A pdb=" N ALA E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 Processing helix chain 'E' and resid 554 through 568 Processing helix chain 'E' and resid 571 through 580 Processing helix chain 'E' and resid 595 through 608 removed outlier: 3.673A pdb=" N ASP E 608 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 637 Processing helix chain 'E' and resid 655 through 658 Processing helix chain 'E' and resid 659 through 686 removed outlier: 3.620A pdb=" N GLU E 684 " --> pdb=" O SER E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 713 removed outlier: 3.896A pdb=" N LEU E 702 " --> pdb=" O THR E 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 103 removed outlier: 4.353A pdb=" N LEU F 102 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 240 through 254 Processing helix chain 'F' and resid 257 through 265 Processing helix chain 'F' and resid 272 through 290 Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'F' and resid 311 through 327 removed outlier: 4.005A pdb=" N GLU F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 348 Processing helix chain 'F' and resid 349 through 365 removed outlier: 3.581A pdb=" N MET F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 391 Processing helix chain 'C' and resid 431 through 457 removed outlier: 3.785A pdb=" N ASN C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 504 through 512 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 642 through 665 removed outlier: 3.777A pdb=" N ALA C 665 " --> pdb=" O GLN C 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'A' and resid 3409 through 3411 removed outlier: 6.795A pdb=" N THR A3455 " --> pdb=" O THR A3470 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A3470 " --> pdb=" O THR A3455 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR A3470 " --> pdb=" O PHE A3452 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE A3452 " --> pdb=" O THR A3470 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG A3472 " --> pdb=" O GLU A3450 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3409 through 3411 removed outlier: 6.795A pdb=" N THR A3455 " --> pdb=" O THR A3470 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A3470 " --> pdb=" O THR A3455 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A3467 " --> pdb=" O VAL A3483 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A3534 " --> pdb=" O GLN A3484 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A3535 " --> pdb=" O PRO A3528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3650 through 3652 Processing sheet with id=AA5, first strand: chain 'A' and resid 3668 through 3670 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.715A pdb=" N ALA B 20 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 32 " --> pdb=" O CYS B 18 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 10 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 107 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN B 13 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 134 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 136 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 removed outlier: 3.887A pdb=" N ARG B 38 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 67 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB2, first strand: chain 'B' and resid 166 through 167 removed outlier: 3.553A pdb=" N TYR B 167 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.511A pdb=" N ILE G 137 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU G 109 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 24 through 27 removed outlier: 3.575A pdb=" N LEU G 37 " --> pdb=" O ILE G 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 42 through 46 Processing sheet with id=AB7, first strand: chain 'G' and resid 171 through 172 Processing sheet with id=AB8, first strand: chain 'G' and resid 171 through 172 removed outlier: 3.586A pdb=" N VAL G 154 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE G 387 " --> pdb=" O HIS G 419 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 208 through 211 removed outlier: 3.614A pdb=" N SER G 210 " --> pdb=" O GLU G 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 273 through 276 removed outlier: 3.530A pdb=" N VAL G 283 " --> pdb=" O PHE G 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 527 through 528 removed outlier: 3.733A pdb=" N CYS C 552 " --> pdb=" O ILE E 502 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS C 553 " --> pdb=" O LYS C 568 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 568 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 213 through 215 Processing sheet with id=AC4, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'C' and resid 472 through 473 removed outlier: 3.621A pdb=" N GLN C 472 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 557 through 558 2308 hydrogen bonds defined for protein. 6768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.29 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6341 1.31 - 1.43: 9900 1.43 - 1.56: 22175 1.56 - 1.69: 10 1.69 - 1.82: 228 Bond restraints: 38654 Sorted by residual: bond pdb=" CA SER F 309 " pdb=" CB SER F 309 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.32e-02 5.74e+03 2.52e+01 bond pdb=" C ASN G 14 " pdb=" O ASN G 14 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.26e-02 6.30e+03 2.13e+01 bond pdb=" N THR E 330 " pdb=" CA THR E 330 " ideal model delta sigma weight residual 1.459 1.516 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" N PRO F 107 " pdb=" CA PRO F 107 " ideal model delta sigma weight residual 1.469 1.412 0.056 1.28e-02 6.10e+03 1.95e+01 bond pdb=" CA SER F 301 " pdb=" CB SER F 301 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.59e-02 3.96e+03 1.53e+01 ... (remaining 38649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 52042 3.48 - 6.95: 399 6.95 - 10.43: 48 10.43 - 13.91: 7 13.91 - 17.38: 1 Bond angle restraints: 52497 Sorted by residual: angle pdb=" CA PHE F 310 " pdb=" CB PHE F 310 " pdb=" CG PHE F 310 " ideal model delta sigma weight residual 113.80 124.12 -10.32 1.00e+00 1.00e+00 1.07e+02 angle pdb=" CA GLY E 332 " pdb=" C GLY E 332 " pdb=" O GLY E 332 " ideal model delta sigma weight residual 122.52 114.58 7.94 7.90e-01 1.60e+00 1.01e+02 angle pdb=" N GLU F 101 " pdb=" CA GLU F 101 " pdb=" C GLU F 101 " ideal model delta sigma weight residual 112.54 100.37 12.17 1.22e+00 6.72e-01 9.96e+01 angle pdb=" N PRO E 412 " pdb=" CA PRO E 412 " pdb=" CB PRO E 412 " ideal model delta sigma weight residual 103.25 113.10 -9.85 1.05e+00 9.07e-01 8.81e+01 angle pdb=" N GLU H 396 " pdb=" CA GLU H 396 " pdb=" C GLU H 396 " ideal model delta sigma weight residual 111.28 101.65 9.63 1.09e+00 8.42e-01 7.80e+01 ... (remaining 52492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21091 17.90 - 35.80: 1911 35.80 - 53.70: 327 53.70 - 71.59: 61 71.59 - 89.49: 41 Dihedral angle restraints: 23431 sinusoidal: 8815 harmonic: 14616 Sorted by residual: dihedral pdb=" N ALA G 10 " pdb=" C ALA G 10 " pdb=" CA ALA G 10 " pdb=" CB ALA G 10 " ideal model delta harmonic sigma weight residual 122.90 106.51 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PHE F 310 " pdb=" C PHE F 310 " pdb=" CA PHE F 310 " pdb=" CB PHE F 310 " ideal model delta harmonic sigma weight residual 122.80 108.19 14.61 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA GLN A1511 " pdb=" C GLN A1511 " pdb=" N PRO A1512 " pdb=" CA PRO A1512 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 23428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5708 0.093 - 0.186: 278 0.186 - 0.279: 31 0.279 - 0.372: 14 0.372 - 0.464: 5 Chirality restraints: 6036 Sorted by residual: chirality pdb=" CA GLN H 391 " pdb=" N GLN H 391 " pdb=" C GLN H 391 " pdb=" CB GLN H 391 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA PHE F 310 " pdb=" N PHE F 310 " pdb=" C PHE F 310 " pdb=" CB PHE F 310 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ASP E 414 " pdb=" N ASP E 414 " pdb=" C ASP E 414 " pdb=" CB ASP E 414 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 6033 not shown) Planarity restraints: 6755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 300 " 0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C MET E 300 " -0.103 2.00e-02 2.50e+03 pdb=" O MET E 300 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS E 301 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 329 " 0.026 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C TRP E 329 " -0.086 2.00e-02 2.50e+03 pdb=" O TRP E 329 " 0.032 2.00e-02 2.50e+03 pdb=" N THR E 330 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 87 " -0.034 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" CG TRP B 87 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B 87 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 87 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 87 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 87 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 87 " -0.003 2.00e-02 2.50e+03 ... (remaining 6752 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 344 2.58 - 3.16: 32901 3.16 - 3.74: 61648 3.74 - 4.32: 76124 4.32 - 4.90: 126270 Nonbonded interactions: 297287 Sorted by model distance: nonbonded pdb=" O2B ATP G 501 " pdb="MG MG G 502 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG B 402 " model vdw 2.093 2.170 nonbonded pdb=" O1B ATP B 401 " pdb="MG MG B 402 " model vdw 2.096 2.170 nonbonded pdb=" OG SER G 22 " pdb="MG MG G 502 " model vdw 2.105 2.170 nonbonded pdb=" O3B ATP G 501 " pdb="MG MG G 502 " model vdw 2.123 2.170 ... (remaining 297282 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=1.00 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: 7.890 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: 0.040 Extract box with map and model: 0.870 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 36.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 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 : 0.004 0.066 38654 Z= 0.222 Angle : 0.752 17.385 52497 Z= 0.450 Chirality : 0.049 0.464 6036 Planarity : 0.005 0.105 6755 Dihedral : 14.406 89.492 13873 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.82 % Allowed : 0.90 % Favored : 98.29 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.13), residues: 4851 helix: 2.18 (0.10), residues: 3035 sheet: -0.62 (0.37), residues: 202 loop : -0.62 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 292 TYR 0.033 0.001 TYR F 291 PHE 0.043 0.001 PHE F 79 TRP 0.077 0.002 TRP B 87 HIS 0.007 0.001 HIS G 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.22 (38654) covalent geometry : angle 0.75243 / 0.45 (52497) hydrogen bonds : bond 0.13458 / 9.57 ( 2300) hydrogen bonds : angle 5.23233 / 3.86 ( 6768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 1447 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.7882 (ppp) cc_final: 0.7265 (ppp) REVERT: A 418 LEU cc_start: 0.9100 (mp) cc_final: 0.8687 (mp) REVERT: A 436 MET cc_start: 0.8533 (mmp) cc_final: 0.8290 (tpp) REVERT: A 440 ASP cc_start: 0.8037 (t0) cc_final: 0.7491 (t0) REVERT: A 572 LEU cc_start: 0.8736 (mt) cc_final: 0.8380 (mt) REVERT: A 612 LYS cc_start: 0.8765 (tttt) cc_final: 0.8450 (tttt) REVERT: A 656 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5602 (mt-10) REVERT: A 666 MET cc_start: 0.7438 (ptm) cc_final: 0.6094 (ptm) REVERT: A 677 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7356 (tt0) REVERT: A 681 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 693 PHE cc_start: 0.7013 (m-80) cc_final: 0.5860 (m-80) REVERT: A 747 PHE cc_start: 0.6955 (m-10) cc_final: 0.6511 (m-80) REVERT: A 792 LEU cc_start: 0.8538 (tp) cc_final: 0.8219 (tp) REVERT: A 795 SER cc_start: 0.7913 (m) cc_final: 0.7457 (t) REVERT: A 888 GLU cc_start: 0.6785 (pm20) cc_final: 0.6523 (pm20) REVERT: A 912 LEU cc_start: 0.5732 (tp) cc_final: 0.5389 (tt) REVERT: A 925 ILE cc_start: 0.6930 (mm) cc_final: 0.6599 (mm) REVERT: A 926 LEU cc_start: 0.7335 (mt) cc_final: 0.6943 (mt) REVERT: A 971 THR cc_start: 0.8142 (p) cc_final: 0.7769 (t) REVERT: A 1023 MET cc_start: 0.8557 (ptp) cc_final: 0.8071 (mtp) REVERT: A 1170 LEU cc_start: 0.8704 (mm) cc_final: 0.8457 (mp) REVERT: A 1248 LEU cc_start: 0.6412 (tp) cc_final: 0.6139 (tp) REVERT: A 1416 ILE cc_start: 0.6244 (mm) cc_final: 0.5773 (mt) REVERT: A 1417 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.6867 (ptp90) REVERT: A 1554 MET cc_start: 0.7626 (tpp) cc_final: 0.7160 (tmm) REVERT: A 1588 PHE cc_start: 0.8618 (t80) cc_final: 0.8308 (t80) REVERT: A 1594 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8595 (tp30) REVERT: A 1738 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 1766 MET cc_start: 0.8488 (ppp) cc_final: 0.8219 (ppp) REVERT: A 1773 LEU cc_start: 0.8524 (mm) cc_final: 0.8216 (mp) REVERT: A 1819 ASP cc_start: 0.7967 (m-30) cc_final: 0.7668 (p0) REVERT: A 1840 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7789 (mmt180) REVERT: A 1843 LEU cc_start: 0.7839 (mt) cc_final: 0.7515 (mt) REVERT: A 1851 ILE cc_start: 0.8347 (mt) cc_final: 0.7839 (tt) REVERT: A 1872 TYR cc_start: 0.7569 (m-80) cc_final: 0.6985 (m-80) REVERT: A 1888 THR cc_start: 0.6757 (m) cc_final: 0.6162 (p) REVERT: A 1974 PHE cc_start: 0.8411 (m-80) cc_final: 0.8185 (m-80) REVERT: A 2428 LEU cc_start: 0.6629 (mt) cc_final: 0.6376 (mt) REVERT: A 2459 ASP cc_start: 0.7718 (m-30) cc_final: 0.7313 (m-30) REVERT: A 2589 LEU cc_start: 0.6738 (mt) cc_final: 0.6452 (mt) REVERT: A 2673 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6614 (mm-30) REVERT: A 2675 ASP cc_start: 0.7327 (m-30) cc_final: 0.7045 (m-30) REVERT: A 2862 SER cc_start: 0.7628 (t) cc_final: 0.7037 (p) REVERT: A 2902 ASP cc_start: 0.7184 (t70) cc_final: 0.6864 (t0) REVERT: A 2958 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6778 (mmtt) REVERT: A 2963 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 3138 PHE cc_start: 0.6172 (m-10) cc_final: 0.5880 (m-80) REVERT: A 3500 LEU cc_start: 0.7537 (tp) cc_final: 0.7217 (tt) REVERT: A 3562 GLU cc_start: 0.7325 (tp30) cc_final: 0.7099 (tp30) REVERT: A 3614 SER cc_start: 0.7120 (t) cc_final: 0.6911 (p) REVERT: A 3622 PHE cc_start: 0.7483 (t80) cc_final: 0.7018 (t80) REVERT: A 3624 LYS cc_start: 0.7181 (tttp) cc_final: 0.6754 (mtpp) REVERT: A 3726 ILE cc_start: 0.7053 (mt) cc_final: 0.6641 (mt) REVERT: B 84 GLU cc_start: 0.7449 (pp20) cc_final: 0.7179 (tm-30) REVERT: B 108 GLU cc_start: 0.7383 (pp20) cc_final: 0.6680 (pp20) REVERT: B 213 ILE cc_start: 0.7934 (mt) cc_final: 0.7708 (mt) REVERT: B 297 ASN cc_start: 0.8398 (m-40) cc_final: 0.8023 (m-40) REVERT: B 300 MET cc_start: 0.6930 (tmm) cc_final: 0.6573 (tmm) REVERT: B 306 MET cc_start: 0.6516 (ppp) cc_final: 0.6120 (ppp) REVERT: B 314 MET cc_start: 0.8072 (tpt) cc_final: 0.7526 (tpp) REVERT: B 318 LEU cc_start: 0.8524 (tt) cc_final: 0.8084 (mm) REVERT: B 362 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7795 (mm-30) REVERT: G 115 TYR cc_start: 0.6588 (t80) cc_final: 0.6340 (t80) REVERT: G 246 GLU cc_start: 0.6947 (mp0) cc_final: 0.6425 (mp0) REVERT: G 285 PHE cc_start: 0.8296 (m-80) cc_final: 0.8048 (m-80) REVERT: G 390 THR cc_start: 0.8344 (m) cc_final: 0.7912 (t) REVERT: G 403 LEU cc_start: 0.8584 (tp) cc_final: 0.8015 (tp) REVERT: E 200 LYS cc_start: 0.8162 (mttt) cc_final: 0.7326 (mttt) REVERT: E 236 LEU cc_start: 0.8133 (mt) cc_final: 0.7907 (mt) REVERT: E 349 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7735 (mt-10) REVERT: E 519 GLN cc_start: 0.6963 (tt0) cc_final: 0.6308 (tm-30) REVERT: E 523 PHE cc_start: 0.6315 (p90) cc_final: 0.3749 (m-10) REVERT: F 77 VAL cc_start: 0.8864 (m) cc_final: 0.8573 (m) REVERT: F 266 GLU cc_start: 0.7928 (pm20) cc_final: 0.7492 (pm20) REVERT: F 272 MET cc_start: 0.7006 (tmm) cc_final: 0.6524 (tmm) REVERT: F 307 LEU cc_start: 0.9220 (tp) cc_final: 0.9015 (tp) REVERT: F 333 ILE cc_start: 0.8509 (tt) cc_final: 0.8167 (tp) REVERT: C 419 MET cc_start: 0.1135 (ttt) cc_final: 0.0917 (ttt) REVERT: C 429 THR cc_start: 0.5999 (t) cc_final: 0.5686 (m) REVERT: C 451 GLN cc_start: 0.7417 (tt0) cc_final: 0.7069 (tt0) REVERT: C 504 ASP cc_start: 0.7947 (t0) cc_final: 0.7496 (t0) REVERT: C 511 ILE cc_start: 0.8331 (mm) cc_final: 0.8111 (mm) REVERT: C 617 LEU cc_start: 0.8072 (mt) cc_final: 0.7832 (mt) outliers start: 31 outliers final: 8 residues processed: 1464 average time/residue: 0.2308 time to fit residues: 537.6391 Evaluate side-chains 971 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 963 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain C residue 565 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.0670 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1718 HIS A1769 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2594 HIS ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3435 GLN A3442 ASN A3443 ASN A3760 HIS B 29 HIS B 116 ASN G 6 GLN G 113 ASN G 386 ASN ** G 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN E 578 HIS E 590 ASN E 655 HIS F 93 HIS C 468 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.178528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139123 restraints weight = 76195.755| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.03 r_work: 0.3659 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38654 Z= 0.152 Angle : 0.679 14.457 52497 Z= 0.341 Chirality : 0.042 0.200 6036 Planarity : 0.005 0.073 6755 Dihedral : 4.860 77.482 5324 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 2.50 % Allowed : 14.51 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.12), residues: 4851 helix: 2.05 (0.09), residues: 3086 sheet: -0.61 (0.37), residues: 185 loop : -0.74 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2576 TYR 0.027 0.002 TYR A 368 PHE 0.058 0.002 PHE A 995 TRP 0.029 0.002 TRP A1821 HIS 0.010 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (38654) covalent geometry : angle 0.67939 / 0.34 (52497) hydrogen bonds : bond 0.04036 / 2.88 ( 2300) hydrogen bonds : angle 4.31483 / 3.22 ( 6768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1043 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9324 (tp) cc_final: 0.8966 (pt) REVERT: A 348 ASP cc_start: 0.7788 (t0) cc_final: 0.7551 (t0) REVERT: A 603 PHE cc_start: 0.8410 (m-10) cc_final: 0.8148 (m-10) REVERT: A 612 LYS cc_start: 0.9275 (tttt) cc_final: 0.8914 (ttpt) REVERT: A 665 THR cc_start: 0.8509 (m) cc_final: 0.8255 (t) REVERT: A 677 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7572 (tt0) REVERT: A 680 ARG cc_start: 0.8831 (tmm-80) cc_final: 0.8519 (ttp80) REVERT: A 681 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 686 MET cc_start: 0.8504 (tpp) cc_final: 0.8003 (tpp) REVERT: A 690 MET cc_start: 0.8283 (mpp) cc_final: 0.7060 (mpp) REVERT: A 693 PHE cc_start: 0.7689 (m-80) cc_final: 0.7344 (m-80) REVERT: A 747 PHE cc_start: 0.7321 (m-10) cc_final: 0.6619 (m-80) REVERT: A 858 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7532 (mmmm) REVERT: A 895 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 912 LEU cc_start: 0.6030 (tp) cc_final: 0.5533 (tt) REVERT: A 926 LEU cc_start: 0.7976 (mt) cc_final: 0.7698 (mt) REVERT: A 1023 MET cc_start: 0.8815 (ptp) cc_final: 0.8427 (mtp) REVERT: A 1170 LEU cc_start: 0.8782 (mm) cc_final: 0.8567 (mp) REVERT: A 1222 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7633 (t80) REVERT: A 1416 ILE cc_start: 0.6394 (mm) cc_final: 0.6167 (mm) REVERT: A 1417 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.7195 (ptp90) REVERT: A 1522 ASP cc_start: 0.7272 (m-30) cc_final: 0.7002 (m-30) REVERT: A 1554 MET cc_start: 0.7863 (tpp) cc_final: 0.7465 (tpt) REVERT: A 1586 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8279 (mp0) REVERT: A 1649 ASP cc_start: 0.8594 (t0) cc_final: 0.8166 (t0) REVERT: A 1716 LEU cc_start: 0.8367 (mp) cc_final: 0.8066 (tp) REVERT: A 1718 HIS cc_start: 0.7286 (p90) cc_final: 0.6618 (p90) REVERT: A 1722 PHE cc_start: 0.8447 (m-80) cc_final: 0.7959 (m-80) REVERT: A 1735 PHE cc_start: 0.6952 (t80) cc_final: 0.6569 (t80) REVERT: A 1738 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 1740 ASP cc_start: 0.8692 (m-30) cc_final: 0.8405 (m-30) REVERT: A 1851 ILE cc_start: 0.8493 (mt) cc_final: 0.8055 (tt) REVERT: A 1927 LEU cc_start: 0.8417 (tp) cc_final: 0.8070 (tp) REVERT: A 2418 MET cc_start: 0.6844 (mmm) cc_final: 0.6116 (ptm) REVERT: A 2459 ASP cc_start: 0.7967 (m-30) cc_final: 0.7710 (m-30) REVERT: A 2578 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7637 (tp30) REVERT: A 2587 LYS cc_start: 0.7474 (mttt) cc_final: 0.7241 (mmmt) REVERT: A 2589 LEU cc_start: 0.7192 (mt) cc_final: 0.6790 (mt) REVERT: A 2763 GLU cc_start: 0.7812 (pp20) cc_final: 0.7420 (pt0) REVERT: A 2792 ARG cc_start: 0.8300 (tpt-90) cc_final: 0.8085 (tpt170) REVERT: A 2862 SER cc_start: 0.7474 (t) cc_final: 0.7007 (p) REVERT: A 2898 ASN cc_start: 0.7342 (m-40) cc_final: 0.6687 (m-40) REVERT: A 2958 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7099 (mmtt) REVERT: A 3087 TYR cc_start: 0.6884 (m-10) cc_final: 0.6555 (m-80) REVERT: A 3442 ASN cc_start: 0.7394 (m-40) cc_final: 0.7168 (m110) REVERT: A 3495 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 3498 PHE cc_start: 0.7431 (m-10) cc_final: 0.7214 (m-10) REVERT: A 3500 LEU cc_start: 0.7940 (tp) cc_final: 0.7688 (tt) REVERT: A 3537 ASN cc_start: 0.7725 (p0) cc_final: 0.7517 (p0) REVERT: A 3562 GLU cc_start: 0.8198 (tp30) cc_final: 0.7897 (tp30) REVERT: A 3622 PHE cc_start: 0.7974 (t80) cc_final: 0.7770 (t80) REVERT: A 3726 ILE cc_start: 0.8052 (mt) cc_final: 0.7643 (mt) REVERT: A 3729 ILE cc_start: 0.7930 (mt) cc_final: 0.7714 (mt) REVERT: B 108 GLU cc_start: 0.7839 (pp20) cc_final: 0.7205 (pp20) REVERT: B 123 ILE cc_start: 0.7980 (tt) cc_final: 0.7705 (pt) REVERT: B 126 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8163 (mm-30) REVERT: B 144 TYR cc_start: 0.6634 (m-10) cc_final: 0.6421 (m-80) REVERT: B 192 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7751 (ptpp) REVERT: B 216 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8693 (pptt) REVERT: B 226 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8332 (mm-40) REVERT: B 229 GLN cc_start: 0.7951 (pp30) cc_final: 0.7741 (pt0) REVERT: B 254 GLU cc_start: 0.8089 (mp0) cc_final: 0.7649 (mp0) REVERT: B 293 GLU cc_start: 0.8245 (mp0) cc_final: 0.7866 (mp0) REVERT: B 297 ASN cc_start: 0.8643 (m-40) cc_final: 0.8013 (m-40) REVERT: B 318 LEU cc_start: 0.8714 (tt) cc_final: 0.8076 (mm) REVERT: B 347 LEU cc_start: 0.8811 (tp) cc_final: 0.8473 (mt) REVERT: G 107 VAL cc_start: 0.8812 (t) cc_final: 0.8553 (p) REVERT: G 113 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7534 (m110) REVERT: G 285 PHE cc_start: 0.8199 (m-80) cc_final: 0.7812 (m-80) REVERT: G 297 LEU cc_start: 0.7755 (mt) cc_final: 0.7476 (mt) REVERT: G 403 LEU cc_start: 0.8585 (tp) cc_final: 0.7973 (tp) REVERT: G 407 LEU cc_start: 0.8357 (mt) cc_final: 0.8152 (mt) REVERT: G 462 LEU cc_start: 0.8612 (tp) cc_final: 0.8396 (tp) REVERT: E 203 ILE cc_start: 0.8602 (mm) cc_final: 0.8393 (mm) REVERT: E 228 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6755 (mp10) REVERT: E 249 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7249 (mm-30) REVERT: E 426 MET cc_start: 0.8119 (tpp) cc_final: 0.7754 (tpp) REVERT: F 111 GLU cc_start: 0.8566 (tt0) cc_final: 0.7981 (tt0) REVERT: F 266 GLU cc_start: 0.8128 (pm20) cc_final: 0.7891 (pm20) REVERT: F 307 LEU cc_start: 0.8901 (tp) cc_final: 0.8687 (tp) REVERT: F 333 ILE cc_start: 0.8504 (tt) cc_final: 0.8273 (mt) REVERT: F 342 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 419 MET cc_start: 0.1388 (ttt) cc_final: 0.1075 (ttt) REVERT: C 429 THR cc_start: 0.6292 (t) cc_final: 0.6010 (m) REVERT: C 437 LYS cc_start: 0.6983 (pptt) cc_final: 0.6573 (pptt) REVERT: C 439 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 472 GLN cc_start: 0.8128 (mt0) cc_final: 0.7832 (mt0) REVERT: C 511 ILE cc_start: 0.8301 (mm) cc_final: 0.7979 (mm) REVERT: C 512 LYS cc_start: 0.8196 (tppt) cc_final: 0.7844 (ttpt) REVERT: C 513 ASP cc_start: 0.7013 (t0) cc_final: 0.6764 (t70) REVERT: C 556 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8598 (ttpt) outliers start: 95 outliers final: 48 residues processed: 1088 average time/residue: 0.2309 time to fit residues: 414.7259 Evaluate side-chains 936 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 886 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1511 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1795 HIS Chi-restraints excluded: chain A residue 1846 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2811 THR Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3539 ASP Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 619 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 122 optimal weight: 5.9990 chunk 306 optimal weight: 0.3980 chunk 345 optimal weight: 0.9990 chunk 263 optimal weight: 0.0670 chunk 14 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 