Starting phenix.real_space_refine on Wed Mar 4 15:47:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vhh_21205/03_2026/6vhh_21205.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vhh_21205/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vhh_21205/03_2026/6vhh_21205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vhh_21205/03_2026/6vhh_21205.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vhh_21205/03_2026/6vhh_21205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vhh_21205/03_2026/6vhh_21205.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.10, per 1000 atoms: 0.22 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: 1.58 Conformation dependent library (CDL) restraints added in 644.3 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: 1.33 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: 6.33 Time building geometry restraints manager: 2.06 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 - 23.76: 8337 23.76 - 47.51: 432 47.51 - 71.27: 35 71.27 - 95.02: 18 95.02 - 118.78: 18 Dihedral angle restraints: 8840 sinusoidal: 3551 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 8837 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: 1.010 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.930 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 15.414 118.776 5450 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 covalent geometry : bond 0.01508 (14522) covalent geometry : angle 1.06803 (19742) SS BOND : bond 0.00751 ( 8) SS BOND : angle 1.30571 ( 16) hydrogen bonds : bond 0.17114 ( 486) hydrogen bonds : angle 8.45011 ( 1686) link_ALPHA1-4 : bond 0.00381 ( 1) link_ALPHA1-4 : angle 1.10802 ( 3) link_BETA1-4 : bond 0.00208 ( 6) link_BETA1-4 : angle 1.17095 ( 18) link_NAG-ASN : bond 0.02617 ( 8) link_NAG-ASN : angle 7.91425 ( 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 : 0.531 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: 0.5359 time to fit residues: 112.0207 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 : 0.554 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 A2407 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.115009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080045 restraints weight = 34271.868| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.91 r_work: 0.3094 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14545 Z= 0.159 Angle : 0.783 12.814 19803 Z= 0.383 Chirality : 0.051 0.538 2272 Planarity : 0.005 0.038 2520 Dihedral : 10.572 96.920 2346 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.03 % Allowed : 12.58 % 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: -1.76 (0.18), residues: 1813 helix: -1.00 (0.48), residues: 111 sheet: -0.27 (0.21), residues: 584 loop : -1.77 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.007 0.001 HIS A2027 Details of bonding type rmsd covalent geometry : bond 0.00348 (14522) covalent geometry : angle 0.74834 (19742) SS BOND : bond 0.00815 ( 8) SS BOND : angle 1.77497 ( 16) hydrogen bonds : bond 0.04058 ( 486) hydrogen bonds : angle 6.07624 ( 1686) link_ALPHA1-4 : bond 0.01086 ( 1) link_ALPHA1-4 : angle 1.76938 ( 3) link_BETA1-4 : bond 0.01350 ( 6) link_BETA1-4 : angle 4.09435 ( 18) link_NAG-ASN : bond 0.00982 ( 8) link_NAG-ASN : angle 5.48576 ( 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 164 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9499 (mtm) cc_final: 0.9081 (mtm) REVERT: A 983 MET cc_start: 0.9233 (mmm) cc_final: 0.8739 (mmm) REVERT: A 1096 MET cc_start: 0.6882 (ttt) cc_final: 0.6651 (ttt) REVERT: A 1161 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7753 (p-80) REVERT: A 1186 ARG cc_start: 0.6058 (tmm-80) cc_final: 0.5690 (tmm-80) REVERT: A 1554 MET cc_start: 0.9184 (mpp) cc_final: 0.8815 (mpt) REVERT: A 1615 ASP cc_start: 0.9431 (t0) cc_final: 0.9142 (t0) REVERT: A 1732 GLU cc_start: 0.9060 (tt0) cc_final: 0.8842 (tp30) REVERT: A 2415 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8641 (mp0) REVERT: A 2472 SER cc_start: 0.9413 (t) cc_final: 0.9112 (p) REVERT: A 2546 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7731 (t80) outliers start: 30 outliers final: 7 residues processed: 154 average time/residue: 0.4986 time to fit residues: 85.9165 Evaluate side-chains 127 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1719 ASN A1820 GLN A2084 GLN A2363 GLN A2407 HIS A2433 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.111376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077217 restraints weight = 34860.646| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.80 