Starting phenix.real_space_refine on Sat Sep 12 08:06:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vhh_21205/09_2026/6vhh_21205.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8999 2.51 5 N 2446 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14219 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1723, 13243 Classifications: {'peptide': 1723} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 63, 'TRANS': 1659} Chain breaks: 2 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 13, 'ASN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 28, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 291 Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 772 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.82, per 1000 atoms: 0.20 Number of scatterers: 14219 At special positions: 0 Unit cell: (108, 119.88, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2712 8.00 N 2446 7.00 C 8999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1218 " distance=2.03 Simple disulfide: pdb=" SG CYS A1277 " - pdb=" SG CYS A1330 " distance=2.03 Simple disulfide: pdb=" SG CYS A1394 " - pdb=" SG CYS A1402 " distance=2.03 Simple disulfide: pdb=" SG CYS A1396 " - pdb=" SG CYS A1404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 66 " distance=2.05 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 110 " distance=2.02 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 97 " distance=2.03 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 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A2704 " - " ASN A1586 " " NAG A2705 " - " ASN A2071 " " NAG A2706 " - " ASN A1867 " " NAG C 1 " - " ASN A1681 " " NAG D 1 " - " ASN A2211 " " NAG E 1 " - " ASN A1766 " " NAG F 1 " - " ASN A1490 " " NAG G 1 " - " ASN A1647 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 589.0 milliseconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3366 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 23 sheets defined 9.0% alpha, 51.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1216 through 1220 Processing helix chain 'A' and resid 1411 through 1415 removed outlier: 3.573A pdb=" N ASP A1414 " --> pdb=" O TYR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2284 through 2288 removed outlier: 3.549A pdb=" N GLY A2288 " --> pdb=" O PHE A2285 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2322 removed outlier: 3.618A pdb=" N TRP A2319 " --> pdb=" O TYR A2316 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A2320 " --> pdb=" O THR A2317 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A2322 " --> pdb=" O TRP A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2334 through 2338 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2353 through 2360 Processing helix chain 'A' and resid 2363 through 2367 Processing helix chain 'A' and resid 2382 through 2390 Processing helix chain 'A' and resid 2398 through 2412 Processing helix chain 'A' and resid 2464 through 2475 Processing helix chain 'A' and resid 2500 through 2509 removed outlier: 4.045A pdb=" N ASP A2504 " --> pdb=" O SER A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2558 through 2561 Processing helix chain 'A' and resid 2562 through 2592 removed outlier: 3.526A pdb=" N GLN A2572 " --> pdb=" O ARG A2568 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A2580 " --> pdb=" O ARG A2576 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A2588 " --> pdb=" O LYS A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2602 through 2610 Processing helix chain 'A' and resid 2627 through 2631 removed outlier: 3.623A pdb=" N ALA A2631 " --> pdb=" O PRO A2628 " (cutoff:3.500A) Processing helix chain 'A' and resid 2633 through 2635 No H-bonds generated for 'chain 'A' and resid 2633 through 2635' Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.873A pdb=" N MET B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 74' Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.625A pdb=" N ILE B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 88 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 911 through 914 Processing sheet with id=AA2, first strand: chain 'A' and resid 930 through 931 Processing sheet with id=AA3, first strand: chain 'A' and resid 991 through 996 removed outlier: 5.443A pdb=" N GLY A1019 " --> pdb=" O GLY A1049 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1067 through 1069 Processing sheet with id=AA5, first strand: chain 'A' and resid 1091 through 1096 removed outlier: 6.386A pdb=" N ILE A1441 " --> pdb=" O ILE A1095 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A1422 " --> pdb=" O ALA A1434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1111 through 1112 removed outlier: 6.724A pdb=" N ILE A1140 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1163 through 1167 Processing sheet with id=AA8, first strand: chain 'A' and resid 1233 through 1237 removed outlier: 5.299A pdb=" N GLY A1234 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A1246 " --> pdb=" O GLY A1234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1294 through 1295 removed outlier: 6.546A pdb=" N ILE A1311 " --> pdb=" O ILE A1323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1351 through 1356 removed outlier: 6.681A pdb=" N THR A1365 " --> pdb=" O SER A1352 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A1354 " --> pdb=" O TYR A1363 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A1363 " --> pdb=" O ILE A1354 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN A1377 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A1386 " --> pdb=" O GLN A1377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1461 removed outlier: 5.742A pdb=" N GLN A1477 " --> pdb=" O PHE A1491 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A1481 " --> pdb=" O TYR A1487 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A1487 " --> pdb=" O SER A1481 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A1490 " --> pdb=" O LEU A1502 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A1502 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A1492 " --> pdb=" O THR A1500 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR A1500 " --> pdb=" O ILE A1512 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A1511 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A1523 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A1513 " --> pdb=" O ARG A1521 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG A1521 " --> pdb=" O LEU A1533 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A1532 " --> pdb=" O VAL A1544 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A1544 " --> pdb=" O THR A1532 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1534 " --> pdb=" O LYS A1542 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS A1542 " --> pdb=" O MET A1554 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A1553 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A1566 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A1555 " --> pdb=" O ALA A1564 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU A1562 " --> pdb=" O ASP A1557 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N LEU A1562 " --> pdb=" O TYR A1578 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR A1578 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A1564 " --> pdb=" O TYR A1576 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A1575 " --> pdb=" O VAL A1587 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A1587 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A1577 " --> pdb=" O THR A1585 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR A1585 " --> pdb=" O LEU A1597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A1659 " --> pdb=" O ILE A1682 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A1682 " --> pdb=" O GLY A1659 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER A1661 " --> pdb=" O CYS A1680 