456 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2901 ASN A3558 GLN A3596 GLN A3643 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN G 386 ASN ** G 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 GLN E 655 HIS C 468 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.175698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133765 restraints weight = 75409.584| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.09 r_work: 0.3596 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38654 Z= 0.148 Angle : 0.638 12.640 52497 Z= 0.321 Chirality : 0.041 0.182 6036 Planarity : 0.005 0.058 6755 Dihedral : 4.753 74.254 5318 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.21 % Allowed : 17.80 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.12), residues: 4851 helix: 2.06 (0.09), residues: 3089 sheet: -0.73 (0.36), residues: 186 loop : -0.77 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 63 TYR 0.024 0.002 TYR A1559 PHE 0.038 0.002 PHE A1549 TRP 0.038 0.002 TRP B 87 HIS 0.034 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (38654) covalent geometry : angle 0.63843 / 0.32 (52497) hydrogen bonds : bond 0.03737 / 2.67 ( 2300) hydrogen bonds : angle 4.13659 / 3.07 ( 6768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 972 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9304 (tp) cc_final: 0.8989 (pt) REVERT: A 325 HIS cc_start: 0.7653 (m-70) cc_final: 0.6886 (m-70) REVERT: A 410 MET cc_start: 0.8223 (ppp) cc_final: 0.7918 (ppp) REVERT: A 453 TYR cc_start: 0.8143 (t80) cc_final: 0.7551 (t80) REVERT: A 612 LYS cc_start: 0.9280 (tttt) cc_final: 0.8874 (tttt) REVERT: A 615 PHE cc_start: 0.8901 (t80) cc_final: 0.8682 (t80) REVERT: A 665 THR cc_start: 0.8613 (m) cc_final: 0.8403 (t) REVERT: A 666 MET cc_start: 0.7963 (ptp) cc_final: 0.6687 (ptp) REVERT: A 677 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7692 (tt0) REVERT: A 680 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8604 (ttp-110) REVERT: A 681 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 686 MET cc_start: 0.8513 (tpp) cc_final: 0.7828 (tpp) REVERT: A 690 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.6755 (mpp) REVERT: A 693 PHE cc_start: 0.7671 (m-80) cc_final: 0.7395 (m-80) REVERT: A 747 PHE cc_start: 0.7164 (m-10) cc_final: 0.6636 (m-80) REVERT: A 871 VAL cc_start: 0.9061 (t) cc_final: 0.8840 (t) REVERT: A 912 LEU cc_start: 0.6242 (tp) cc_final: 0.5769 (tt) REVERT: A 956 MET cc_start: 0.8861 (mmm) cc_final: 0.8499 (mmm) REVERT: A 970 ILE cc_start: 0.8634 (tp) cc_final: 0.8426 (tp) REVERT: A 1023 MET cc_start: 0.8812 (ptp) cc_final: 0.8398 (mtp) REVERT: A 1222 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 1554 MET cc_start: 0.7867 (tpp) cc_final: 0.7414 (tpt) REVERT: A 1558 LEU cc_start: 0.9001 (tp) cc_final: 0.8591 (tp) REVERT: A 1562 ASN cc_start: 0.8239 (p0) cc_final: 0.7916 (p0) REVERT: A 1600 ILE cc_start: 0.8332 (mm) cc_final: 0.8128 (mp) REVERT: A 1649 ASP cc_start: 0.8829 (t0) cc_final: 0.8427 (t0) REVERT: A 1735 PHE cc_start: 0.7078 (t80) cc_final: 0.6710 (t80) REVERT: A 1738 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 1872 TYR cc_start: 0.7307 (m-80) cc_final: 0.7045 (m-10) REVERT: A 2418 MET cc_start: 0.7013 (mmm) cc_final: 0.6188 (ptm) REVERT: A 2459 ASP cc_start: 0.8219 (m-30) cc_final: 0.7974 (m-30) REVERT: A 2578 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7771 (tp30) REVERT: A 2589 LEU cc_start: 0.7496 (mt) cc_final: 0.7122 (mt) REVERT: A 2595 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 2645 LEU cc_start: 0.7195 (mp) cc_final: 0.6971 (mp) REVERT: A 2763 GLU cc_start: 0.8085 (pp20) cc_final: 0.7781 (pt0) REVERT: A 2835 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 2836 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7702 (ttm110) REVERT: A 2862 SER cc_start: 0.7811 (t) cc_final: 0.7300 (p) REVERT: A 2898 ASN cc_start: 0.7732 (m-40) cc_final: 0.7368 (m-40) REVERT: A 2902 ASP cc_start: 0.8439 (t0) cc_final: 0.8083 (m-30) REVERT: A 2958 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7549 (mmtt) REVERT: A 2963 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 3087 TYR cc_start: 0.7275 (m-10) cc_final: 0.7067 (m-80) REVERT: A 3420 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7225 (m) REVERT: A 3442 ASN cc_start: 0.7417 (m-40) cc_final: 0.7179 (m110) REVERT: A 3537 ASN cc_start: 0.8022 (p0) cc_final: 0.7811 (p0) REVERT: A 3538 ASP cc_start: 0.8462 (t0) cc_final: 0.8153 (t0) REVERT: A 3562 GLU cc_start: 0.8330 (tp30) cc_final: 0.8044 (tp30) REVERT: A 3603 THR cc_start: 0.7603 (p) cc_final: 0.7377 (p) REVERT: A 3709 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 3726 ILE cc_start: 0.8398 (mt) cc_final: 0.8027 (mt) REVERT: A 3772 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 17 MET cc_start: 0.7091 (mtt) cc_final: 0.6849 (mtm) REVERT: B 72 ILE cc_start: 0.8936 (tp) cc_final: 0.8722 (tt) REVERT: B 108 GLU cc_start: 0.7800 (pp20) cc_final: 0.7142 (pp20) REVERT: B 123 ILE cc_start: 0.7829 (tt) cc_final: 0.7617 (pt) REVERT: B 154 LEU cc_start: 0.8265 (tt) cc_final: 0.7975 (tt) REVERT: B 160 VAL cc_start: 0.8526 (t) cc_final: 0.8277 (p) REVERT: B 192 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7775 (ptpp) REVERT: B 226 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8268 (mm-40) REVERT: B 253 ASN cc_start: 0.8959 (m-40) cc_final: 0.8735 (t0) REVERT: B 254 GLU cc_start: 0.8097 (mp0) cc_final: 0.7643 (mp0) REVERT: B 281 ASN cc_start: 0.8323 (m-40) cc_final: 0.7992 (m-40) REVERT: B 293 GLU cc_start: 0.8357 (mp0) cc_final: 0.8010 (mp0) REVERT: B 297 ASN cc_start: 0.8687 (m-40) cc_final: 0.8129 (m-40) REVERT: B 318 LEU cc_start: 0.8732 (tt) cc_final: 0.8335 (mm) REVERT: B 362 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8102 (mm-30) REVERT: G 109 GLU cc_start: 0.7874 (pp20) cc_final: 0.7385 (pp20) REVERT: G 285 PHE cc_start: 0.8297 (m-80) cc_final: 0.7964 (m-80) REVERT: G 297 LEU cc_start: 0.7906 (mt) cc_final: 0.7632 (mt) REVERT: G 403 LEU cc_start: 0.8544 (tp) cc_final: 0.8323 (tp) REVERT: G 407 LEU cc_start: 0.8462 (mt) cc_final: 0.8166 (mt) REVERT: G 417 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7854 (ttp-170) REVERT: G 450 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8635 (p) REVERT: G 462 LEU cc_start: 0.8666 (tp) cc_final: 0.8419 (tp) REVERT: E 200 LYS cc_start: 0.8348 (mttt) cc_final: 0.8100 (mtpt) REVERT: E 228 GLN cc_start: 0.7203 (mm110) cc_final: 0.6978 (mp10) REVERT: E 249 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7315 (mm-30) REVERT: E 260 LEU cc_start: 0.8803 (mt) cc_final: 0.8554 (mt) REVERT: E 426 MET cc_start: 0.8214 (tpp) cc_final: 0.7785 (tpp) REVERT: E 467 ASP cc_start: 0.7201 (p0) cc_final: 0.6884 (p0) REVERT: F 111 GLU cc_start: 0.8490 (tt0) cc_final: 0.7882 (tt0) REVERT: F 128 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8011 (t0) REVERT: F 266 GLU cc_start: 0.8110 (pm20) cc_final: 0.7899 (pm20) REVERT: F 285 ARG cc_start: 0.8632 (ptm160) cc_final: 0.8201 (ptp-170) REVERT: F 320 GLN cc_start: 0.8586 (tp40) cc_final: 0.8043 (tm-30) REVERT: F 332 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7739 (tt0) REVERT: F 333 ILE cc_start: 0.8551 (tt) cc_final: 0.8284 (mt) REVERT: F 337 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8277 (mt-10) REVERT: F 340 VAL cc_start: 0.8653 (t) cc_final: 0.8282 (m) REVERT: F 342 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7713 (mm-30) REVERT: C 419 MET cc_start: 0.1342 (ttt) cc_final: 0.0984 (ttt) REVERT: C 429 THR cc_start: 0.6200 (t) cc_final: 0.5993 (m) REVERT: C 437 LYS cc_start: 0.6871 (pptt) cc_final: 0.6385 (pptt) REVERT: C 439 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7806 (mm-30) REVERT: C 472 GLN cc_start: 0.8174 (mt0) cc_final: 0.7846 (mt0) REVERT: C 504 ASP cc_start: 0.7923 (t70) cc_final: 0.7145 (t0) REVERT: C 506 GLU cc_start: 0.8283 (mp0) cc_final: 0.7954 (mp0) REVERT: C 511 ILE cc_start: 0.8413 (mm) cc_final: 0.8138 (mm) REVERT: C 575 LEU cc_start: 0.7085 (tp) cc_final: 0.6487 (tt) REVERT: C 617 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8077 (mm) outliers start: 122 outliers final: 68 residues processed: 1030 average time/residue: 0.2203 time to fit residues: 377.0016 Evaluate side-chains 959 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 882 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1592 PHE Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1795 HIS Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2811 THR Chi-restraints excluded: chain A residue 3141 GLN Chi-restraints excluded: chain A residue 3146 LEU Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3667 THR Chi-restraints excluded: chain A residue 3709 ILE Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3772 ILE Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 44 optimal weight: 2.9990 chunk 301 optimal weight: 0.5980 chunk 417 optimal weight: 0.0040 chunk 222 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 387 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 327 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 GLN A 757 ASN A 873 GLN A 920 HIS ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN ** A1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3558 GLN A3596 GLN ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3651 HIS B 29 HIS B 162 HIS ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 HIS E 240 HIS E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.174617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132580 restraints weight = 75439.276| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.06 r_work: 0.3565 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38654 Z= 0.135 Angle : 0.638 14.467 52497 Z= 0.314 Chirality : 0.041 0.232 6036 Planarity : 0.005 0.069 6755 Dihedral : 4.645 73.054 5315 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 3.50 % Allowed : 19.17 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.12), residues: 4851 helix: 2.09 (0.09), residues: 3093 sheet: -0.78 (0.35), residues: 186 loop : -0.75 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2576 TYR 0.021 0.001 TYR A1559 PHE 0.034 0.002 PHE A1549 TRP 0.026 0.001 TRP A2906 HIS 0.011 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (38654) covalent geometry : angle 0.63753 / 0.31 (52497) hydrogen bonds : bond 0.03442 / 2.47 ( 2300) hydrogen bonds : angle 4.03354 / 3.00 ( 6768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 935 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9239 (tp) cc_final: 0.8990 (pt) REVERT: A 325 HIS cc_start: 0.7645 (m-70) cc_final: 0.6874 (m-70) REVERT: A 357 PHE cc_start: 0.8666 (t80) cc_final: 0.8442 (t80) REVERT: A 360 TYR cc_start: 0.8244 (t80) cc_final: 0.7920 (t80) REVERT: A 612 LYS cc_start: 0.9297 (tttt) cc_final: 0.8922 (tttt) REVERT: A 667 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7741 (t80) REVERT: A 677 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7721 (tt0) REVERT: A 680 ARG cc_start: 0.8940 (tmm-80) cc_final: 0.8673 (ttp-110) REVERT: A 681 GLU cc_start: 0.8672 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 686 MET cc_start: 0.8558 (tpp) cc_final: 0.7793 (tpp) REVERT: A 690 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: A 693 PHE cc_start: 0.7785 (m-80) cc_final: 0.7546 (m-80) REVERT: A 747 PHE cc_start: 0.7203 (m-10) cc_final: 0.6647 (m-80) REVERT: A 748 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6988 (mpp) REVERT: A 804 LEU cc_start: 0.8626 (mm) cc_final: 0.8379 (mt) REVERT: A 838 LEU cc_start: 0.8572 (mm) cc_final: 0.8255 (mm) REVERT: A 858 LYS cc_start: 0.8364 (tppt) cc_final: 0.7808 (mmmm) REVERT: A 903 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 912 LEU cc_start: 0.6353 (tp) cc_final: 0.5853 (tt) REVERT: A 928 LYS cc_start: 0.7795 (tttm) cc_final: 0.7589 (mttm) REVERT: A 1023 MET cc_start: 0.8842 (ptp) cc_final: 0.8414 (mtp) REVERT: A 1222 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7829 (t80) REVERT: A 1357 LEU cc_start: 0.7901 (mp) cc_final: 0.7579 (tp) REVERT: A 1554 MET cc_start: 0.7765 (tpp) cc_final: 0.7347 (tpt) REVERT: A 1558 LEU cc_start: 0.9028 (tp) cc_final: 0.8693 (tp) REVERT: A 1586 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8496 (mp0) REVERT: A 1649 ASP cc_start: 0.8863 (t0) cc_final: 0.8363 (t0) REVERT: A 1709 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 1740 ASP cc_start: 0.8679 (m-30) cc_final: 0.8324 (m-30) REVERT: A 1766 MET cc_start: 0.8239 (tmm) cc_final: 0.7898 (tmm) REVERT: A 1843 LEU cc_start: 0.7818 (mt) cc_final: 0.7474 (mt) REVERT: A 1874 LYS cc_start: 0.8332 (mttm) cc_final: 0.7758 (mttm) REVERT: A 2418 MET cc_start: 0.7058 (mmm) cc_final: 0.6226 (ptt) REVERT: A 2459 ASP cc_start: 0.8251 (m-30) cc_final: 0.8027 (m-30) REVERT: A 2578 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 2589 LEU cc_start: 0.7668 (mt) cc_final: 0.7327 (mt) REVERT: A 2595 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 2643 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5915 (mt-10) REVERT: A 2645 LEU cc_start: 0.7338 (mp) cc_final: 0.7090 (mp) REVERT: A 2763 GLU cc_start: 0.8053 (pp20) cc_final: 0.7410 (pt0) REVERT: A 2902 ASP cc_start: 0.8528 (t0) cc_final: 0.8197 (m-30) REVERT: A 2958 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7622 (mmtt) REVERT: A 3098 LYS cc_start: 0.8026 (pptt) cc_final: 0.7585 (pttt) REVERT: A 3129 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 3442 ASN cc_start: 0.7589 (m-40) cc_final: 0.7354 (m110) REVERT: A 3562 GLU cc_start: 0.8388 (tp30) cc_final: 0.8051 (tp30) REVERT: A 3594 SER cc_start: 0.9082 (m) cc_final: 0.8864 (p) REVERT: A 3603 THR cc_start: 0.7905 (p) cc_final: 0.7671 (p) REVERT: A 3673 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7389 (mptt) REVERT: A 3705 LEU cc_start: 0.8404 (tp) cc_final: 0.8202 (tt) REVERT: A 3726 ILE cc_start: 0.8553 (mt) cc_final: 0.8139 (mt) REVERT: B 17 MET cc_start: 0.7396 (mtt) cc_final: 0.7177 (mtm) REVERT: B 108 GLU cc_start: 0.7898 (pp20) cc_final: 0.7307 (pp20) REVERT: B 123 ILE cc_start: 0.7817 (tt) cc_final: 0.7608 (pt) REVERT: B 154 LEU cc_start: 0.8317 (tt) cc_final: 0.7952 (tt) REVERT: B 192 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7814 (ptpp) REVERT: B 253 ASN cc_start: 0.8983 (m-40) cc_final: 0.8763 (t0) REVERT: B 254 GLU cc_start: 0.8037 (mp0) cc_final: 0.7622 (mp0) REVERT: B 281 ASN cc_start: 0.8421 (m-40) cc_final: 0.8173 (m-40) REVERT: B 293 GLU cc_start: 0.8400 (mp0) cc_final: 0.8151 (mp0) REVERT: B 297 ASN cc_start: 0.8791 (m-40) cc_final: 0.8267 (m-40) REVERT: B 347 LEU cc_start: 0.8692 (tp) cc_final: 0.8419 (mt) REVERT: B 362 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8154 (mm-30) REVERT: G 21 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.7302 (t) REVERT: G 74 MET cc_start: 0.9219 (mmm) cc_final: 0.8969 (tpt) REVERT: G 285 PHE cc_start: 0.8254 (m-80) cc_final: 0.7901 (m-80) REVERT: G 401 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7323 (tm-30) REVERT: G 405 GLN cc_start: 0.8295 (mm110) cc_final: 0.8019 (mm110) REVERT: G 406 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7939 (mt-10) REVERT: G 407 LEU cc_start: 0.8543 (mt) cc_final: 0.8322 (mt) REVERT: G 450 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8692 (p) REVERT: E 200 LYS cc_start: 0.8401 (mttt) cc_final: 0.8141 (mtpt) REVERT: E 228 GLN cc_start: 0.7264 (mm110) cc_final: 0.7062 (mp10) REVERT: E 300 MET cc_start: 0.7320 (tpp) cc_final: 0.7037 (tpp) REVERT: E 426 MET cc_start: 0.8214 (tpp) cc_final: 0.7854 (tpp) REVERT: E 467 ASP cc_start: 0.7347 (p0) cc_final: 0.7002 (p0) REVERT: E 474 LYS cc_start: 0.6691 (tttp) cc_final: 0.6107 (ptpp) REVERT: E 582 ARG cc_start: 0.7208 (mmp80) cc_final: 0.6983 (mmp80) REVERT: F 111 GLU cc_start: 0.8487 (tt0) cc_final: 0.7906 (tt0) REVERT: F 115 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: F 128 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7963 (t0) REVERT: F 255 ASP cc_start: 0.7923 (m-30) cc_final: 0.7666 (m-30) REVERT: F 266 GLU cc_start: 0.8187 (pm20) cc_final: 0.7983 (pm20) REVERT: F 285 ARG cc_start: 0.8668 (ptm160) cc_final: 0.8254 (ptm160) REVERT: F 321 TYR cc_start: 0.8974 (t80) cc_final: 0.8460 (t80) REVERT: F 332 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7792 (tt0) REVERT: F 333 ILE cc_start: 0.8578 (tt) cc_final: 0.8362 (mt) REVERT: F 342 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7345 (mm-30) REVERT: C 419 MET cc_start: 0.1385 (ttt) cc_final: 0.1153 (ttt) REVERT: C 429 THR cc_start: 0.6193 (t) cc_final: 0.5990 (m) REVERT: C 437 LYS cc_start: 0.6877 (pptt) cc_final: 0.6394 (pptt) REVERT: C 439 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 511 ILE cc_start: 0.8393 (mm) cc_final: 0.8119 (mm) REVERT: C 563 LEU cc_start: 0.8215 (mp) cc_final: 0.7824 (tt) REVERT: C 575 LEU cc_start: 0.7075 (tp) cc_final: 0.6471 (tt) REVERT: C 652 CYS cc_start: 0.7822 (t) cc_final: 0.7227 (m) outliers start: 133 outliers final: 76 residues processed: 999 average time/residue: 0.2288 time to fit residues: 378.8241 Evaluate side-chains 977 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 890 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1592 PHE Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1913 HIS Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 3129 GLU Chi-restraints excluded: chain A residue 3141 GLN Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 612 PHE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 266 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 178 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 322 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 HIS ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1530 GLN ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3127 HIS ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.170176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127801 restraints weight = 74670.284| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.74 r_work: 0.3498 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38654 Z= 0.190 Angle : 0.678 13.519 52497 Z= 0.338 Chirality : 0.043 0.263 6036 Planarity : 0.005 0.080 6755 Dihedral : 4.765 69.178 5315 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 4.19 % Allowed : 20.59 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 4851 helix: 1.95 (0.09), residues: 3072 sheet: -0.82 (0.34), residues: 196 loop : -0.71 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.022 0.002 TYR A2696 PHE 0.044 0.002 PHE A 995 TRP 0.029 0.002 TRP A2906 HIS 0.046 0.002 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (38654) covalent geometry : angle 0.67841 / 0.34 (52497) hydrogen bonds : bond 0.03924 / 2.82 ( 2300) hydrogen bonds : angle 4.16670 / 3.09 ( 6768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 944 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8773 (tp) cc_final: 0.8369 (mp) REVERT: A 325 HIS cc_start: 0.7840 (m-70) cc_final: 0.6964 (m-70) REVERT: A 357 PHE cc_start: 0.8870 (t80) cc_final: 0.8623 (t80) REVERT: A 571 PHE cc_start: 0.8960 (m-80) cc_final: 0.8693 (m-80) REVERT: A 612 LYS cc_start: 0.9294 (tttt) cc_final: 0.8952 (ttpt) REVERT: A 615 PHE cc_start: 0.8864 (t80) cc_final: 0.8592 (t80) REVERT: A 662 ILE cc_start: 0.9195 (tt) cc_final: 0.8949 (pt) REVERT: A 666 MET cc_start: 0.8353 (ptt) cc_final: 0.7885 (ptt) REVERT: A 667 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 677 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7851 (tt0) REVERT: A 681 GLU cc_start: 0.8696 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 686 MET cc_start: 0.8527 (tpp) cc_final: 0.7784 (tpp) REVERT: A 689 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8833 (mm-40) REVERT: A 690 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7108 (mpp) REVERT: A 701 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 702 PHE cc_start: 0.8673 (m-80) cc_final: 0.8288 (m-80) REVERT: A 748 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6943 (mmt) REVERT: A 804 LEU cc_start: 0.8712 (mm) cc_final: 0.8445 (mt) REVERT: A 929 LEU cc_start: 0.8941 (mt) cc_final: 0.8719 (mt) REVERT: A 1142 MET cc_start: 0.8292 (tpp) cc_final: 0.7939 (tpp) REVERT: A 1145 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 1194 ILE cc_start: 0.8524 (tt) cc_final: 0.8299 (pt) REVERT: A 1335 ASP cc_start: 0.8527 (t0) cc_final: 0.7845 (t0) REVERT: A 1554 MET cc_start: 0.7653 (tpp) cc_final: 0.7345 (tpt) REVERT: A 1558 LEU cc_start: 0.8972 (tp) cc_final: 0.8705 (tp) REVERT: A 1600 ILE cc_start: 0.8308 (mm) cc_final: 0.8088 (mp) REVERT: A 1617 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7271 (ptp-170) REVERT: A 1649 ASP cc_start: 0.8888 (t0) cc_final: 0.8316 (t0) REVERT: A 1740 ASP cc_start: 0.8681 (m-30) cc_final: 0.8395 (m-30) REVERT: A 1766 MET cc_start: 0.8286 (tmm) cc_final: 0.8049 (tmm) REVERT: A 1843 LEU cc_start: 0.8067 (mt) cc_final: 0.7746 (mt) REVERT: A 1874 LYS cc_start: 0.8354 (mttm) cc_final: 0.7793 (mttm) REVERT: A 1920 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 2418 MET cc_start: 0.7054 (mmm) cc_final: 0.6684 (mmp) REVERT: A 2423 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 2459 ASP cc_start: 0.8364 (m-30) cc_final: 0.8128 (m-30) REVERT: A 2542 ASP cc_start: 0.7781 (t0) cc_final: 0.7452 (t0) REVERT: A 2578 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 2589 LEU cc_start: 0.8167 (mt) cc_final: 0.7827 (mt) REVERT: A 2595 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 2643 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6267 (mt-10) REVERT: A 2763 GLU cc_start: 0.8051 (pp20) cc_final: 0.7739 (pp20) REVERT: A 2884 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7912 (mm-40) REVERT: A 2958 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7956 (mmtt) REVERT: A 3087 TYR cc_start: 0.8335 (m-80) cc_final: 0.8129 (m-80) REVERT: A 3098 LYS cc_start: 0.8183 (pptt) cc_final: 0.7881 (pttt) REVERT: A 3114 ASP cc_start: 0.5951 (t0) cc_final: 0.5704 (t0) REVERT: A 3129 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: A 3146 LEU cc_start: 0.8521 (tp) cc_final: 0.8285 (tp) REVERT: A 3443 ASN cc_start: 0.7469 (t0) cc_final: 0.7032 (t0) REVERT: A 3538 ASP cc_start: 0.8488 (t0) cc_final: 0.8160 (t0) REVERT: A 3603 THR cc_start: 0.8621 (p) cc_final: 0.7746 (p) REVERT: A 3607 ASP cc_start: 0.8147 (m-30) cc_final: 0.7743 (m-30) REVERT: A 3624 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8044 (ttpp) REVERT: A 3673 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7775 (mptt) REVERT: A 3726 ILE cc_start: 0.8689 (mt) cc_final: 0.8254 (mm) REVERT: B 108 GLU cc_start: 0.7893 (pp20) cc_final: 0.7333 (pp20) REVERT: B 123 ILE cc_start: 0.7969 (tt) cc_final: 0.7697 (pt) REVERT: B 154 LEU cc_start: 0.8367 (tt) cc_final: 0.7909 (tt) REVERT: B 166 ILE cc_start: 0.9078 (mt) cc_final: 0.8573 (mm) REVERT: B 167 TYR cc_start: 0.7100 (t80) cc_final: 0.6277 (t80) REVERT: B 192 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7863 (ptpp) REVERT: B 226 GLN cc_start: 0.8911 (tp40) cc_final: 0.8495 (mm-40) REVERT: B 229 GLN cc_start: 0.7987 (pp30) cc_final: 0.7775 (pt0) REVERT: B 254 GLU cc_start: 0.8019 (mp0) cc_final: 0.7534 (mp0) REVERT: B 281 ASN cc_start: 0.8637 (m-40) cc_final: 0.8341 (m-40) REVERT: B 297 ASN cc_start: 0.8856 (m-40) cc_final: 0.8409 (m-40) REVERT: B 318 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8465 (mm) REVERT: B 362 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8188 (mm-30) REVERT: G 21 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7709 (t) REVERT: G 74 MET cc_start: 0.9214 (mmm) cc_final: 0.8855 (tpt) REVERT: G 109 GLU cc_start: 0.7817 (pp20) cc_final: 0.7251 (pp20) REVERT: G 205 VAL cc_start: 0.8597 (t) cc_final: 0.8083 (p) REVERT: G 285 PHE cc_start: 0.8313 (m-80) cc_final: 0.8085 (m-80) REVERT: G 297 LEU cc_start: 0.8231 (mt) cc_final: 0.7786 (mt) REVERT: G 401 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7211 (tm-30) REVERT: G 405 GLN cc_start: 0.8349 (mm110) cc_final: 0.7971 (mm110) REVERT: G 406 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8129 (mt-10) REVERT: E 228 GLN cc_start: 0.7562 (mm110) cc_final: 0.7249 (tm-30) REVERT: E 253 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7683 (mt) REVERT: E 260 LEU cc_start: 0.8967 (mt) cc_final: 0.8672 (mm) REVERT: E 300 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7367 (tpp) REVERT: E 426 MET cc_start: 0.8345 (tpp) cc_final: 0.7951 (tpp) REVERT: E 467 ASP cc_start: 0.7202 (p0) cc_final: 0.6897 (p0) REVERT: E 480 GLU cc_start: 0.8561 (tt0) cc_final: 0.8291 (tp30) REVERT: E 567 GLU cc_start: 0.7763 (pt0) cc_final: 0.7515 (pt0) REVERT: E 582 ARG cc_start: 0.7308 (mmp80) cc_final: 0.6617 (mmp80) REVERT: E 587 TYR cc_start: 0.7615 (m-80) cc_final: 0.7045 (m-80) REVERT: E 605 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: F 111 GLU cc_start: 0.8437 (tt0) cc_final: 0.7898 (tt0) REVERT: F 