r_work: 0.3047 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14545 Z= 0.223 Angle : 0.711 11.174 19803 Z= 0.353 Chirality : 0.049 0.375 2272 Planarity : 0.004 0.038 2520 Dihedral : 9.073 79.981 2336 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.11 % Allowed : 13.80 % Favored : 83.09 % 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: -1.22 (0.19), residues: 1813 helix: 0.00 (0.49), residues: 119 sheet: -0.12 (0.21), residues: 602 loop : -1.34 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2147 TYR 0.032 0.002 TYR A2011 PHE 0.017 0.001 PHE B 106 TRP 0.010 0.001 TRP A2311 HIS 0.006 0.001 HIS A2031 Details of bonding type rmsd covalent geometry : bond 0.00493 (14522) covalent geometry : angle 0.68604 (19742) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.62279 ( 16) hydrogen bonds : bond 0.03739 ( 486) hydrogen bonds : angle 5.49758 ( 1686) link_ALPHA1-4 : bond 0.00543 ( 1) link_ALPHA1-4 : angle 1.74690 ( 3) link_BETA1-4 : bond 0.01394 ( 6) link_BETA1-4 : angle 3.41690 ( 18) link_NAG-ASN : bond 0.00589 ( 8) link_NAG-ASN : angle 4.31043 ( 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 172 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9530 (mtm) cc_final: 0.9063 (mtm) REVERT: A 983 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8830 (tpp) REVERT: A 1096 MET cc_start: 0.7098 (ttt) cc_final: 0.6852 (ttt) REVERT: A 1161 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7766 (p-80) REVERT: A 1186 ARG cc_start: 0.6224 (tmm-80) cc_final: 0.5856 (tmm-80) REVERT: A 1394 CYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6466 (t) REVERT: A 1554 MET cc_start: 0.9179 (mpp) cc_final: 0.8851 (mpt) REVERT: A 1615 ASP cc_start: 0.9466 (t0) cc_final: 0.9083 (t0) REVERT: A 1718 ARG cc_start: 0.9270 (mtt-85) cc_final: 0.9067 (mmt-90) REVERT: A 1783 MET cc_start: 0.8689 (ptt) cc_final: 0.8359 (ptp) REVERT: A 2046 MET cc_start: 0.9090 (mmt) cc_final: 0.8747 (mmp) REVERT: A 2056 MET cc_start: 0.8875 (mmm) cc_final: 0.8557 (mmt) REVERT: A 2447 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8503 (tmm) REVERT: A 2472 SER cc_start: 0.9431 (t) cc_final: 0.9130 (p) REVERT: A 2546 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7717 (t80) REVERT: B 30 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 52 MET cc_start: 0.8236 (ppp) cc_final: 0.7962 (ppp) REVERT: B 69 ASP cc_start: 0.7860 (m-30) cc_final: 0.7644 (m-30) REVERT: B 79 TYR cc_start: 0.7304 (m-80) cc_final: 0.6883 (m-80) REVERT: B 92 ASN cc_start: 0.8481 (m110) cc_final: 0.8120 (m110) REVERT: B 115 LYS cc_start: 0.6309 (ptmm) cc_final: 0.6058 (ptmm) outliers start: 46 outliers final: 20 residues processed: 156 average time/residue: 0.4651 time to fit residues: 81.5540 Evaluate side-chains 142 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 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 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 1565 THR 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 2486 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 43 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 54 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 127 optimal weight: 0.0020 chunk 152 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1199 ASN ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1820 GLN A2084 GLN ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2407 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.112682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078348 restraints weight = 34589.862| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.83 r_work: 0.3080 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14545 Z= 0.130 Angle : 0.664 10.393 19803 Z= 0.327 Chirality : 0.048 0.354 2272 Planarity : 0.004 0.049 2520 Dihedral : 8.408 75.045 2336 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.84 % Allowed : 15.02 % Favored : 82.14 % 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: -0.94 (0.19), residues: 1813 helix: 0.60 (0.51), residues: 118 sheet: -0.02 (0.20), residues: 630 loop : -1.17 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 90 TYR 0.013 0.001 TYR B 121 PHE 0.010 0.001 PHE B 106 TRP 0.009 0.001 TRP A1756 HIS 0.004 0.001 HIS A2027 Details of bonding type rmsd covalent geometry : bond 0.00286 (14522) covalent geometry : angle 0.64196 (19742) SS BOND : bond 0.00145 ( 8) SS BOND : angle 1.17236 ( 16) hydrogen bonds : bond 0.03294 ( 486) hydrogen bonds : angle 5.19969 ( 1686) link_ALPHA1-4 : bond 0.00434 ( 1) link_ALPHA1-4 : angle 2.19841 ( 3) link_BETA1-4 : bond 0.01237 ( 6) link_BETA1-4 : angle 3.31203 ( 18) link_NAG-ASN : bond 0.00596 ( 8) link_NAG-ASN : angle 3.92109 ( 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 167 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9560 (mtm) cc_final: 0.9206 (mtm) REVERT: A 983 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8893 (tpp) REVERT: A 1096 MET cc_start: 0.7151 (ttt) cc_final: 0.6874 (ttt) REVERT: A 1144 PHE cc_start: 0.9371 (m-80) cc_final: 0.8896 (m-80) REVERT: A 1161 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7592 (p-80) REVERT: A 1186 ARG cc_start: 0.6467 (tmm-80) cc_final: 0.6014 (tmm-80) REVERT: A 1228 THR cc_start: 0.3411 (OUTLIER) cc_final: 0.3036 (p) REVERT: A 1250 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5397 (mmm) REVERT: A 1394 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6439 (t) REVERT: A 1554 MET cc_start: 0.9125 (mpp) cc_final: 0.8791 (mpt) REVERT: A 1615 ASP cc_start: 0.9407 (t0) cc_final: 0.9026 (t0) REVERT: A 1783 MET cc_start: 0.8695 (ptt) cc_final: 0.8417 (ptp) REVERT: A 2056 MET cc_start: 0.8928 (mmm) cc_final: 0.8677 (mmt) REVERT: A 2415 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8590 (mp0) REVERT: A 2447 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8557 (tmm) REVERT: A 2472 SER cc_start: 0.9461 (t) cc_final: 0.9166 (p) REVERT: A 2546 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7730 (t80) REVERT: A 2620 TYR cc_start: 0.8560 (m-80) cc_final: 0.8015 (m-80) REVERT: B 52 MET cc_start: 0.8454 (ppp) cc_final: 0.8229 (ppp) REVERT: B 79 TYR cc_start: 0.7369 (m-80) cc_final: 0.6902 (m-80) REVERT: B 84 TYR cc_start: 0.8476 (t80) cc_final: 0.8149 (t80) REVERT: B 92 ASN cc_start: 0.8410 (m110) cc_final: 0.8137 (m110) REVERT: B 115 LYS cc_start: 0.6409 (ptmm) cc_final: 0.6049 (ptmm) outliers start: 42 outliers final: 11 residues processed: 154 average time/residue: 0.4985 time to fit residues: 86.0632 Evaluate side-chains 134 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 1250 MET 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 2286 HIS Chi-restraints excluded: chain A residue 2306 VAL 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 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: 9.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1301 ASN ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 ASN ** A1691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1820 GLN A2084 GLN ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2407 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.109673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074954 restraints weight = 35278.800| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.81 r_work: 0.3003 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 14545 Z= 0.336 Angle : 0.755 10.925 19803 Z= 0.374 Chirality : 0.050 0.346 2272 Planarity : 0.004 0.051 2520 Dihedral : 8.173 72.347 2336 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.04 % Allowed : 16.10 % Favored : 80.85 % 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: -1.00 (0.19), residues: 1813 helix: 0.51 (0.50), residues: 118 sheet: -0.17 (0.20), residues: 626 loop : -1.11 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2406 TYR 0.034 0.002 TYR B 121 PHE 0.018 0.002 PHE A1662 TRP 0.013 0.002 TRP A2311 HIS 0.006 0.001 HIS A1476 Details of bonding type rmsd covalent geometry : bond 0.00755 (14522) covalent geometry : angle 0.73450 (19742) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.53352 ( 16) hydrogen bonds : bond 0.03855 ( 486) hydrogen bonds : angle 5.37055 ( 1686) link_ALPHA1-4 : bond 0.00240 ( 1) link_ALPHA1-4 : angle 2.28203 ( 3) link_BETA1-4 : bond 0.01301 ( 6) link_BETA1-4 : angle 3.48233 ( 18) link_NAG-ASN : bond 0.00617 ( 8) link_NAG-ASN : angle 3.96471 ( 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 162 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 968 MET cc_start: 0.9550 (mtm) cc_final: 0.9080 (mtm) REVERT: A 983 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8769 (tpp) REVERT: A 1161 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7574 (p-80) REVERT: A 1186 ARG cc_start: 0.6411 (tmm-80) cc_final: 0.5973 (tmm-80) REVERT: A 1315 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 1394 CYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6549 (t) REVERT: A 1554 MET cc_start: 0.9239 (mpp) cc_final: 0.8883 (mpt) REVERT: A 1995 GLU cc_start: 0.9312 (mp0) cc_final: 0.8901 (pm20) REVERT: A 2011 TYR cc_start: 0.8859 (p90) cc_final: 0.8362 (p90) REVERT: A 2056 MET cc_start: 0.8959 (mmm) cc_final: 