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS A1680 " --> pdb=" O SER A1661 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS A1663 " --> pdb=" O GLY A1678 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A1674 " --> pdb=" O HIS A1667 " (cutoff:3.500A) removed outlier: 19.407A pdb=" N THR A1672 " --> pdb=" O GLN A1701 " (cutoff:3.500A) removed outlier: 20.713A pdb=" N GLN A1701 " --> pdb=" O THR A1672 " (cutoff:3.500A) removed outlier: 17.172A pdb=" N THR A1674 " --> pdb=" O LYS A1699 " (cutoff:3.500A) removed outlier: 13.317A pdb=" N LYS A1699 " --> pdb=" O THR A1674 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N THR A1676 " --> pdb=" O LEU A1697 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU A1697 " --> pdb=" O THR A1676 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY A1678 " --> pdb=" O TRP A1695 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A1692 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A1715 " --> pdb=" O SER A1692 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A1694 " --> pdb=" O LEU A1713 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A1713 " --> pdb=" O GLU A1694 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A1696 " --> pdb=" O ARG A1711 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A1711 " --> pdb=" O ARG A1696 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A1698 " --> pdb=" O PHE A1709 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A1709 " --> pdb=" O ARG A1698 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A1700 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1721 " --> pdb=" O LEU A1713 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A1715 " --> pdb=" O ASN A1719 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASN A1719 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1755 " --> pdb=" O ILE A1746 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE A1754 " --> pdb=" O VAL A1767 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A1766 " --> pdb=" O LEU A1778 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A1778 " --> pdb=" O ASN A1766 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER A1768 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A1776 " --> pdb=" O THR A1787 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A1797 " --> pdb=" O ASP A1788 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL A1796 " --> pdb=" O TYR A1808 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A1826 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1838 " --> pdb=" O ILE A1826 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A1828 " --> pdb=" O LEU A1836 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A1836 " --> pdb=" O MET A1848 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A1871 " --> pdb=" O THR A1883 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A1883 " --> pdb=" O ILE A1871 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP A1873 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A1881 " --> pdb=" O TYR A1894 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN A1891 " --> pdb=" O TYR A1907 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR A1907 " --> pdb=" O GLN A1891 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A1893 " --> pdb=" O ILE A1905 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A1905 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A1895 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER A1903 " --> pdb=" O PHE A1914 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A1911 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A1928 " --> pdb=" O ALA A1911 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A1913 " --> pdb=" O VAL A1926 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A1926 " --> pdb=" O THR A1913 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY A1915 " --> pdb=" O LYS A1924 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A1924 " --> pdb=" O TYR A1939 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A1934 " --> pdb=" O PHE A1953 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE A1953 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A1936 " --> pdb=" O TYR A1951 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A1951 " --> pdb=" O THR A1936 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A1938 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN A1949 " --> pdb=" O ARG A1938 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG A1940 " --> pdb=" O ASP A1947 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N LEU A1945 " --> pdb=" O TYR A1967 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N TYR A1967 " --> pdb=" O LEU A1945 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP A1947 " --> pdb=" O TYR A1965 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A1962 " --> pdb=" O PRO A1979 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A1964 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A1977 " --> pdb=" O ASP A1964 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A1966 " --> pdb=" O ALA A1975 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1457 through 1461 removed outlier: 5.742A pdb=" N GLN A1477 " --> pdb=" O PHE A1491 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A1481 " --> pdb=" O TYR A1487 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A1487 " --> pdb=" O SER A1481 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A1490 " --> pdb=" O LEU A1502 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A1502 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A1492 " --> pdb=" O THR A1500 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR A1500 " --> pdb=" O ILE A1512 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A1511 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A1523 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A1513 " --> pdb=" O ARG A1521 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG A1521 " --> pdb=" O LEU A1533 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A1532 " --> pdb=" O VAL A1544 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A1544 " --> pdb=" O THR A1532 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A1534 " --> pdb=" O LYS A1542 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS A1542 " --> pdb=" O MET A1554 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A1553 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A1566 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A1555 " --> pdb=" O ALA A1564 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU A1562 " --> pdb=" O ASP A1557 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N LEU A1562 " --> pdb=" O TYR A1578 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR A1578 " --> pdb=" O LEU A1562 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A1564 " --> pdb=" O TYR A1576 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A1575 " --> pdb=" O VAL A1587 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A1587 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A1577 " --> pdb=" O THR A1585 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR A1585 " --> pdb=" O LEU A1597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A1659 " --> pdb=" O ILE A1682 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A1682 " --> pdb=" O GLY A1659 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER A1661 " --> pdb=" O CYS A1680 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS A1680 " --> pdb=" O SER A1661 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS A1663 " --> pdb=" O GLY A1678 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A1674 " --> pdb=" O HIS A1667 " (cutoff:3.500A) removed outlier: 19.407A pdb=" N THR A1672 " --> pdb=" O GLN A1701 " (cutoff:3.500A) removed outlier: 20.713A pdb=" N GLN A1701 " --> pdb=" O THR A1672 " (cutoff:3.500A) removed outlier: 17.172A pdb=" N THR A1674 " --> pdb=" O