115 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: F 128 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8037 (t0) REVERT: F 242 ASP cc_start: 0.9036 (m-30) cc_final: 0.8789 (m-30) REVERT: F 266 GLU cc_start: 0.8217 (pm20) cc_final: 0.7963 (pm20) REVERT: F 285 ARG cc_start: 0.8690 (ptm160) cc_final: 0.8327 (ptm160) REVERT: F 292 ARG cc_start: 0.7934 (mmp-170) cc_final: 0.7611 (mmp-170) REVERT: F 321 TYR cc_start: 0.9063 (t80) cc_final: 0.8410 (t80) REVERT: F 332 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7761 (tt0) REVERT: F 340 VAL cc_start: 0.8692 (t) cc_final: 0.8343 (m) REVERT: F 342 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7440 (mm-30) REVERT: F 362 ARG cc_start: 0.6540 (tpt170) cc_final: 0.6326 (tpt170) REVERT: C 419 MET cc_start: 0.1286 (ttt) cc_final: 0.1049 (ttt) REVERT: C 437 LYS cc_start: 0.6654 (pptt) cc_final: 0.6108 (pptt) REVERT: C 439 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 472 GLN cc_start: 0.8256 (mt0) cc_final: 0.7948 (mt0) REVERT: C 496 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7171 (mt-10) REVERT: C 511 ILE cc_start: 0.8455 (mm) cc_final: 0.8160 (mm) REVERT: C 512 LYS cc_start: 0.8027 (tppt) cc_final: 0.7738 (ttpt) REVERT: C 604 MET cc_start: 0.7574 (ptm) cc_final: 0.7373 (ptm) REVERT: C 652 CYS cc_start: 0.7974 (t) cc_final: 0.7315 (m) outliers start: 159 outliers final: 96 residues processed: 1025 average time/residue: 0.2285 time to fit residues: 389.2347 Evaluate side-chains 993 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 880 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1617 ARG Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1648 VAL Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1756 VAL Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2576 ARG Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3129 GLU Chi-restraints excluded: chain A residue 3292 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3652 ILE Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 300 MET Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 605 GLN Chi-restraints excluded: chain E residue 612 PHE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 552 CYS Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 413 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 374 optimal weight: 4.9990 chunk 409 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 HIS ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 ASN ** A3596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN G 176 GLN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.170692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128039 restraints weight = 74764.216| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.97 r_work: 0.3508 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38654 Z= 0.152 Angle : 0.653 13.172 52497 Z= 0.324 Chirality : 0.041 0.230 6036 Planarity : 0.005 0.061 6755 Dihedral : 4.722 68.337 5315 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 3.92 % Allowed : 22.43 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.12), residues: 4851 helix: 2.02 (0.09), residues: 3070 sheet: -0.61 (0.36), residues: 179 loop : -0.74 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 257 TYR 0.018 0.002 TYR A1707 PHE 0.038 0.002 PHE A1549 TRP 0.027 0.001 TRP A2906 HIS 0.012 0.001 HIS A1540 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (38654) covalent geometry : angle 0.65299 / 0.32 (52497) hydrogen bonds : bond 0.03546 / 2.54 ( 2300) hydrogen bonds : angle 4.06705 / 3.02 ( 6768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 926 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8785 (tp) cc_final: 0.8344 (mp) REVERT: A 325 HIS cc_start: 0.7806 (m-70) cc_final: 0.6938 (m-70) REVERT: A 571 PHE cc_start: 0.8969 (m-80) cc_final: 0.8612 (m-80) REVERT: A 612 LYS cc_start: 0.9276 (tttt) cc_final: 0.8971 (ttpt) REVERT: A 662 ILE cc_start: 0.9230 (tt) cc_final: 0.8954 (pt) REVERT: A 667 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7639 (t80) REVERT: A 677 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8049 (tt0) REVERT: A 681 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 686 MET cc_start: 0.8510 (tpp) cc_final: 0.7756 (tpp) REVERT: A 689 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8853 (mm-40) REVERT: A 690 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7015 (mpp) REVERT: A 701 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 702 PHE cc_start: 0.8504 (m-80) cc_final: 0.8270 (m-80) REVERT: A 753 PHE cc_start: 0.5888 (m-10) cc_final: 0.5550 (m-80) REVERT: A 758 GLU cc_start: 0.7920 (pt0) cc_final: 0.7569 (mm-30) REVERT: A 838 LEU cc_start: 0.8829 (mm) cc_final: 0.8371 (mm) REVERT: A 858 LYS cc_start: 0.8823 (tppt) cc_final: 0.8494 (tppt) REVERT: A 929 LEU cc_start: 0.9017 (mt) cc_final: 0.8807 (mt) REVERT: A 944 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8062 (mmmt) REVERT: A 1023 MET cc_start: 0.7808 (ptt) cc_final: 0.7024 (mtp) REVERT: A 1142 MET cc_start: 0.8369 (tpp) cc_final: 0.7943 (tpp) REVERT: A 1145 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 1194 ILE cc_start: 0.8604 (tt) cc_final: 0.8140 (pt) REVERT: A 1335 ASP cc_start: 0.8577 (t0) cc_final: 0.7933 (t0) REVERT: A 1554 MET cc_start: 0.7704 (tpp) cc_final: 0.7333 (tpt) REVERT: A 1558 LEU cc_start: 0.8993 (tp) cc_final: 0.8764 (tp) REVERT: A 1574 GLU cc_start: 0.7891 (pp20) cc_final: 0.7668 (pp20) REVERT: A 1586 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8401 (mp0) REVERT: A 1600 ILE cc_start: 0.8400 (mm) cc_final: 0.8128 (mp) REVERT: A 1649 ASP cc_start: 0.8910 (t0) cc_final: 0.8342 (t0) REVERT: A 1660 GLU cc_start: 0.8520 (mp0) cc_final: 0.8281 (mp0) REVERT: A 1740 ASP cc_start: 0.8653 (m-30) cc_final: 0.8297 (m-30) REVERT: A 1766 MET cc_start: 0.8198 (tmm) cc_final: 0.7973 (tmm) REVERT: A 1844 MET cc_start: 0.8359 (mmt) cc_final: 0.8155 (mmt) REVERT: A 1874 LYS cc_start: 0.8324 (mttm) cc_final: 0.7745 (mttm) REVERT: A 2418 MET cc_start: 0.6992 (mmm) cc_final: 0.6668 (mmp) REVERT: A 2423 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 2542 ASP cc_start: 0.7598 (t0) cc_final: 0.7239 (t0) REVERT: A 2578 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 2589 LEU cc_start: 0.8168 (mt) cc_final: 0.7797 (mt) REVERT: A 2595 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 2643 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6380 (mt-10) REVERT: A 2763 GLU cc_start: 0.8004 (pp20) cc_final: 0.7786 (pp20) REVERT: A 2958 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7935 (mmtt) REVERT: A 3098 LYS cc_start: 0.8149 (pptt) cc_final: 0.7948 (pttt) REVERT: A 3114 ASP cc_start: 0.5652 (t0) cc_final: 0.5439 (p0) REVERT: A 3129 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 3146 LEU cc_start: 0.8644 (tp) cc_final: 0.8363 (tp) REVERT: A 3443 ASN cc_start: 0.7490 (t0) cc_final: 0.7094 (t0) REVERT: A 3538 ASP cc_start: 0.8593 (t0) cc_final: 0.8352 (t0) REVERT: A 3543 THR cc_start: 0.8093 (p) cc_final: 0.7863 (t) REVERT: A 3607 ASP cc_start: 0.8125 (m-30) cc_final: 0.7831 (m-30) REVERT: A 3673 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7703 (mptt) REVERT: A 3676 SER cc_start: 0.7316 (t) cc_final: 0.7036 (t) REVERT: A 3726 ILE cc_start: 0.8686 (mt) cc_final: 0.8328 (mm) REVERT: B 108 GLU cc_start: 0.7788 (pp20) cc_final: 0.7385 (pp20) REVERT: B 123 ILE cc_start: 0.8011 (tt) cc_final: 0.7713 (pt) REVERT: B 154 LEU cc_start: 0.8325 (tt) cc_final: 0.7852 (tt) REVERT: B 166 ILE cc_start: 0.9059 (mt) cc_final: 0.8582 (mm) REVERT: B 192 LYS cc_start: 0.8245 (ptpp) cc_final: 0.7907 (ptpp) REVERT: B 254 GLU cc_start: 0.7965 (mp0) cc_final: 0.7559 (mp0) REVERT: B 281 ASN cc_start: 0.8613 (m-40) cc_final: 0.8282 (m-40) REVERT: B 297 ASN cc_start: 0.8759 (m-40) cc_final: 0.8335 (m-40) REVERT: B 318 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8441 (mm) REVERT: B 335 GLU cc_start: 0.8131 (mp0) cc_final: 0.7744 (pm20) REVERT: B 354 GLN cc_start: 0.8140 (mt0) cc_final: 0.7939 (mp10) REVERT: B 362 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8172 (mm-30) REVERT: G 21 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7618 (t) REVERT: G 109 GLU cc_start: 0.7771 (pp20) cc_final: 0.7313 (pp20) REVERT: G 249 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7028 (mt-10) REVERT: G 252 LEU cc_start: 0.8303 (mm) cc_final: 0.8073 (mt) REVERT: G 285 PHE cc_start: 0.8233 (m-80) cc_final: 0.7972 (m-80) REVERT: G 297 LEU cc_start: 0.8297 (mt) cc_final: 0.7974 (mt) REVERT: G 307 GLU cc_start: 0.8031 (mp0) cc_final: 0.7638 (mp0) REVERT: G 401 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7123 (tm-30) REVERT: G 405 GLN cc_start: 0.8302 (mm110) cc_final: 0.7958 (mm110) REVERT: G 406 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8209 (mt-10) REVERT: E 222 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8088 (tm-30) REVERT: E 228 GLN cc_start: 0.7558 (mm110) cc_final: 0.7286 (tm-30) REVERT: E 243 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8011 (mt) REVERT: E 253 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7586 (mt) REVERT: E 260 LEU cc_start: 0.9012 (mt) cc_final: 0.8714 (mm) REVERT: E 426 MET cc_start: 0.8265 (tpp) cc_final: 0.7962 (tpp) REVERT: E 467 ASP cc_start: 0.7163 (p0) cc_final: 0.6867 (p0) REVERT: E 480 GLU cc_start: 0.8560 (tt0) cc_final: 0.8311 (tp30) REVERT: E 567 GLU cc_start: 0.7759 (pt0) cc_final: 0.7429 (pt0) REVERT: E 587 TYR cc_start: 0.7637 (m-80) cc_final: 0.7230 (m-80) REVERT: E 656 ARG cc_start: 0.7025 (ttt90) cc_final: 0.6758 (ttt90) REVERT: F 111 GLU cc_start: 0.8443 (tt0) cc_final: 0.7866 (tt0) REVERT: F 115 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: F 242 ASP cc_start: 0.9068 (m-30) cc_final: 0.8574 (p0) REVERT: F 253 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8325 (tttt) REVERT: F 266 GLU cc_start: 0.8291 (pm20) cc_final: 0.8016 (pm20) REVERT: F 321 TYR cc_start: 0.9018 (t80) cc_final: 0.8332 (t80) REVERT: F 332 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7764 (tt0) REVERT: F 338 SER cc_start: 0.9299 (t) cc_final: 0.8477 (p) REVERT: F 342 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 437 LYS cc_start: 0.6607 (pptt) cc_final: 0.6133 (pptt) REVERT: C 439 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 472 GLN cc_start: 0.8244 (mt0) cc_final: 0.7911 (mt0) REVERT: C 511 ILE cc_start: 0.8527 (mm) cc_final: 0.8264 (mm) REVERT: C 512 LYS cc_start: 0.8016 (tppt) cc_final: 0.7340 (mtmm) REVERT: C 513 ASP cc_start: 0.6657 (t70) cc_final: 0.6241 (t70) REVERT: C 617 LEU cc_start: 0.8589 (mt) cc_final: 0.8091 (mm) REVERT: C 652 CYS cc_start: 0.7916 (t) cc_final: 0.7220 (m) outliers start: 149 outliers final: 94 residues processed: 999 average time/residue: 0.2207 time to fit residues: 368.1628 Evaluate side-chains 970 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 865 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 899 ASP Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1818 SER Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2576 ARG Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3129 GLU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3292 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3438 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3533 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3654 GLU Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 463 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 123 optimal weight: 20.0000 chunk 310 optimal weight: 0.0270 chunk 236 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 276 optimal weight: 0.4980 chunk 183 optimal weight: 40.0000 chunk 98 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS A1288 GLN ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2807 GLN A2824 GLN ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS E 590 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.167095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122111 restraints weight = 74409.355| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.11 r_work: 0.3412 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 38654 Z= 0.217 Angle : 0.727 15.816 52497 Z= 0.360 Chirality : 0.044 0.237 6036 Planarity : 0.005 0.058 6755 Dihedral : 4.933 80.733 5313 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 4.48 % Allowed : 22.72 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.12), residues: 4851 helix: 1.84 (0.09), residues: 3069 sheet: -0.62 (0.36), residues: 180 loop : -0.80 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 350 TYR 0.036 0.002 TYR A 394 PHE 0.035 0.002 PHE A 995 TRP 0.032 0.002 TRP A2906 HIS 0.007 0.001 HIS A2841 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (38654) covalent geometry : angle 0.72666 / 0.36 (52497) hydrogen bonds : bond 0.04107 / 2.95 ( 2300) hydrogen bonds : angle 4.20684 / 3.13 ( 6768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 898 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8816 (tp) cc_final: 0.8549 (mp) REVERT: A 325 HIS cc_start: 0.7940 (m-70) cc_final: 0.7071 (m-70) REVERT: A 394 TYR cc_start: 0.8257 (m-80) cc_final: 0.7981 (m-80) REVERT: A 571 PHE cc_start: 0.8994 (m-80) cc_final: 0.8732 (m-80) REVERT: A 612 LYS cc_start: 0.9278 (tttt) cc_final: 0.8887 (ttpt) REVERT: A 661 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: A 662 ILE cc_start: 0.9225 (tt) cc_final: 0.8976 (pt) REVERT: A 666 MET cc_start: 0.8095 (ptt) cc_final: 0.7888 (ptt) REVERT: A 667 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7593 (t80) REVERT: A 677 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8124 (tp30) REVERT: A 681 GLU cc_start: 0.8820 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 686 MET cc_start: 0.8567 (tpp) cc_final: 0.7757 (tpp) REVERT: A 689 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8884 (mm-40) REVERT: A 690 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: A 701 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 702 PHE cc_start: 0.8391 (m-80) cc_final: 0.7974 (m-80) REVERT: A 753 PHE cc_start: 0.6235 (m-10) cc_final: 0.5892 (m-80) REVERT: A 758 GLU cc_start: 0.7981 (pt0) cc_final: 0.7535 (mm-30) REVERT: A 838 LEU cc_start: 0.8921 (mm) cc_final: 0.8492 (mm) REVERT: A 944 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8029 (mmmt) REVERT: A 947 SER cc_start: 0.8128 (m) cc_final: 0.7716 (p) REVERT: A 1023 MET cc_start: 0.7929 (ptt) cc_final: 0.7130 (mtp) REVERT: A 1142 MET cc_start: 0.8720 (tpp) cc_final: 0.8146 (tpp) REVERT: A 1184 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 1198 MET cc_start: 0.8351 (tmm) cc_final: 0.8035 (tpt) REVERT: A 1203 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6332 (mt) REVERT: A 1335 ASP cc_start: 0.8681 (t0) cc_final: 0.8095 (t0) REVERT: A 1437 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8592 (mpt-90) REVERT: A 1554 MET cc_start: 0.7735 (tpp) cc_final: 0.7397 (tpt) REVERT: A 1586 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8421 (mp0) REVERT: A 1600 ILE cc_start: 0.8539 (mm) cc_final: 0.8338 (mp) REVERT: A 1628 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.7860 (mtt90) REVERT: A 1649 ASP cc_start: 0.8925 (t0) cc_final: 0.8354 (t0) REVERT: A 1650 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9077 (mm) REVERT: A 1740 ASP cc_start: 0.8721 (m-30) cc_final: 0.8430 (m-30) REVERT: A 1766 MET cc_start: 0.8248 (tmm) cc_final: 0.7993 (tmm) REVERT: A 1874 LYS cc_start: 0.8329 (mttm) cc_final: 0.7741 (mttm) REVERT: A 2418 MET cc_start: 0.7104 (mmm) cc_final: 0.6891 (mmp) REVERT: A 2423 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 2578 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 2589 LEU cc_start: 0.8379 (mt) cc_final: 0.8015 (mt) REVERT: A 2595 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 2643 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 2662 ASP cc_start: 0.8767 (t0) cc_final: 0.8531 (t0) REVERT: A 2958 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7993 (mmtt) REVERT: A 3129 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 3443 ASN cc_start: 0.7908 (t0) cc_final: 0.7537 (t0) REVERT: A 3603 THR cc_start: 0.9090 (p) cc_final: 0.8183 (p) REVERT: A 3607 ASP cc_start: 0.8336 (m-30) cc_final: 0.7910 (m-30) REVERT: A 3624 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: A 3673 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7712 (mptt) REVERT: A 3726 ILE cc_start: 0.8784 (mt) cc_final: 0.8548 (mm) REVERT: B 82 ASP cc_start: 0.8086 (p0) cc_final: 0.7881 (p0) REVERT: B 108 GLU cc_start: 0.7835 (pp20) cc_final: 0.7341 (pp20) REVERT: B 154 LEU cc_start: 0.8479 (tt) cc_final: 0.8021 (tt) REVERT: B 166 ILE cc_start: 0.9021 (mt) cc_final: 0.8594 (mm) REVERT: B 192 LYS cc_start: 0.8249 (ptpp) cc_final: 0.7908 (ptpp) REVERT: B 229 GLN cc_start: 0.7778 (pp30) cc_final: 0.7223 (pt0) REVERT: B 254 GLU cc_start: 0.8049 (mp0) cc_final: 0.7673 (mp0) REVERT: B 297 ASN cc_start: 0.8853 (m-40) cc_final: 0.8566 (m110) REVERT: B 318 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B 335 GLU cc_start: 0.8192 (mp0) cc_final: 0.7879 (pm20) REVERT: B 362 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 109 GLU cc_start: 0.7907 (pp20) cc_final: 0.7350 (pp20) REVERT: G 205 VAL cc_start: 0.8741 (t) cc_final: 0.8483 (p) REVERT: G 249 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7194 (mt-10) REVERT: G 252 LEU cc_start: 0.8447 (mm) cc_final: 0.8158 (mt) REVERT: G 285 PHE cc_start: 0.8347 (m-80) cc_final: 0.8028 (m-80) REVERT: G 297 LEU cc_start: 0.8430 (mt) cc_final: 0.8055 (mt) REVERT: G 307 GLU cc_start: 0.8118 (mp0) cc_final: 0.7694 (mp0) REVERT: G 401 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7379 (tm-30) REVERT: G 405 GLN cc_start: 0.8368 (mm110) cc_final: 0.8155 (mm110) REVERT: G 406 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8407 (mt-10) REVERT: G 415 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8234 (tttp) REVERT: G 421 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8076 (p) REVERT: G 426 GLU cc_start: 0.7513 (tt0) cc_final: 0.7310 (tt0) REVERT: E 189 ARG cc_start: 0.6467 (mtp85) cc_final: 0.6255 (ttp-170) REVERT: E 222 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 243 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8213 (mt) REVERT: E 253 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7773 (mt) REVERT: E 260 LEU cc_start: 0.9080 (mt) cc_final: 0.8755 (mm) REVERT: E 303 LEU cc_start: 0.8555 (tp) cc_final: 0.8334 (tp) REVERT: E 426 MET cc_start: 0.8555 (tpp) cc_final: 0.8301 (tpp) REVERT: E 430 LYS cc_start: 0.8401 (tptp) cc_final: 0.8100 (tptp) REVERT: E 467 ASP cc_start: 0.7155 (p0) cc_final: 0.6849 (p0) REVERT: E 480 GLU cc_start: 0.8622 (tt0) cc_final: 0.8410 (tp30) REVERT: E 567 GLU cc_start: 0.7960 (pt0) cc_final: 0.7657 (pt0) REVERT: E 587 TYR cc_start: 0.7924 (m-80) cc_final: 0.7706 (m-80) REVERT: E 592 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7822 (mt-10) REVERT: F 111 GLU cc_start: 0.8478 (tt0) cc_final: 0.7985 (tt0) REVERT: F 253 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8361 (tttt) REVERT: F 266 GLU cc_start: 0.8433 (pm20) cc_final: 0.7904 (pm20) REVERT: F 285 ARG cc_start: 0.8677 (ptm160) cc_final: 0.8309 (ptm160) REVERT: F 332 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7897 (tt0) REVERT: F 338 SER cc_start: 0.9262 (t) cc_final: 0.8395 (p) REVERT: F 340 VAL cc_start: 0.8789 (t) cc_final: 0.8422 (m) REVERT: F 342 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7894 (mm-30) REVERT: C 439 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 472 GLN cc_start: 0.8277 (mt0) cc_final: 0.7954 (mt0) REVERT: C 511 ILE cc_start: 0.8647 (mm) cc_final: 0.8396 (mm) REVERT: C 512 LYS cc_start: 0.8059 (tppt) cc_final: 0.7660 (mtmt) REVERT: C 617 LEU cc_start: 0.8661 (mt) cc_final: 0.8187 (mm) REVERT: C 652 CYS cc_start: 0.8102 (t) cc_final: 0.7370 (m) outliers start: 170 outliers final: 119 residues processed: 987 average time/residue: 0.2112 time to fit residues: 347.4656 Evaluate side-chains 982 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 850 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 669 HIS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1756 VAL Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2576 ARG Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2670 SER Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3084 ILE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3129 GLU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3136 ILE Chi-restraints excluded: chain A residue 3292 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3438 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3533 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3621 LEU Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3634 ILE Chi-restraints excluded: chain A residue 3652 ILE Chi-restraints excluded: chain A residue 3654 GLU Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 463 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 675 GLU Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Chi-restraints excluded: chain C residue 659 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 228 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 424 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 488 optimal weight: 0.4980 chunk 267 optimal weight: 0.3980 chunk 224 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 387 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2908 GLN ** A3310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3435 GLN ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS B 116 ASN B 281 ASN E 590 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.169344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.124731 restraints weight = 74181.229| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.14 r_work: 0.3456 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38654 Z= 0.135 Angle : 0.678 14.118 52497 Z= 0.331 Chirality : 0.041 0.234 6036 Planarity : 0.005 0.061 6755 Dihedral : 4.806 83.204 5313 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 24.49 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.12), residues: 4851 helix: 1.99 (0.09), residues: 3065 sheet: -0.43 (0.37), residues: 178 loop : -0.78 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A3489 TYR 0.027 0.001 TYR A1559 PHE 0.032 0.002 PHE A1549 TRP 0.035 0.001 TRP A2906 HIS 0.008 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (38654) covalent geometry : angle 0.67827 / 0.33 (52497) hydrogen bonds : bond 0.03484 / 2.49 ( 2300) hydrogen bonds : angle 4.06983 / 3.01 ( 6768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 897 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 HIS cc_start: 0.7934 (m-70) cc_final: 0.7026 (m-70) REVERT: A 350 ARG cc_start: 0.6485 (ttp80) cc_final: 0.6123 (ttp80) REVERT: A 357 PHE cc_start: 0.8573 (t80) cc_final: 0.7535 (t80) REVERT: A 394 TYR cc_start: 0.8186 (m-80) cc_final: 0.7844 (m-80) REVERT: A 452 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8356 (tpp80) REVERT: A 559 LYS cc_start: 0.9100 (tptp) cc_final: 0.8886 (tptp) REVERT: A 571 PHE cc_start: 0.8972 (m-80) cc_final: 0.8698 (m-80) REVERT: A 612 LYS cc_start: 0.9268 (tttt) cc_final: 0.8912 (tttt) REVERT: A 661 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: A 662 ILE cc_start: 0.9158 (tt) cc_final: 0.8937 (pt) REVERT: A 666 MET cc_start: 0.8067 (ptt) cc_final: 0.7848 (ptt) REVERT: A 667 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 677 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8025 (tp30) REVERT: A 680 ARG cc_start: 0.9093 (tmm-80) cc_final: 0.8630 (ttt-90) REVERT: A 681 GLU cc_start: 0.8783 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 686 MET cc_start: 0.8539 (tpp) cc_final: 0.7799 (tpp) REVERT: A 689 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8862 (mm-40) REVERT: A 690 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7025 (mpp) REVERT: A 701 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 702 PHE cc_start: 0.8438 (m-80) cc_final: 0.7977 (m-80) REVERT: A 753 PHE cc_start: 0.6124 (m-10) cc_final: 0.5808 (m-80) REVERT: A 758 GLU cc_start: 0.7955 (pt0) cc_final: 0.7560 (mm-30) REVERT: A 805 TYR cc_start: 0.7397 (m-10) cc_final: 0.7123 (m-10) REVERT: A 838 LEU cc_start: 0.8877 (mm) cc_final: 0.8426 (mm) REVERT: A 875 LEU cc_start: 0.8529 (mt) cc_final: 0.8185 (mt) REVERT: A 944 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8098 (mmmt) REVERT: A 1023 MET cc_start: 0.7913 (ptt) cc_final: 0.7146 (mtp) REVERT: A 1142 MET cc_start: 0.8582 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1184 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 1198 MET cc_start: 0.8353 (tmm) cc_final: 0.8025 (tpt) REVERT: A 1202 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7306 (m) REVERT: A 1335 ASP cc_start: 0.8677 (t0) cc_final: 0.8133 (t0) REVERT: A 1437 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8581 (mpt-90) REVERT: A 1554 MET cc_start: 0.7759 (tpp) cc_final: 0.7348 (tpt) REVERT: A 1586 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8430 (mp0) REVERT: A 1628 ARG cc_start: 0.8129 (ptp-170) cc_final: 0.7691 (mtt90) REVERT: A 1649 ASP cc_start: 0.8888 (t0) cc_final: 0.8323 (t0) REVERT: A 1650 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 1740 ASP cc_start: 0.8612 (m-30) cc_final: 0.8371 (m-30) REVERT: A 1766 MET cc_start: 0.8169 (tmm) cc_final: 0.7922 (tmm) REVERT: A 1844 MET cc_start: 0.8606 (mmt) cc_final: 0.8360 (mmt) REVERT: A 1874 LYS cc_start: 0.8399 (mttm) cc_final: 0.7835 (mttm) REVERT: A 2423 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 2589 LEU cc_start: 0.8310 (mt) cc_final: 0.7909 (mt) REVERT: A 2595 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 2612 VAL cc_start: 0.8719 (t) cc_final: 0.8498 (t) REVERT: A 2643 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6773 (mt-10) REVERT: A 2763 GLU cc_start: 0.7981 (pp20) cc_final: 0.7751 (pp20) REVERT: A 2958 LYS cc_start: 0.8283 (mmtt) cc_final: 0.8002 (mmtt) REVERT: A 3305 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7537 (mp0) REVERT: A 3443 ASN cc_start: 0.7680 (t0) cc_final: 0.7355 (t0) REVERT: A 3562 GLU cc_start: 0.8720 (tt0) cc_final: 0.8270 (mt-10) REVERT: A 3570 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8427 (ttmm) REVERT: A 3603 THR cc_start: 0.9030 (p) cc_final: 0.8203 (p) REVERT: A 3607 ASP cc_start: 0.8311 (m-30) cc_final: 0.7954 (m-30) REVERT: A 3640 MET cc_start: 0.7863 (mmm) cc_final: 0.7538 (mmm) REVERT: A 3673 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7622 (mptt) REVERT: B 108 GLU cc_start: 0.7735 (pp20) cc_final: 0.7296 (pp20) REVERT: B 154 LEU cc_start: 0.8415 (tt) cc_final: 0.7948 (tt) REVERT: B 166 ILE cc_start: 0.9025 (mt) cc_final: 0.8613 (mm) REVERT: B 192 LYS cc_start: 0.8243 (ptpp) cc_final: 0.7908 (ptpp) REVERT: B 254 GLU cc_start: 0.7974 (mp0) cc_final: 0.7607 (mp0) REVERT: B 318 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 329 LYS cc_start: 0.8308 (tttt) cc_final: 0.8063 (mtpt) REVERT: B 335 GLU cc_start: 0.8120 (mp0) cc_final: 0.7824 (pm20) REVERT: B 356 MET cc_start: 0.8530 (mmt) cc_final: 0.8285 (mpp) REVERT: B 362 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8183 (mm-30) REVERT: G 109 GLU cc_start: 0.7914 (pp20) cc_final: 0.7333 (pp20) REVERT: G 205 VAL cc_start: 0.8715 (t) cc_final: 0.8466 (p) REVERT: G 249 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7123 (mt-10) REVERT: G 252 LEU cc_start: 0.8315 (mm) cc_final: 0.8083 (mt) REVERT: G 285 PHE cc_start: 0.8269 (m-80) cc_final: 0.7927 (m-80) REVERT: G 297 LEU cc_start: 0.8409 (mt) cc_final: 0.8084 (mt) REVERT: G 406 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8489 (mt-10) REVERT: G 415 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8236 (tttp) REVERT: E 222 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 243 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 253 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7758 (mt) REVERT: E 260 LEU cc_start: 0.9038 (mt) cc_final: 0.8704 (mm) REVERT: E 303 LEU cc_start: 0.8489 (tp) cc_final: 0.8279 (tp) REVERT: E 426 MET cc_start: 0.8537 (tpp) cc_final: 0.8217 (tpp) REVERT: E 430 LYS cc_start: 0.8350 (tptp) cc_final: 0.8042 (tptp) REVERT: E 467 ASP cc_start: 0.7147 (p0) cc_final: 0.6857 (p0) REVERT: E 480 GLU cc_start: 0.8579 (tt0) cc_final: 0.8359 (tp30) REVERT: E 567 GLU cc_start: 0.8009 (pt0) cc_final: 0.7673 (pt0) REVERT: E 587 TYR cc_start: 0.7857 (m-80) cc_final: 0.7611 (m-80) REVERT: E 592 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7746 (mt-10) REVERT: F 111 GLU cc_start: 0.8481 (tt0) cc_final: 0.7983 (tt0) REVERT: F 253 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8430 (tttt) REVERT: F 255 ASP cc_start: 0.8187 (m-30) cc_final: 0.7973 (m-30) REVERT: F 266 GLU cc_start: 0.8370 (pm20) cc_final: 0.7843 (pm20) REVERT: F 285 ARG cc_start: 0.8671 (ptm160) cc_final: 0.8294 (ptm160) REVERT: F 332 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7817 (tt0) REVERT: F 338 SER cc_start: 0.9282 (t) cc_final: 0.8392 (p) REVERT: F 340 VAL cc_start: 0.8766 (t) cc_final: 0.8412 (m) REVERT: F 342 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7854 (mm-30) REVERT: C 437 LYS cc_start: 0.6713 (pptt) cc_final: 0.6273 (pptt) REVERT: C 439 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7784 (mm-30) REVERT: C 472 GLN cc_start: 0.8265 (mt0) cc_final: 0.7939 (mt0) REVERT: C 511 ILE cc_start: 0.8598 (mm) cc_final: 0.8337 (mm) REVERT: C 512 LYS cc_start: 0.8091 (tppt) cc_final: 0.7548 (mppt) REVERT: C 652 CYS cc_start: 0.8056 (t) cc_final: 0.7358 (m) outliers start: 131 outliers final: 90 residues processed: 960 average time/residue: 0.2130 time to fit residues: 338.4907 Evaluate side-chains 953 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 852 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1887 VAL Chi-restraints excluded: chain A residue 1913 HIS Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3136 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3435 GLN Chi-restraints excluded: chain A residue 3438 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 463 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 207 optimal weight: 0.9990 chunk 479 optimal weight: 4.9990 chunk 454 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 371 optimal weight: 0.9980 chunk 352 optimal weight: 0.0770 chunk 339 optimal weight: 1.9990 chunk 316 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1563 ASN ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3435 GLN ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 297 ASN E 590 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.169516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128305 restraints weight = 74368.693| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.86 r_work: 0.3489 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38654 Z= 0.145 Angle : 0.683 13.297 52497 Z= 0.333 Chirality : 0.042 0.252 6036 Planarity : 0.005 0.060 6755 Dihedral : 4.789 88.215 5313 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 3.45 % Allowed : 25.01 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.12), residues: 4851 helix: 2.01 (0.09), residues: 3069 sheet: -0.33 (0.37), residues: 178 loop : -0.74 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3489 TYR 0.027 0.001 TYR A 394 PHE 0.031 0.002 PHE A 339 TRP 0.054 0.001 TRP B 87 HIS 0.014 0.001 HIS A1540 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (38654) covalent geometry : angle 0.68334 / 0.33 (52497) hydrogen bonds : bond 0.03507 / 2.50 ( 2300) hydrogen bonds : angle 4.06480 / 3.02 ( 6768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 877 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 ARG cc_start: 0.6571 (ttp80) cc_final: 0.6206 (ttp80) REVERT: A 394 TYR cc_start: 0.8274 (m-80) cc_final: 0.7948 (m-80) REVERT: A 410 MET cc_start: 0.8730 (ppp) cc_final: 0.8457 (ppp) REVERT: A 544 TYR cc_start: 0.8622 (m-10) cc_final: 0.8177 (m-10) REVERT: A 559 LYS cc_start: 0.9109 (tptp) cc_final: 0.8903 (tptp) REVERT: A 571 PHE cc_start: 0.8965 (m-80) cc_final: 0.8725 (m-80) REVERT: A 612 LYS cc_start: 0.9196 (tttt) cc_final: 0.8827 (ttpt) REVERT: A 661 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 662 ILE cc_start: 0.9124 (tt) cc_final: 0.8916 (pt) REVERT: A 667 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 680 ARG cc_start: 0.9053 (tmm-80) cc_final: 0.8597 (ttt-90) REVERT: A 681 GLU cc_start: 0.8718 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 686 MET cc_start: 0.8471 (tpp) cc_final: 0.7692 (tpp) REVERT: A 689 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8837 (mm-40) REVERT: A 690 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: A 701 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 702 PHE cc_start: 0.8380 (m-80) cc_final: 0.7873 (m-80) REVERT: A 753 PHE cc_start: 0.6108 (m-10) cc_final: 0.5814 (m-80) REVERT: A 758 GLU cc_start: 0.7881 (pt0) cc_final: 0.7542 (mm-30) REVERT: A 805 TYR cc_start: 0.7396 (m-10) cc_final: 0.7171 (m-10) REVERT: A 838 LEU cc_start: 0.8882 (mm) cc_final: 0.8455 (mm) REVERT: A 875 LEU cc_start: 0.8477 (mt) cc_final: 0.8052 (mt) REVERT: A 944 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8110 (mmmt) REVERT: A 1023 MET cc_start: 0.7873 (ptt) cc_final: 0.7081 (mtp) REVERT: A 1142 MET cc_start: 0.8586 (tpp) cc_final: 0.8217 (tpp) REVERT: A 1184 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 1198 MET cc_start: 0.8371 (tmm) cc_final: 0.8076 (tpt) REVERT: A 1202 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7218 (m) REVERT: A 1203 LEU cc_start: 0.6213 (mm) cc_final: 0.5705 (mt) REVERT: A 1231 GLU cc_start: 0.7848 (pm20) cc_final: 0.7561 (pm20) REVERT: A 1335 ASP cc_start: 0.8622 (t0) cc_final: 0.8108 (t0) REVERT: A 1554 MET cc_start: 0.7706 (tpp) cc_final: 0.7299 (tpt) REVERT: A 1586 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8362 (mp0) REVERT: A 1649 ASP cc_start: 0.8841 (t0) cc_final: 0.8323 (t0) REVERT: A 1650 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 1707 TYR cc_start: 0.7738 (m-10) cc_final: 0.7530 (m-10) REVERT: A 1766 MET cc_start: 0.8140 (tmm) cc_final: 0.7883 (tmm) REVERT: A 1844 MET cc_start: 0.8462 (mmt) cc_final: 0.8202 (mmt) REVERT: A 1874 LYS cc_start: 0.8431 (mttm) cc_final: 0.7868 (mttm) REVERT: A 2418 MET cc_start: 0.6521 (mmp) cc_final: 0.5967 (ptm) REVERT: A 2423 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7990 (mt) REVERT: A 2589 LEU cc_start: 0.8315 (mt) cc_final: 0.7973 (mt) REVERT: A 2595 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 2612 VAL cc_start: 0.8699 (t) cc_final: 0.8478 (t) REVERT: A 2643 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 2763 GLU cc_start: 0.7918 (pp20) cc_final: 0.7694 (pp20) REVERT: A 2895 ASP cc_start: 0.8475 (m-30) cc_final: 0.8197 (m-30) REVERT: A 2958 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7834 (mmtt) REVERT: A 3431 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 3443 ASN cc_start: 0.7681 (t0) cc_final: 0.7306 (t0) REVERT: A 3556 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8932 (mmmm) REVERT: A 3562 GLU cc_start: 0.8603 (tt0) cc_final: 0.8179 (mt-10) REVERT: A 3603 THR cc_start: 0.9079 (p) cc_final: 0.8238 (p) REVERT: A 3607 ASP cc_start: 0.8208 (m-30) cc_final: 0.7865 (m-30) REVERT: A 3624 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8031 (ttpp) REVERT: A 3640 MET cc_start: 0.7843 (mmm) cc_final: 0.7582 (mmm) REVERT: A 3673 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7617 (mptt) REVERT: B 108 GLU cc_start: 0.7663 (pp20) cc_final: 0.7237 (pp20) REVERT: B 166 ILE cc_start: 0.9037 (mt) cc_final: 0.8658 (mm) REVERT: B 192 LYS cc_start: 0.8255 (ptpp) cc_final: 0.7928 (ptpp) REVERT: B 254 GLU cc_start: 0.7933 (mp0) cc_final: 0.7585 (mp0) REVERT: B 318 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 329 LYS cc_start: 0.8274 (tttt) cc_final: 0.8026 (mtpt) REVERT: B 335 GLU cc_start: 0.8048 (mp0) cc_final: 0.7763 (pm20) REVERT: B 362 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8138 (mm-30) REVERT: G 109 GLU cc_start: 0.7766 (pp20) cc_final: 0.7223 (pp20) REVERT: G 205 VAL cc_start: 0.8707 (t) cc_final: 0.8465 (p) REVERT: G 252 LEU cc_start: 0.8306 (mm) cc_final: 0.8064 (mt) REVERT: G 285 PHE cc_start: 0.8281 (m-80) cc_final: 0.7934 (m-80) REVERT: G 297 LEU cc_start: 0.8425 (mt) cc_final: 0.8087 (mt) REVERT: G 406 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8606 (mt-10) REVERT: G 415 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8263 (tttp) REVERT: G 426 GLU cc_start: 0.7392 (tt0) cc_final: 0.6982 (mt-10) REVERT: E 213 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8311 (pttp) REVERT: E 222 GLU cc_start: 0.8213 (tm-30) cc_final: 0.8011 (tm-30) REVERT: E 243 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8146 (mt) REVERT: E 253 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7776 (mt) REVERT: E 260 LEU cc_start: 0.9054 (mt) cc_final: 0.8730 (mm) REVERT: E 280 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7893 (ptt-90) REVERT: E 303 LEU cc_start: 0.8541 (tp) cc_final: 0.8262 (tp) REVERT: E 426 MET cc_start: 0.8524 (tpp) cc_final: 0.8236 (tpp) REVERT: E 430 LYS cc_start: 0.8326 (tptp) cc_final: 0.8058 (tptp) REVERT: E 467 ASP cc_start: 0.7001 (p0) cc_final: 0.6736 (p0) REVERT: E 582 ARG cc_start: 0.7307 (mmp80) cc_final: 0.7071 (mmp80) REVERT: E 587 TYR