0.8637 (mmm) REVERT: A 2447 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8504 (tmm) REVERT: A 2546 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 2620 TYR cc_start: 0.8710 (m-80) cc_final: 0.8506 (m-80) REVERT: B 52 MET cc_start: 0.8700 (ppp) cc_final: 0.8437 (ppp) REVERT: B 79 TYR cc_start: 0.7536 (m-80) cc_final: 0.7061 (m-80) REVERT: B 92 ASN cc_start: 0.8059 (m110) cc_final: 0.7630 (m110) REVERT: B 115 LYS cc_start: 0.6894 (ptmm) cc_final: 0.6492 (ptmm) REVERT: B 120 GLN cc_start: 0.6204 (tt0) cc_final: 0.5640 (tm-30) outliers start: 45 outliers final: 19 residues processed: 148 average time/residue: 0.4971 time to fit residues: 82.4232 Evaluate side-chains 135 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 1315 THR Chi-restraints excluded: chain A residue 1373 ASN Chi-restraints excluded: chain A residue 1394 CYS Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1446 LYS Chi-restraints excluded: chain A residue 1478 TYR Chi-restraints excluded: chain A residue 1620 VAL 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 2333 MET Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2486 SER 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 43 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 179 optimal weight: 0.0010 chunk 49 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1199 ASN A1373 ASN A1646 ASN A1820 GLN A2027 HIS ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2407 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.113187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078701 restraints weight = 34647.156| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.82 r_work: 0.3060 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14545 Z= 0.154 Angle : 0.659 10.295 19803 Z= 0.326 Chirality : 0.047 0.346 2272 Planarity : 0.004 0.053 2520 Dihedral : 7.796 68.264 2334 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.64 % Allowed : 16.98 % Favored : 80.38 % 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: -0.82 (0.19), residues: 1813 helix: 0.82 (0.51), residues: 118 sheet: -0.09 (0.20), residues: 639 loop : -0.99 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.030 0.001 TYR A2011 PHE 0.011 0.001 PHE A1662 TRP 0.012 0.001 TRP A1572 HIS 0.004 0.001 HIS A2027 Details of bonding type rmsd covalent geometry : bond 0.00342 (14522) covalent geometry : angle 0.63910 (19742) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.99643 ( 16) hydrogen bonds : bond 0.03272 ( 486) hydrogen bonds : angle 5.09838 ( 1686) link_ALPHA1-4 : bond 0.00418 ( 1) link_ALPHA1-4 : angle 2.28273 ( 3) link_BETA1-4 : bond 0.01263 ( 6) link_BETA1-4 : angle 3.31641 ( 18) link_NAG-ASN : bond 0.00537 ( 8) link_NAG-ASN : angle 3.55896 ( 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 167 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.593 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: 0.9154 (mtm) REVERT: A 983 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8779 (tpp) REVERT: A 1096 MET cc_start: 0.6892 (ttt) cc_final: 0.6648 (ttt) REVERT: A 1161 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7568 (p-80) REVERT: A 1228 THR cc_start: 0.4744 (OUTLIER) cc_final: 0.4289 (t) REVERT: A 1255 ASP cc_start: 0.9134 (t0) cc_final: 0.8929 (t70) REVERT: A 1315 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 1373 ASN cc_start: 0.6280 (OUTLIER) cc_final: 0.6070 (m110) REVERT: A 1394 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6625 (t) REVERT: A 1554 MET cc_start: 0.9185 (mpp) cc_final: 0.8845 (mpt) REVERT: A 2056 MET cc_start: 0.9010 (mmm) cc_final: 0.8725 (mmt) REVERT: A 2411 PHE cc_start: 0.9098 (t80) cc_final: 0.8853 (t80) REVERT: A 2415 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8585 (mp0) REVERT: A 2447 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8496 (tmm) REVERT: A 2472 SER cc_start: 0.9422 (t) cc_final: 0.9132 (p) REVERT: A 2546 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7797 (t80) REVERT: A 2620 TYR cc_start: 0.8713 (m-80) cc_final: 0.8185 (m-80) REVERT: B 52 MET cc_start: 0.8730 (ppp) cc_final: 0.8459 (ppp) REVERT: B 79 TYR cc_start: 0.7649 (m-80) cc_final: 0.7158 (m-80) REVERT: B 92 ASN cc_start: 0.7876 (m110) cc_final: 0.7456 (m110) REVERT: B 115 LYS cc_start: 0.6877 (ptmm) cc_final: 0.6438 (ptmm) outliers start: 39 outliers final: 11 residues processed: 156 average time/residue: 0.4974 time to fit residues: 87.1954 Evaluate side-chains 138 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 2018 THR 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 