LYS A1699 " (cutoff:3.500A) removed outlier: 13.317A pdb=" N LYS A1699 " --> pdb=" O THR A1674 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N THR A1676 " --> pdb=" O LEU A1697 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU A1697 " --> pdb=" O THR A1676 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLY A1678 " --> pdb=" O TRP A1695 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A1692 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A1715 " --> pdb=" O SER A1692 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU A1694 " --> pdb=" O LEU A1713 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A1713 " --> pdb=" O GLU A1694 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A1696 " --> pdb=" O ARG A1711 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A1711 " --> pdb=" O ARG A1696 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A1698 " --> pdb=" O PHE A1709 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A1709 " --> pdb=" O ARG A1698 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A1700 " --> pdb=" O THR A1707 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1721 " --> pdb=" O LEU A1713 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A1715 " --> pdb=" O ASN A1719 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASN A1719 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1755 " --> pdb=" O ILE A1746 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE A1754 " --> pdb=" O VAL A1767 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A1766 " --> pdb=" O LEU A1778 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A1778 " --> pdb=" O ASN A1766 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER A1768 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA A1776 " --> pdb=" O THR A1787 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A1797 " --> pdb=" O ASP A1788 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL A1796 " --> pdb=" O TYR A1808 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A1826 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1838 " --> pdb=" O ILE A1826 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A1828 " --> pdb=" O LEU A1836 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A1836 " --> pdb=" O MET A1848 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A1871 " --> pdb=" O THR A1883 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A1883 " --> pdb=" O ILE A1871 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP A1873 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A1881 " --> pdb=" O TYR A1894 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN A1891 " --> pdb=" O TYR A1907 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR A1907 " --> pdb=" O GLN A1891 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A1893 " --> pdb=" O ILE A1905 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A1905 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A1895 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER A1903 " --> pdb=" O PHE A1914 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A1911 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A1928 " --> pdb=" O ALA A1911 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A1913 " --> pdb=" O VAL A1926 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A1926 " --> pdb=" O THR A1913 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY A1915 " --> pdb=" O LYS A1924 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS A1924 " --> pdb=" O TYR A1939 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER A1934 " --> pdb=" O PHE A1953 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE A1953 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A1936 " --> pdb=" O TYR A1951 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A1951 " --> pdb=" O THR A1936 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A1938 " --> pdb=" O GLN A1949 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN A1949 " --> pdb=" O ARG A1938 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG A1940 " --> pdb=" O ASP A1947 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N LEU A1945 " --> pdb=" O TYR A1967 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N TYR A1967 " --> pdb=" O LEU A1945 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP A1947 " --> pdb=" O TYR A1965 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A1962 " --> pdb=" O PRO A1979 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A1964 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A1977 " --> pdb=" O ASP A1964 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A1966 " --> pdb=" O ALA A1975 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA A1975 " --> pdb=" O TYR A1991 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A1990 " --> pdb=" O PHE A2003 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A2003 " --> pdb=" O LEU A1990 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG A1992 " --> pdb=" O GLU A2001 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLU A2001 " --> pdb=" O VAL A2008 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS A2035 " --> pdb=" O VAL A2051 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET A2041 " --> pdb=" O LEU A2045 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A2045 " --> pdb=" O MET A2041 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N MET A2046 " --> pdb=" O LEU A2066 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A2066 " --> pdb=" O MET A2046 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP A2048 " --> pdb=" O LEU A2064 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A2064 " --> pdb=" O TRP A2048 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR A2050 " --> pdb=" O ARG A2062 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG A2062 " --> pdb=" O THR A2050 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A2052 " --> pdb=" O ILE A2060 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE A2060 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A2074 " --> pdb=" O VAL A2090 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL A2090 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A2076 " --> pdb=" O VAL A2088 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A2088 " --> pdb=" O THR A2076 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A2078 " --> pdb=" O GLN A2086 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A2090 " --> pdb=" O PRO A2094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2099 through 2100 removed outlier: 3.678A pdb=" N LEU A2108 " --> pdb=" O SER A2099 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N HIS A2107 " --> pdb=" O LEU A2120 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A2131 " --> pdb=" O PRO A2119 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG A2121 " --> pdb=" O THR A2129 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR A2129 " --> pdb=" O TYR A2136 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A2134 " --> pdb=" O LEU A2131 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN A2135 " --> pdb=" O ARG A2147 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A2147 " --> pdb=" O GLN A2135 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A2137 " --> pdb=" O CYS A2145 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N CYS A2145 " --> pdb=" O PHE A2152 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A2162 " --> pdb=" O GLU A2153 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR A2161 " --> pdb=" O TYR A2174 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER A2171 " --> pdb=" O THR A2187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A2187 " --> pdb=" O SER A2171 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A2173 " --> pdb=" O TYR A2185 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A2185 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A2175 " --> pdb=" O ALA A2183 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA A2183 " --> pdb=" O TYR A2195 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A2217 " --> pdb=" O SER A2233 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A2233 " --> pdb=" O ILE A2217 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER A2219 " --> pdb=" O MET A2231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A2231 " --> pdb=" O SER A2219 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A2221 " --> pdb=" O PHE A2229 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A2229 " --> pdb=" O VAL A2241 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLU A2238 " --> pdb=" O SER A2254 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER A2254 " --> pdb=" O GLU A2238 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A2240 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A2252 " --> pdb=" O TYR A2240 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A2242 " --> pdb=" O LEU A2250 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A2250 " --> pdb=" O LEU A2263 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A2254 " --> pdb=" O MET A2259 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET A2259 " --> pdb=" O SER A2254 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN A2262 " --> pdb=" O ASP A2274 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP A2274 " --> pdb=" O GLN A2262 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A2264 " --> pdb=" O TYR A2272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2289 through 2291 removed outlier: 3.756A pdb=" N LEU A2296 " --> pdb=" O ASP A2291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A2310 " --> pdb=" O ASP A2305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2446 through 2450 Processing sheet with id=AB7, first strand: chain 'A' and resid 2478 through 2479 Processing sheet with id=AB8, first strand: chain 'A' and resid 2478 through 2479 removed outlier: 5.977A pdb=" N ASP A2491 " --> pdb=" O LEU A2550 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER A2552 " --> pdb=" O ASP A2491 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A2493 " --> pdb=" O SER A2552 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ARG A2554 " --> pdb=" O HIS A2493 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE A2495 " --> pdb=" O ARG A2554 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR A2540 " --> pdb=" O TYR A2555 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2529 through 2532 Processing sheet with id=AC1, first strand: chain 'A' and resid 2616 through 2620 Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AC4, first strand: chain 'B' and resid 41 through 44 Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 51 656 hydrogen bonds defined for protein. 1686 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: 6.24 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3164 1.32 - 1.45: 3390 1.45 - 1.57: 7865 1.57 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 14522 Sorted by residual: bond pdb=" N CYS A1106 " pdb=" CA CYS A1106 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.10e-03 1.21e+04 1.19e+01 bond pdb=" N ILE B 65 " pdb=" CA ILE B 65 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.22e-02 6.72e+03 1.15e+01 bond pdb=" N ASN A1138 " pdb=" CA ASN A1138 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 bond pdb=" N LYS A1448 " pdb=" CA LYS A1448 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.12e+01 bond pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.18e-02 7.18e+03 9.80e+00 ... (remaining 14517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 18269 1.91 - 3.82: 1300 3.82 - 5.73: 143 5.73 - 7.65: 27 7.65 - 9.56: 3 Bond angle restraints: 19742 Sorted by residual: angle pdb=" C ALA A1160 " pdb=" N HIS A1161 " pdb=" CA HIS A1161 " ideal model delta sigma weight residual 121.19 127.88 -6.69 1.59e+00 3.96e-01 1.77e+01 angle pdb=" N VAL A1544 " pdb=" CA VAL A1544 " pdb=" C VAL A1544 " ideal model delta sigma weight residual 107.80 101.84 5.96 1.45e+00 4.76e-01 1.69e+01 angle pdb=" CA VAL A1134 " pdb=" C VAL A1134 " pdb=" N GLY A1135 " ideal model delta sigma weight residual 116.37 111.57 4.80 1.22e+00 6.72e-01 1.55e+01 angle pdb=" C SER A1445 " pdb=" N LYS A1446 " pdb=" CA LYS A1446 " ideal model delta sigma weight residual 120.82 126.19 -5.37 1.41e+00 5.03e-01 1.45e+01 angle pdb=" CA GLY A1540 " pdb=" C GLY A1540 " pdb=" O GLY A1540 " ideal model delta sigma weight residual 120.75 117.28 3.47 9.40e-01 1.13e+00 1.36e+01 ... (remaining 19737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7682 17.19 - 34.38: 700 34.38 - 51.57: 125 51.57 - 68.75: 18 68.75 - 85.94: 4 Dihedral angle restraints: 8529 sinusoidal: 3240 harmonic: 5289 Sorted by residual: dihedral pdb=" CB CYS A1394 " pdb=" SG CYS A1394 " pdb=" SG CYS A1402 " pdb=" CB CYS A1402 " ideal model delta sinusoidal sigma weight residual -86.00 -148.59 62.59 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ARG A1233 " pdb=" C ARG A1233 " pdb=" N GLY A1234 " pdb=" CA GLY A1234 " ideal model delta harmonic sigma weight residual 180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN A1438 " pdb=" C ASN A1438 " pdb=" N ILE A1439 " pdb=" CA ILE A1439 " ideal model delta harmonic sigma weight residual 180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 8526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.917: 2269 0.917 - 1.834: 0 1.834 - 2.751: 0 2.751 - 3.668: 0 3.668 - 4.584: 3 Chirality restraints: 2272 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.01 -4.41 2.00e-02 2.50e+03 4.86e+04 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A1766 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 2.18 -4.58 2.00e-01 2.50e+01 5.25e+02 chirality pdb=" C1 NAG A2705 " pdb=" ND2 ASN A2071 " pdb=" C2 NAG A2705 " pdb=" O5 NAG A2705 " both_signs ideal model delta sigma weight residual False -2.40 2.13 -4.53 2.00e-01 2.50e+01 5.14e+02 ... (remaining 2269 not shown) Planarity restraints: 2528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG E 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.080 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2704 " -0.339 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A2704 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A2704 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG A2704 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A2704 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2705 " 0.339 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A2705 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A2705 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG A2705 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG A2705 " 0.079 2.00e-02 2.50e+03 ... (remaining 2525 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 165 2.62 - 3.19: 12081 3.19 - 3.76: 20453 3.76 - 4.33: 30271 4.33 - 4.90: 52205 Nonbonded interactions: 115175 Sorted by model distance: nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.053 3.040 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.054 3.040 nonbonded pdb=" O3 NAG C 2 " pdb=" O7 NAG C 2 " model vdw 2.058 3.040 nonbonded pdb=" NH2 ARG A1233 " pdb=" O PRO A1291 " model vdw 2.199 3.120 nonbonded pdb=" OG SER B 35 " pdb=" O TYR B 39 " model vdw 2.201 3.040 ... (remaining 115170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.015 0.100 14545 Z= 0.668 Angle : 1.103 27.502 19803 Z= 0.628 Chirality : 0.178 4.584 2272 Planarity : 0.014 0.302 2520 Dihedral : 13.390 85.942 5139 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.83 % Favored : 92.00 % Rotamer: Outliers : 0.95 % Allowed : 7.58 % Favored : 91.47 % Cbeta Deviations : 0.06 % 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: -2.75 (0.17), residues: 1813 helix: -2.96 (0.39), residues: 116 sheet: -0.75 (0.21), residues: 557 loop : -2.39 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1823 TYR 0.039 0.004 TYR A2478 PHE 0.024 0.003 PHE A2003 TRP 0.025 0.003 TRP A2311 HIS 0.027 0.003 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.01508 / 0.67 (14522) covalent geometry : angle 1.06803 / 0.62 (19742) SS BOND : bond 0.00751 / 0.60 ( 8) SS BOND : angle 1.30571 / 0.82 ( 16) hydrogen bonds : bond 0.17114 / 11.63 ( 486) hydrogen bonds : angle 8.45011 / 5.66 ( 1686) link_ALPHA1-4 : bond 0.00381 / 0.20 ( 1) link_ALPHA1-4 : angle 1.10802 / 0.44 ( 3) link_BETA1-4 : bond 0.00208 / 0.11 ( 6) link_BETA1-4 : angle 1.17095 / 0.73 ( 18) link_NAG-ASN : bond 0.02617 / 1.77 ( 8) link_NAG-ASN : angle 7.91425 / 4.