cc_start: 0.7799 (m-80) cc_final: 0.7572 (m-80) REVERT: E 592 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7591 (mt-10) REVERT: F 111 GLU cc_start: 0.8414 (tt0) cc_final: 0.7879 (tt0) REVERT: F 253 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8441 (tttt) REVERT: F 255 ASP cc_start: 0.8164 (m-30) cc_final: 0.7962 (m-30) REVERT: F 266 GLU cc_start: 0.8322 (pm20) cc_final: 0.7785 (pm20) REVERT: F 285 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8417 (ptp-170) REVERT: F 332 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7802 (tt0) REVERT: F 338 SER cc_start: 0.9300 (t) cc_final: 0.8369 (p) REVERT: F 340 VAL cc_start: 0.8763 (t) cc_final: 0.8393 (m) REVERT: F 342 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 439 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7754 (mm-30) REVERT: C 511 ILE cc_start: 0.8606 (mm) cc_final: 0.8336 (mm) REVERT: C 512 LYS cc_start: 0.8070 (tppt) cc_final: 0.7624 (mtmt) REVERT: C 652 CYS cc_start: 0.8039 (t) cc_final: 0.7351 (m) outliers start: 131 outliers final: 89 residues processed: 945 average time/residue: 0.2076 time to fit residues: 325.1784 Evaluate side-chains 956 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 853 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2576 ARG Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2645 LEU Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3136 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3431 GLU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3621 LEU Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3701 VAL Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 463 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 213 LYS Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 619 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 63 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 463 optimal weight: 0.6980 chunk 450 optimal weight: 0.0030 chunk 184 optimal weight: 30.0000 chunk 274 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1882 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3089 GLN ** A3310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 297 ASN ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.169330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127399 restraints weight = 73776.439| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.75 r_work: 0.3490 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 38654 Z= 0.154 Angle : 0.705 18.748 52497 Z= 0.344 Chirality : 0.042 0.299 6036 Planarity : 0.005 0.063 6755 Dihedral : 4.812 87.270 5313 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 3.21 % Allowed : 25.62 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 4851 helix: 1.99 (0.09), residues: 3066 sheet: -0.32 (0.37), residues: 178 loop : -0.72 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A3489 TYR 0.029 0.001 TYR A 394 PHE 0.034 0.002 PHE A 339 TRP 0.059 0.002 TRP B 87 HIS 0.008 0.001 HIS A2619 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (38654) covalent geometry : angle 0.70521 / 0.34 (52497) hydrogen bonds : bond 0.03561 / 2.54 ( 2300) hydrogen bonds : angle 4.09372 / 3.04 ( 6768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 867 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 TYR cc_start: 0.8309 (m-80) cc_final: 0.8003 (m-80) REVERT: A 410 MET cc_start: 0.8781 (ppp) cc_final: 0.8504 (ppp) REVERT: A 544 TYR cc_start: 0.8629 (m-10) cc_final: 0.8128 (m-10) REVERT: A 559 LYS cc_start: 0.9105 (tptp) cc_final: 0.8897 (tptp) REVERT: A 571 PHE cc_start: 0.8986 (m-80) cc_final: 0.8766 (m-80) REVERT: A 608 ILE cc_start: 0.9501 (mm) cc_final: 0.8781 (mm) REVERT: A 609 ASN cc_start: 0.8319 (m-40) cc_final: 0.7987 (m110) REVERT: A 661 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: A 667 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7703 (t80) REVERT: A 677 GLU cc_start: 0.8492 (tp30) cc_final: 0.7987 (tt0) REVERT: A 680 ARG cc_start: 0.9077 (tmm-80) cc_final: 0.8605 (ttt-90) REVERT: A 681 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 686 MET cc_start: 0.8444 (tpp) cc_final: 0.7496 (tpp) REVERT: A 690 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.6962 (mpp) REVERT: A 701 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 702 PHE cc_start: 0.8344 (m-80) cc_final: 0.7809 (m-80) REVERT: A 753 PHE cc_start: 0.6106 (m-10) cc_final: 0.5816 (m-80) REVERT: A 758 GLU cc_start: 0.7847 (pt0) cc_final: 0.7498 (mm-30) REVERT: A 805 TYR cc_start: 0.7368 (m-10) cc_final: 0.7120 (m-10) REVERT: A 838 LEU cc_start: 0.8865 (mm) cc_final: 0.8452 (mm) REVERT: A 875 LEU cc_start: 0.8489 (mt) cc_final: 0.8067 (mt) REVERT: A 944 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8204 (mmmt) REVERT: A 1023 MET cc_start: 0.7856 (ptt) cc_final: 0.7056 (mtp) REVERT: A 1142 MET cc_start: 0.8671 (tpp) cc_final: 0.8262 (tpp) REVERT: A 1184 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 1198 MET cc_start: 0.8371 (tmm) cc_final: 0.8079 (tpt) REVERT: A 1202 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7199 (m) REVERT: A 1203 LEU cc_start: 0.6238 (mm) cc_final: 0.5727 (mt) REVERT: A 1231 GLU cc_start: 0.7888 (pm20) cc_final: 0.7597 (pm20) REVERT: A 1335 ASP cc_start: 0.8679 (t0) cc_final: 0.8163 (t0) REVERT: A 1554 MET cc_start: 0.7687 (tpp) cc_final: 0.7255 (tpt) REVERT: A 1562 ASN cc_start: 0.8478 (p0) cc_final: 0.8098 (p0) REVERT: A 1586 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8389 (mp0) REVERT: A 1649 ASP cc_start: 0.8898 (t0) cc_final: 0.8364 (t0) REVERT: A 1650 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8917 (mm) REVERT: A 1707 TYR cc_start: 0.7751 (m-10) cc_final: 0.7533 (m-10) REVERT: A 1740 ASP cc_start: 0.8559 (m-30) cc_final: 0.8193 (m-30) REVERT: A 1766 MET cc_start: 0.8239 (tmm) cc_final: 0.7992 (tmm) REVERT: A 1844 MET cc_start: 0.8444 (mmt) cc_final: 0.8149 (mmt) REVERT: A 1874 LYS cc_start: 0.8441 (mttm) cc_final: 0.7904 (mttm) REVERT: A 1935 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7252 (mmt90) REVERT: A 2418 MET cc_start: 0.6528 (mmp) cc_final: 0.5939 (ptm) REVERT: A 2423 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7938 (mt) REVERT: A 2589 LEU cc_start: 0.8348 (mt) cc_final: 0.8009 (mt) REVERT: A 2595 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 2643 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6729 (mt-10) REVERT: A 2763 GLU cc_start: 0.7959 (pp20) cc_final: 0.7729 (pp20) REVERT: A 2895 ASP cc_start: 0.8543 (m-30) cc_final: 0.8264 (m-30) REVERT: A 2958 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7847 (mmtt) REVERT: A 3443 ASN cc_start: 0.7707 (t0) cc_final: 0.7413 (t0) REVERT: A 3562 GLU cc_start: 0.8601 (tt0) cc_final: 0.8157 (mt-10) REVERT: A 3603 THR cc_start: 0.9118 (p) cc_final: 0.8284 (p) REVERT: A 3607 ASP cc_start: 0.8236 (m-30) cc_final: 0.7855 (m-30) REVERT: A 3624 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7987 (ttpp) REVERT: A 3640 MET cc_start: 0.7904 (mmm) cc_final: 0.7666 (mmm) REVERT: A 3673 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7639 (mptt) REVERT: A 3782 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7998 (mttt) REVERT: B 108 GLU cc_start: 0.7637 (pp20) cc_final: 0.7185 (pp20) REVERT: B 154 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 166 ILE cc_start: 0.9034 (mt) cc_final: 0.8659 (mm) REVERT: B 192 LYS cc_start: 0.8244 (ptpp) cc_final: 0.7908 (ptpp) REVERT: B 254 GLU cc_start: 0.7944 (mp0) cc_final: 0.7096 (mp0) REVERT: B 318 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8472 (mm) REVERT: B 329 LYS cc_start: 0.8227 (tttt) cc_final: 0.7998 (mtpt) REVERT: B 362 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 109 GLU cc_start: 0.7766 (pp20) cc_final: 0.7244 (pp20) REVERT: G 194 LEU cc_start: 0.8556 (tt) cc_final: 0.8316 (tt) REVERT: G 246 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8142 (tt0) REVERT: G 252 LEU cc_start: 0.8319 (mm) cc_final: 0.8082 (mt) REVERT: G 285 PHE cc_start: 0.8262 (m-80) cc_final: 0.7934 (m-80) REVERT: G 297 LEU cc_start: 0.8467 (mt) cc_final: 0.8135 (mt) REVERT: G 406 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8637 (mt-10) REVERT: G 415 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8312 (tttp) REVERT: G 426 GLU cc_start: 0.7454 (tt0) cc_final: 0.7026 (mt-10) REVERT: E 189 ARG cc_start: 0.6456 (mtp85) cc_final: 0.6219 (ttp-170) REVERT: E 243 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 253 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7809 (mt) REVERT: E 260 LEU cc_start: 0.9087 (mt) cc_final: 0.8765 (mm) REVERT: E 280 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7855 (ptt-90) REVERT: E 303 LEU cc_start: 0.8482 (tp) cc_final: 0.8182 (tp) REVERT: E 426 MET cc_start: 0.8542 (tpp) cc_final: 0.8269 (tpp) REVERT: E 430 LYS cc_start: 0.8324 (tptp) cc_final: 0.8026 (tptp) REVERT: E 467 ASP cc_start: 0.7023 (p0) cc_final: 0.6750 (p0) REVERT: E 592 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7623 (mt-10) REVERT: F 111 GLU cc_start: 0.8402 (tt0) cc_final: 0.7857 (tt0) REVERT: F 253 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8377 (tttt) REVERT: F 266 GLU cc_start: 0.8396 (pm20) cc_final: 0.7874 (pm20) REVERT: F 285 ARG cc_start: 0.8684 (ptm160) cc_final: 0.8399 (ptp-170) REVERT: F 288 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8652 (mmm160) REVERT: F 332 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7918 (tt0) REVERT: F 338 SER cc_start: 0.9275 (t) cc_final: 0.8289 (p) REVERT: F 340 VAL cc_start: 0.8751 (t) cc_final: 0.8354 (m) REVERT: F 342 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 439 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7797 (mm-30) REVERT: C 472 GLN cc_start: 0.8313 (mt0) cc_final: 0.7982 (mt0) REVERT: C 511 ILE cc_start: 0.8607 (mm) cc_final: 0.8338 (mm) REVERT: C 512 LYS cc_start: 0.8029 (tppt) cc_final: 0.7561 (mtmt) REVERT: C 617 LEU cc_start: 0.8496 (mt) cc_final: 0.8023 (mm) REVERT: C 652 CYS cc_start: 0.8059 (t) cc_final: 0.7332 (m) outliers start: 122 outliers final: 92 residues processed: 926 average time/residue: 0.2185 time to fit residues: 335.8806 Evaluate side-chains 954 residues out of total 4459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 847 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 GLN Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1739 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2544 LEU Chi-restraints excluded: chain A residue 2576 ARG Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2645 LEU Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3132 VAL Chi-restraints excluded: chain A residue 3292 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3621 LEU Chi-restraints excluded: chain A residue 3624 LYS Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3701 VAL Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3782 LYS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 698 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 619 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 17 optimal weight: 0.3980 chunk 390 optimal weight: 3.9990 chunk 461 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 268 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 238 optimal weight: 0.5980 chunk 299 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN G 181 HIS ** E 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.170023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127148 restraints weight = 73962.197| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.76 r_work: 0.3447 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38654 Z= 0.151 Angle : 0.708 14.845 52497 Z= 0.347 Chirality : 0.043 0.277 6036 Planarity : 0.005 0.069 6755 Dihedral : 4.795 84.119 5313 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 3.11 % Allowed : 25.86 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.12), residues: 4851 helix: 2.00 (0.09), residues: 3066 sheet: -0.35 (0.37), residues: 178 loop : -0.71 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A2881 TYR 0.028 0.001 TYR A 394 PHE 0.042 0.002 PHE A1604 TRP 0.055 0.001 TRP B 87 HIS 0.005 0.001 HIS A1547 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (38654) covalent geometry : angle 0.70802 / 0.35 (52497) hydrogen bonds : bond 0.03523 / 2.51 ( 2300) hydrogen bonds : angle 4.09436 / 3.04 ( 6768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12243.00 seconds wall clock time: 209 minutes 32.02 seconds (12572.02 seconds total)