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1238 ASP cc_start: 0.7892 (t70) cc_final: 0.7543 (t70) REVERT: B 73 MET cc_start: 0.6127 (mpp) cc_final: 0.5801 (mtt) outliers start: 14 outliers final: 7 residues processed: 189 average time/residue: 0.5398 time to fit residues: 113.2690 Evaluate side-chains 124 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1867 ASN Chi-restraints excluded: chain A residue 2105 ASN Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2487 ILE Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain B residue 84 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN A 938 HIS A1048 GLN A1065 HIS A1301 ASN A1377 GLN A1438 ASN A1476 HIS A1506 ASN A1508 ASN A1522 HIS A1667 HIS A1719 ASN A1820 GLN A1927 ASN A2031 HIS A2084 GLN A2105 ASN A2363 GLN A2407 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.113685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079402 restraints weight = 33861.297| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.76 r_work: 0.3106 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 14545 Z= 0.163 Angle : 0.774 12.707 19803 Z= 0.381 Chirality : 0.052 0.682 2272 Planarity : 0.005 0.038 2520 Dihedral : 5.827 45.663 2035 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.10 % Allowed : 12.52 % Favored : 85.39 % 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: -1.78 (0.18), residues: 1813 helix: -0.98 (0.48), residues: 111 sheet: -0.29 (0.21), residues: 586 loop : -1.78 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1614 TYR 0.020 0.001 TYR A2478 PHE 0.012 0.001 PHE A1050 TRP 0.008 0.001 TRP A1695 HIS 0.006 0.001 HIS A2027 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (14522) covalent geometry : angle 0.74062 / 0.37 (19742) SS BOND : bond 0.00663 / 0.53 ( 8) SS BOND : angle 2.18598 / 1.31 ( 16) hydrogen bonds : bond 0.04147 / 2.80 ( 486) hydrogen bonds : angle 6.09220 / 4.11 ( 1686) link_ALPHA1-4 : bond 0.00604 / 0.32 ( 1) link_ALPHA1-4 : angle 1.53273 / 0.81 ( 3) link_BETA1-4 : bond 0.01161 / 0.61 ( 6) link_BETA1-4 : angle 3.55919 / 2.66 ( 18) link_NAG-ASN : bond 0.01026 / 0.70 ( 8) link_NAG-ASN : angle 5.45924 / 3.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9520 (mtm) cc_final: 0.9134 (mtm) REVERT: A 983 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8695 (mmm) REVERT: A 1096 MET cc_start: 0.6985 (ttt) cc_final: 0.6745 (ttt) REVERT: A 1161 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7766 (p-80) REVERT: A 1186 ARG cc_start: 0.6042 (tmm-80) cc_final: 0.5631 (tmm-80) REVERT: A 1554 MET cc_start: 0.9184 (mpp) cc_final: 0.8814 (mpt) REVERT: A 1615 ASP cc_start: 0.9407 (t0) cc_final: 0.9126 (t0) REVERT: A 1732 GLU cc_start: 0.9026 (tt0) cc_final: 0.8823 (tp30) REVERT: A 2472 SER cc_start: 0.9416 (t) cc_final: 0.9116 (p) REVERT: A 2546 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7737 (t80) outliers start: 31 outliers final: 7 residues processed: 153 average time/residue: 0.5056 time to fit residues: 86.7385 Evaluate side-chains 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2486 SER Chi-restraints excluded: chain A residue 2487 ILE Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 0.3980 chunk 180 optimal weight: 8.9990 chunk 96 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1820 GLN A2027 HIS A2407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.114120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079958 restraints weight = 34531.124| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.83 r_work: 0.3118 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14545 Z= 0.122 Angle : 0.667 10.704 19803 Z= 0.330 Chirality : 0.049 0.457 2272 Planarity : 0.004 0.038 2520 Dihedral : 5.127 46.815 2025 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.84 % Allowed : 13.46 % Favored : 83.69 % 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: -1.16 (0.19), residues: 1813 helix: 0.00 (0.49), residues: 119 sheet: -0.01 (0.21), residues: 607 loop : -1.35 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2147 TYR 0.033 0.001 TYR A2011 PHE 0.009 0.001 PHE B 106 TRP 0.006 0.001 TRP A1695 HIS 0.004 0.001 HIS A2027 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14522) covalent geometry : angle 0.64518 / 0.33 (19742) SS BOND : bond 0.00423 / 0.34 ( 8) SS BOND : angle 1.26293 / 0.75 ( 16) hydrogen bonds : bond 0.03415 / 2.27 ( 486) hydrogen bonds : angle 5.39020 / 3.65 ( 1686) link_ALPHA1-4 : bond 0.00653 / 0.34 ( 1) link_ALPHA1-4 : angle 1.46448 / 0.79 ( 3) link_BETA1-4 : bond 0.01084 / 0.57 ( 6) link_BETA1-4 : angle 2.56219 / 1.89 ( 18) link_NAG-ASN : bond 0.00645 / 0.39 ( 8) link_NAG-ASN : angle 4.27310 / 2.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9562 (mtm) cc_final: 0.9094 (mtm) REVERT: A 983 MET cc_start: 0.9216 (mmm) cc_final: 0.8740 (mmm) REVERT: A 1096 MET cc_start: 0.7024 (ttt) cc_final: 0.6813 (ttt) REVERT: A 1161 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7771 (p-80) REVERT: A 1186 ARG cc_start: 0.6168 (tmm-80) cc_final: 0.5828 (tmm-80) REVERT: A 1394 CYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6367 (t) REVERT: A 1541 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (pt) REVERT: A 1554 MET cc_start: 0.9053 (mpp) cc_final: 0.8716 (mpt) REVERT: A 1615 ASP cc_start: 0.9421 (t0) cc_final: 0.9090 (t0) REVERT: A 1732 GLU cc_start: 0.9071 (tt0) cc_final: 0.8840 (tp30) REVERT: A 1783 MET cc_start: 0.8610 (ptt) cc_final: 0.8332 (ptp) REVERT: A 2056 MET cc_start: 0.8846 (mmm) cc_final: 0.8592 (mmt) REVERT: A 2447 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8490 (tmm) REVERT: A 2472 SER cc_start: 0.9445 (t) cc_final: 0.9159 (p) REVERT: A 2546 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 2620 TYR cc_start: 0.8349 (m-80) cc_final: 0.7808 (m-80) REVERT: B 30 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 52 MET cc_start: 0.8311 (ppp) cc_final: 0.8061 (ppp) REVERT: B 69 ASP cc_start: 0.7753 (m-30) cc_final: 0.7514 (m-30) REVERT: B 79 TYR cc_start: 0.6986 (m-80) cc_final: 0.6616 (m-80) REVERT: B 92 ASN cc_start: 0.8466 (m110) cc_final: 0.8093 (m110) outliers start: 42 outliers final: 15 residues processed: 158 average time/residue: 0.4751 time to fit residues: 85.2469 Evaluate side-chains 139 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1373 ASN Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2487 ILE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2622 LEU Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 61 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1199 ASN ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1820 GLN ** A2194 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 = 0.3929 r_free = 0.3929 target = 0.113006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078867 restraints weight = 34604.909| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.83 r_work: 0.3077 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14545 Z= 0.166 Angle : 0.656 10.480 19803 Z= 0.326 Chirality : 0.048 0.358 2272 Planarity : 0.004 0.037 2520 Dihedral : 5.012 46.629 2025 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.77 % Allowed : 14.48 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.19), residues: 1813 helix: 0.72 (0.51), residues: 118 sheet: 0.05 (0.21), residues: 612 loop : -1.11 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1043 TYR 0.017 0.001 TYR B 121 PHE 0.012 0.001 PHE A1662 TRP 0.008 0.001 TRP A2311 HIS 0.003 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (14522) covalent geometry : angle 0.63868 / 0.32 (19742) SS BOND : bond 0.00279 / 0.22 ( 8) SS BOND : angle 1.17895 / 0.71 ( 16) hydrogen bonds : bond 0.03349 / 2.24 ( 486) hydrogen bonds : angle 5.15307 / 3.49 ( 1686) link_ALPHA1-4 : bond 0.00631 / 0.33 ( 1) link_ALPHA1-4 : angle 1.73125 / 0.93 ( 3) link_BETA1-4 : bond 0.00960 / 0.51 ( 6) link_BETA1-4 : angle 2.48109 / 1.84 ( 18) link_NAG-ASN : bond 0.00511 / 0.29 ( 8) link_NAG-ASN : angle 3.76129 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9571 (mtm) cc_final: 0.9234 (mtm) REVERT: A 983 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8706 (mmm) REVERT: A 1096 MET cc_start: 0.7062 (ttt) cc_final: 0.6823 (ttt) REVERT: A 1161 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7639 (p-80) REVERT: A 1186 ARG cc_start: 0.6341 (tmm-80) cc_final: 0.5915 (tmm-80) REVERT: A 1250 MET cc_start: 0.5930 (mmm) cc_final: 0.5528 (mmm) REVERT: A 1394 CYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6452 (t) REVERT: A 1541 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (pt) REVERT: A 1554 MET cc_start: 0.9114 (mpp) cc_final: 0.8787 (mpt) REVERT: A 1615 ASP cc_start: 0.9419 (t0) cc_final: 0.9063 (t0) REVERT: A 1783 MET cc_start: 0.8672 (ptt) cc_final: 0.8395 (ptp) REVERT: A 2011 TYR cc_start: 0.8831 (p90) cc_final: 0.8496 (p90) REVERT: A 2056 MET cc_start: 0.8895 (mmm) cc_final: 0.8655 (mmm) REVERT: A 2415 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: A 2447 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8537 (tmm) REVERT: A 2472 SER cc_start: 0.9480 (t) cc_final: 0.9195 (p) REVERT: A 2546 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7730 (t80) REVERT: A 2620 TYR cc_start: 0.8553 (m-80) cc_final: 0.7997 (m-80) REVERT: B 52 MET cc_start: 0.8595 (ppp) cc_final: 0.8349 (ppp) REVERT: B 79 TYR cc_start: 0.7372 (m-80) cc_final: 0.6922 (m-80) REVERT: B 84 TYR cc_start: 0.8466 (t80) cc_final: 0.8129 (t80) outliers start: 41 outliers final: 14 residues processed: 151 average time/residue: 0.4965 time to fit residues: 84.5388 Evaluate side-chains 135 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1373 ASN Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2333 MET Chi-restraints excluded: chain A residue 2415 GLU Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2487 ILE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2622 LEU Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 99 optimal weight: 0.1980 chunk 169 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 167 optimal weight: 0.3980 chunk 123 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 ASN A1820 GLN ** A2194 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 = 0.3946 r_free = 0.3946 target = 0.113938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079326 restraints weight = 34600.015| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.83 r_work: 0.3102 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14545 Z= 0.121 Angle : 0.634 9.973 19803 Z= 0.314 Chirality : 0.047 0.343 2272 Planarity : 0.004 0.041 2520 Dihedral : 4.837 47.034 2025 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.84 % Allowed : 15.70 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1813 helix: 0.82 (0.51), residues: 118 sheet: 0.15 (0.20), residues: 639 loop : -1.00 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2406 TYR 0.027 0.001 TYR B 121 PHE 0.010 0.001 PHE A1245 TRP 0.008 0.001 TRP A1572 HIS 0.003 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14522) covalent geometry : angle 0.61799 / 0.31 (19742) SS BOND : bond 0.00173 / 0.12 ( 8) SS BOND : angle 1.06187 / 0.64 ( 16) hydrogen bonds : bond 0.03099 / 2.07 ( 486) hydrogen bonds : angle 4.96881 / 3.35 ( 1686) link_ALPHA1-4 : bond 0.00624 / 0.33 ( 1) link_ALPHA1-4 : angle 1.69485 / 0.92 ( 3) link_BETA1-4 : bond 0.00950 / 0.51 ( 6) link_BETA1-4 : angle 2.37702 / 1.76 ( 18) link_NAG-ASN : bond 0.00544 / 0.31 ( 8) link_NAG-ASN : angle 3.42949 / 1.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9575 (mtm) cc_final: 0.9290 (mtm) REVERT: A 983 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8693 (mmm) REVERT: A 1096 MET cc_start: 0.7166 (ttt) cc_final: 0.6901 (ttt) REVERT: A 1161 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7629 (p-80) REVERT: A 1186 ARG cc_start: 0.6536 (tmm-80) cc_final: 0.6002 (tmm-80) REVERT: A 1228 THR cc_start: 0.3624 (OUTLIER) cc_final: 0.3392 (p) REVERT: A 1255 ASP cc_start: 0.9206 (t0) cc_final: 0.8964 (t70) REVERT: A 1315 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8895 (p) REVERT: A 1394 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6579 (t) REVERT: A 1541 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8211 (pt) REVERT: A 1554 MET cc_start: 0.9086 (mpp) cc_final: 0.8750 (mpt) REVERT: A 1615 ASP cc_start: 0.9384 (t0) cc_final: 0.9034 (t0) REVERT: A 1994 ASP cc_start: 0.8840 (t0) cc_final: 0.8571 (t70) REVERT: A 2011 TYR cc_start: 0.8807 (p90) cc_final: 0.8444 (p90) REVERT: A 2056 MET cc_start: 0.8880 (mmm) cc_final: 0.8646 (mmt) REVERT: A 2447 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8554 (tmm) REVERT: A 2472 SER cc_start: 0.9476 (t) cc_final: 0.9185 (p) REVERT: A 2546 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 2620 TYR cc_start: 0.8540 (m-80) cc_final: 0.8006 (m-80) REVERT: B 52 MET cc_start: 0.8770 (ppp) cc_final: 0.8563 (ppp) REVERT: B 79 TYR cc_start: 0.7482 (m-80) cc_final: 0.6971 (m-80) REVERT: B 115 LYS cc_start: 0.6306 (ptmm) cc_final: 0.5930 (ttpp) REVERT: B 120 GLN cc_start: 0.6348 (tt0) cc_final: 0.5747 (tm-30) outliers start: 42 outliers final: 11 residues processed: 155 average time/residue: 0.4830 time to fit residues: 84.6646 Evaluate side-chains 135 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1373 ASN Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1446 LYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain B residue 43 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1345 HIS ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 ASN A1667 HIS A1820 GLN ** A2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 ASN A2433 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.112376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077920 restraints weight = 34772.742| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.85 r_work: 0.3061 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14545 Z= 0.199 Angle : 0.651 10.047 19803 Z= 0.325 Chirality : 0.047 0.336 2272 Planarity : 0.004 0.039 2520 Dihedral : 4.777 46.180 2023 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.71 % Allowed : 15.76 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1813 helix: 0.99 (0.52), residues: 118 sheet: 0.08 (0.21), residues: 631 loop : -0.90 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 90 TYR 0.025 0.001 TYR B 121 PHE 0.012 0.001 PHE A1662 TRP 0.009 0.001 TRP A2311 HIS 0.004 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (14522) covalent geometry : angle 0.63575 / 0.32 (19742) SS BOND : bond 0.00204 / 0.15 ( 8) SS BOND : angle 1.09642 / 0.67 ( 16) hydrogen bonds : bond 0.03286 / 2.21 ( 486) hydrogen bonds : angle 4.98838 / 3.37 ( 1686) link_ALPHA1-4 : bond 0.00540 / 0.28 ( 1) link_ALPHA1-4 : angle 1.80124 / 0.99 ( 3) link_BETA1-4 : bond 0.00951 / 0.50 ( 6) link_BETA1-4 : angle 2.45233 / 1.84 ( 18) link_NAG-ASN : bond 0.00475 / 0.27 ( 8) link_NAG-ASN : angle 3.31403 / 1.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9563 (mtm) cc_final: 0.9236 (mtm) REVERT: A 983 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8680 (mmm) REVERT: A 1096 MET cc_start: 0.6964 (ttt) cc_final: 0.6759 (ttt) REVERT: A 1161 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7562 (p-80) REVERT: A 1228 THR cc_start: 0.3534 (OUTLIER) cc_final: 0.3169 (p) REVERT: A 1315 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8850 (p) REVERT: A 1394 CYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6642 (t) REVERT: A 1554 MET cc_start: 0.9108 (mpp) cc_final: 0.8762 (mpt) REVERT: A 1994 ASP cc_start: 0.8931 (t0) cc_final: 0.8605 (t70) REVERT: A 2056 MET cc_start: 0.8924 (mmm) cc_final: 0.8677 (mmm) REVERT: A 2411 PHE cc_start: 0.9088 (t80) cc_final: 0.8810 (t80) REVERT: A 2415 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: A 2447 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8511 (tmm) REVERT: A 2472 SER cc_start: 0.9443 (t) cc_final: 0.9158 (p) REVERT: A 2546 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 2620 TYR cc_start: 0.8657 (m-80) cc_final: 0.8063 (m-80) REVERT: B 52 MET cc_start: 0.8813 (ppp) cc_final: 0.8569 (ppp) REVERT: B 79 TYR cc_start: 0.7569 (m-80) cc_final: 0.7108 (m-80) REVERT: B 115 LYS cc_start: 0.6566 (ptmm) cc_final: 0.6123 (ttpp) REVERT: B 120 GLN cc_start: 0.6416 (tt0) cc_final: 0.5838 (tm-30) outliers start: 40 outliers final: 11 residues processed: 149 average time/residue: 0.5056 time to fit residues: 84.6863 Evaluate side-chains 134 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1373 ASN Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2415 GLU Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 66 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1373 ASN A1646 ASN A1667 HIS A1820 GLN A2084 GLN ** A2194 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 = 0.3916 r_free = 0.3916 target = 0.111447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077159 restraints weight = 34806.850| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.78 r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14545 Z= 0.170 Angle : 0.644 10.382 19803 Z= 0.319 Chirality : 0.047 0.330 2272 Planarity : 0.003 0.037 2520 Dihedral : 4.699 46.472 2023 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.44 % Allowed : 17.32 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1813 helix: 1.13 (0.52), residues: 117 sheet: 0.08 (0.20), residues: 652 loop : -0.81 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2406 TYR 0.033 0.001 TYR B 121 PHE 0.010 0.001 PHE A1662 TRP 0.010 0.001 TRP A1572 HIS 0.003 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14522) covalent geometry : angle 0.63016 / 0.32 (19742) SS BOND : bond 0.00172 / 0.13 ( 8) SS BOND : angle 1.03026 / 0.63 ( 16) hydrogen bonds : bond 0.03179 / 2.12 ( 486) hydrogen bonds : angle 4.94404 / 3.33 ( 1686) link_ALPHA1-4 : bond 0.00443 / 0.23 ( 1) link_ALPHA1-4 : angle 1.76016 / 0.96 ( 3) link_BETA1-4 : bond 0.00974 / 0.52 ( 6) link_BETA1-4 : angle 2.39973 / 1.80 ( 18) link_NAG-ASN : bond 0.00464 / 0.25 ( 8) link_NAG-ASN : angle 3.17878 / 1.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9556 (mtm) cc_final: 0.9238 (mtm) REVERT: A 983 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8725 (mmm) REVERT: A 1096 MET cc_start: 0.6926 (ttt) cc_final: 0.6701 (ttt) REVERT: A 1161 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7574 (p-80) REVERT: A 1228 THR cc_start: 0.4210 (OUTLIER) cc_final: 0.3876 (p) REVERT: A 1394 CYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6656 (t) REVERT: A 1554 MET cc_start: 0.9095 (mpp) cc_final: 0.8751 (mpt) REVERT: A 1994 ASP cc_start: 0.8966 (t0) cc_final: 0.8661 (t70) REVERT: A 2056 MET cc_start: 0.9002 (mmm) cc_final: 0.8757 (mmm) REVERT: A 2411 PHE cc_start: 0.9044 (t80) cc_final: 0.8755 (t80) REVERT: A 2415 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: A 2447 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8480 (tmm) REVERT: A 2472 SER cc_start: 0.9450 (t) cc_final: 0.9163 (p) REVERT: A 2546 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 2620 TYR cc_start: 0.8678 (m-80) cc_final: 0.8134 (m-80) REVERT: B 52 MET cc_start: 0.8759 (ppp) cc_final: 0.8523 (ppp) REVERT: B 79 TYR cc_start: 0.7644 (m-80) cc_final: 0.7155 (m-80) REVERT: B 115 LYS cc_start: 0.6506 (ptmm) cc_final: 0.6230 (ttpp) outliers start: 36 outliers final: 16 residues processed: 145 average time/residue: 0.4805 time to fit residues: 78.7576 Evaluate side-chains 137 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 2018 THR Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2415 GLU Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2622 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1373 ASN A1646 ASN A1820 GLN ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078408 restraints weight = 34631.914| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.79 r_work: 0.3096 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14545 Z= 0.123 Angle : 0.634 9.682 19803 Z= 0.314 Chirality : 0.047 0.328 2272 Planarity : 0.003 0.037 2520 Dihedral : 4.594 46.677 2023 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.30 % Allowed : 17.39 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1813 helix: 1.31 (0.53), residues: 117 sheet: 0.23 (0.21), residues: 621 loop : -0.80 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2406 TYR 0.023 0.001 TYR B 121 PHE 0.009 0.001 PHE A1245 TRP 0.011 0.001 TRP A1572 HIS 0.002 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14522) covalent geometry : angle 0.62133 / 0.31 (19742) SS BOND : bond 0.00126 / 0.08 ( 8) SS BOND : angle 0.91679 / 0.56 ( 16) hydrogen bonds : bond 0.03016 / 2.01 ( 486) hydrogen bonds : angle 4.82414 / 3.26 ( 1686) link_ALPHA1-4 : bond 0.00487 / 0.26 ( 1) link_ALPHA1-4 : angle 1.71453 / 0.93 ( 3) link_BETA1-4 : bond 0.00931 / 0.49 ( 6) link_BETA1-4 : angle 2.33538 / 1.75 ( 18) link_NAG-ASN : bond 0.00559 / 0.30 ( 8) link_NAG-ASN : angle 3.05966 / 1.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9557 (mtm) cc_final: 0.9261 (mtm) REVERT: A 983 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8989 (tpp) REVERT: A 1096 MET cc_start: 0.6894 (ttt) cc_final: 0.6675 (ttt) REVERT: A 1161 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7578 (p-80) REVERT: A 1228 THR cc_start: 0.4332 (OUTLIER) cc_final: 0.4124 (p) REVERT: A 1394 CYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6623 (t) REVERT: A 1554 MET cc_start: 0.9084 (mpp) cc_final: 0.8738 (mpt) REVERT: A 1918 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: A 1994 ASP cc_start: 0.8970 (t0) cc_final: 0.8635 (t70) REVERT: A 2056 MET cc_start: 0.9002 (mmm) cc_final: 0.8769 (mmm) REVERT: A 2333 MET cc_start: 0.9565 (ttm) cc_final: 0.9278 (ptm) REVERT: A 2411 PHE cc_start: 0.8989 (t80) cc_final: 0.8688 (t80) REVERT: A 2447 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: A 2472 SER cc_start: 0.9445 (t) cc_final: 0.9155 (p) REVERT: A 2546 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7766 (t80) REVERT: A 2620 TYR cc_start: 0.8661 (m-80) cc_final: 0.8130 (m-80) REVERT: B 52 MET cc_start: 0.8864 (ppp) cc_final: 0.8601 (ppp) REVERT: B 79 TYR cc_start: 0.7699 (m-80) cc_final: 0.7201 (m-80) REVERT: B 115 LYS cc_start: 0.6495 (ptmm) cc_final: 0.6023 (ttpp) outliers start: 34 outliers final: 16 residues processed: 147 average time/residue: 0.4974 time to fit residues: 82.2029 Evaluate side-chains 136 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1857 ILE Chi-restraints excluded: chain A residue 1918 GLU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2546 TYR Chi-restraints excluded: chain A residue 2553 ILE Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1373 ASN A1646 ASN A1667 HIS A1820 GLN ** A2194 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 = 0.3920 r_free = 0.3920 target = 0.111471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077010 restraints weight = 35032.464| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.87 r_work: 0.3063 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14545 Z= 0.183 Angle : 0.654 9.752 19803 Z= 0.325 Chirality : 0.047 0.324 2272 Planarity : 0.004 0.037 2520 Dihedral : 4.619 45.835 2023 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.96 % Allowed : 18.00 % Favored : 80.04 % 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: -0.45 (0.20), residues: 1813 helix: 1.36 (0.53), residues: 117 sheet: 0.24 (0.21), residues: 610 loop : -0.80 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2406 TYR 0.017 0.001 TYR B 121 PHE 0.011 0.001 PHE A1470 TRP 0.011 0.001 TRP A1572 HIS 0.003 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (14522) covalent geometry : angle 0.64155 / 0.32 (19742) SS BOND : bond 0.00176 / 0.13 ( 8) SS BOND : angle 0.97176 / 0.59 ( 16) hydrogen bonds : bond 0.03128 / 2.09 ( 486) hydrogen bonds : angle 4.85325 / 3.28 ( 1686) link_ALPHA1-4 : bond 0.00404 / 0.21 ( 1) link_ALPHA1-4 : angle 1.73183 / 0.94 ( 3) link_BETA1-4 : bond 0.00945 / 0.49 ( 6) link_BETA1-4 : angle 2.39631 / 1.81 ( 18) link_NAG-ASN : bond 0.00476 / 0.26 ( 8) link_NAG-ASN : angle 3.06557 / 1.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9550 (mtm) cc_final: 0.9258 (mtm) REVERT: A 983 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8732 (mmm) REVERT: A 1096 MET cc_start: 0.6887 (ttt) cc_final: 0.6661 (ttt) REVERT: A 1161 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7582 (p-80) REVERT: A 1186 ARG cc_start: 0.6672 (tmm-80) cc_final: 0.6405 (tmm-80) REVERT: A 1228 THR cc_start: 0.4872 (OUTLIER) cc_final: 0.4585 (p) REVERT: A 1394 CYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6634 (t) REVERT: A 1554 MET cc_start: 0.9130 (mpp) cc_final: 0.8793 (mpt) REVERT: A 1994 ASP cc_start: 0.8963 (t0) cc_final: 0.8660 (t70) REVERT: A 2056 MET cc_start: 0.9022 (mmm) cc_final: 0.8754 (mmm) REVERT: A 2411 PHE cc_start: 0.9029 (t80) cc_final: 0.8725 (t80) REVERT: A 2429 GLU cc_start: 0.8626 (pm20) cc_final: 0.8416 (mp0) REVERT: A 2447 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8555 (tmm) REVERT: A 2472 SER cc_start: 0.9458 (t) cc_final: 0.9171 (p) REVERT: A 2620 TYR cc_start: 0.8699 (m-80) cc_final: 0.8219 (m-80) REVERT: B 52 MET cc_start: 0.8894 (ppp) cc_final: 0.8641 (ppp) REVERT: B 79 TYR cc_start: 0.7786 (m-80) cc_final: 0.7251 (m-80) REVERT: B 87 MET cc_start: 0.8477 (pp-130) cc_final: 0.8217 (ppp) REVERT: B 115 LYS cc_start: 0.6447 (ptmm) cc_final: 0.6040 (ttpp) REVERT: B 120 GLN cc_start: 0.6401 (tt0) cc_final: 0.5801 (tm-30) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.5141 time to fit residues: 78.7108 Evaluate side-chains 139 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1857 ILE Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2553 ILE Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2622 LEU Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 2.9990 chunk 167 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 144 optimal weight: 0.0470 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1646 ASN A1820 GLN ** A2194 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 = 0.3950 r_free = 0.3950 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078659 restraints weight = 34505.616| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.88 r_work: 0.3104 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14545 Z= 0.111 Angle : 0.644 10.285 19803 Z= 0.318 Chirality : 0.047 0.326 2272 Planarity : 0.003 0.036 2520 Dihedral : 4.502 46.088 2023 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.42 % Allowed : 18.61 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1813 helix: 1.22 (0.52), residues: 117 sheet: 0.29 (0.21), residues: 618 loop : -0.73 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2406 TYR 0.018 0.001 TYR B 121 PHE 0.009 0.001 PHE A1245 TRP 0.013 0.001 TRP A1572 HIS 0.002 0.000 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14522) covalent geometry : angle 0.63235 / 0.31 (19742) SS BOND : bond 0.00155 / 0.12 ( 8) SS BOND : angle 0.92399 / 0.60 ( 16) hydrogen bonds : bond 0.02919 / 1.95 ( 486) hydrogen bonds : angle 4.69851 / 3.19 ( 1686) link_ALPHA1-4 : bond 0.00555 / 0.29 ( 1) link_ALPHA1-4 : angle 1.67671 / 0.90 ( 3) link_BETA1-4 : bond 0.00895 / 0.47 ( 6) link_BETA1-4 : angle 2.29204 / 1.72 ( 18) link_NAG-ASN : bond 0.00531 / 0.29 ( 8) link_NAG-ASN : angle 2.93884 / 1.65 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9552 (mtm) cc_final: 0.9307 (mtm) REVERT: A 983 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8987 (tpp) REVERT: A 1161 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7513 (p-80) REVERT: A 1186 ARG cc_start: 0.6623 (tmm-80) cc_final: 0.6374 (tmm-80) REVERT: A 1228 THR cc_start: 0.4819 (OUTLIER) cc_final: 0.4560 (p) REVERT: A 1394 CYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6597 (t) REVERT: A 1554 MET cc_start: 0.9059 (mpp) cc_final: 0.8701 (mpt) REVERT: A 1732 GLU cc_start: 0.8990 (tt0) cc_final: 0.8776 (tp30) REVERT: A 1918 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: A 1994 ASP cc_start: 0.8901 (t0) cc_final: 0.8625 (t70) REVERT: A 2056 MET cc_start: 0.9011 (mmm) cc_final: 0.8743 (mmm) REVERT: A 2333 MET cc_start: 0.9562 (ttm) cc_final: 0.9325 (ptm) REVERT: A 2411 PHE cc_start: 0.9009 (t80) cc_final: 0.8665 (t80) REVERT: A 2429 GLU cc_start: 0.8698 (pm20) cc_final: 0.8472 (mp0) REVERT: A 2447 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8538 (tmm) REVERT: A 2472 SER cc_start: 0.9461 (t) cc_final: 0.9170 (p) REVERT: A 2620 TYR cc_start: 0.8653 (m-80) cc_final: 0.8178 (m-80) REVERT: B 31 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7467 (mtm-85) REVERT: B 52 MET cc_start: 0.8910 (ppp) cc_final: 0.8637 (ppp) REVERT: B 79 TYR cc_start: 0.7792 (m-80) cc_final: 0.7210 (m-80) REVERT: B 115 LYS cc_start: 0.6447 (ptmm) cc_final: 0.6076 (ttpp) REVERT: B 120 GLN cc_start: 0.6437 (tt0) cc_final: 0.5798 (tm-30) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.5066 time to fit residues: 80.5033 Evaluate side-chains 141 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1161 HIS Chi-restraints excluded: chain A residue 1228 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1356 ILE Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1918 GLU Chi-restraints excluded: chain A residue 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL Chi-restraints excluded: chain A residue 2359 MET Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2553 ILE Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2630 LEU Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 176 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1319 GLN A1820 GLN ** A2194 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 = 0.3935 r_free = 0.3935 target = 0.112212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078029 restraints weight = 34628.385| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.84 r_work: 0.3094 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14545 Z= 0.148 Angle : 0.650 11.078 19803 Z= 0.322 Chirality : 0.047 0.322 2272 Planarity : 0.004 0.037 2520 Dihedral : 4.494 45.711 2023 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.62 % Allowed : 18.88 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1813 helix: 1.28 (0.53), residues: 117 sheet: 0.23 (0.21), residues: 632 loop : -0.69 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2406 TYR 0.018 0.001 TYR B 121 PHE 0.010 0.001 PHE A1470 TRP 0.014 0.001 TRP A1572 HIS 0.003 0.001 HIS A2227 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14522) covalent geometry : angle 0.63827 / 0.32 (19742) SS BOND : bond 0.00153 / 0.12 ( 8) SS BOND : angle 1.06453 / 0.73 ( 16) hydrogen bonds : bond 0.03021 / 2.02 ( 486) hydrogen bonds : angle 4.71094 / 3.19 ( 1686) link_ALPHA1-4 : bond 0.00395 / 0.21 ( 1) link_ALPHA1-4 : angle 1.70800 / 0.92 ( 3) link_BETA1-4 : bond 0.00923 / 0.49 ( 6) link_BETA1-4 : angle 2.36471 / 1.77 ( 18) link_NAG-ASN : bond 0.00474 / 0.25 ( 8) link_NAG-ASN : angle 2.92038 / 1.64 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.86 seconds wall clock time: 78 minutes 25.74 seconds (4705.74 seconds total)