2557 LEU Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain B residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1373 ASN A1646 ASN A1820 GLN ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2407 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.109344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075026 restraints weight = 35124.198| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.78 r_work: 0.3021 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14545 Z= 0.271 Angle : 0.711 10.547 19803 Z= 0.352 Chirality : 0.048 0.337 2272 Planarity : 0.004 0.053 2520 Dihedral : 7.671 66.137 2334 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.91 % Allowed : 17.66 % Favored : 79.43 % 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: -0.81 (0.20), residues: 1813 helix: 0.83 (0.52), residues: 118 sheet: -0.04 (0.21), residues: 618 loop : -1.00 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2406 TYR 0.017 0.001 TYR B 121 PHE 0.014 0.001 PHE A1662 TRP 0.012 0.001 TRP A1572 HIS 0.004 0.001 HIS A2227 Details of bonding type rmsd covalent geometry : bond 0.00608 (14522) covalent geometry : angle 0.69203 (19742) SS BOND : bond 0.00265 ( 8) SS BOND : angle 1.24386 ( 16) hydrogen bonds : bond 0.03530 ( 486) hydrogen bonds : angle 5.16184 ( 1686) link_ALPHA1-4 : bond 0.00322 ( 1) link_ALPHA1-4 : angle 2.31897 ( 3) link_BETA1-4 : bond 0.01277 ( 6) link_BETA1-4 : angle 3.39125 ( 18) link_NAG-ASN : bond 0.00543 ( 8) link_NAG-ASN : angle 3.60003 ( 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 166 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9532 (mtm) cc_final: 0.9085 (mtm) REVERT: A 983 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8806 (tpp) REVERT: A 1096 MET cc_start: 0.6991 (ttt) cc_final: 0.6659 (ttt) REVERT: A 1161 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7625 (p-80) REVERT: A 1315 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (p) REVERT: A 1394 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6778 (t) REVERT: A 1554 MET cc_start: 0.9208 (mpp) cc_final: 0.8844 (mpt) REVERT: A 2056 MET cc_start: 0.9013 (mmm) cc_final: 0.8733 (mmm) REVERT: A 2411 PHE cc_start: 0.9114 (t80) cc_final: 0.8835 (t80) REVERT: A 2472 SER cc_start: 0.9426 (t) cc_final: 0.9128 (p) REVERT: A 2620 TYR cc_start: 0.8763 (m-80) cc_final: 0.8520 (m-80) REVERT: B 52 MET cc_start: 0.8750 (ppp) cc_final: 0.8475 (ppp) REVERT: B 79 TYR cc_start: 0.7645 (m-80) cc_final: 0.7134 (m-80) REVERT: B 92 ASN cc_start: 0.8150 (m110) cc_final: 0.7703 (m110) REVERT: B 115 LYS cc_start: 0.6885 (ptmm) cc_final: 0.6446 (ptmm) outliers start: 43 outliers final: 22 residues processed: 150 average time/residue: 0.5019 time to fit residues: 84.1663 Evaluate side-chains 142 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 1315 THR Chi-restraints excluded: chain A residue 1356 ILE 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 1601 MET 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 1934 SER 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 2398 THR Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2557 LEU 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 45 CYS 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: 0.7980 chunk 4 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 1 optimal weight: 0.0040 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 11 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1345 HIS A1646 ASN A1820 GLN A2107 HIS ** A2194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2407 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078060 restraints weight = 34741.805| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.75 r_work: 0.3092 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14545 Z= 0.109 Angle : 0.662 9.931 19803 Z= 0.325 Chirality : 0.047 0.341 2272 Planarity : 0.004 0.054 2520 Dihedral : 7.394 62.018 2334 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.96 % Allowed : 19.15 % Favored : 78.89 % 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: -0.62 (0.20), residues: 1813 helix: 0.97 (0.53), residues: 117 sheet: 0.07 (0.21), residues: 631 loop : -0.86 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2406 TYR 0.021 0.001 TYR B 121 PHE 0.010 0.001 PHE A1245 TRP 0.012 0.001 TRP A1572 HIS 0.002 0.001 HIS A1846 Details of bonding type rmsd covalent geometry : bond 0.00240 (14522) covalent geometry : angle 0.64375 (19742) SS BOND : bond 0.00168 ( 8) SS BOND : angle 0.91423 ( 16) hydrogen bonds : bond 0.03060 ( 486) hydrogen bonds : angle 4.93857 ( 1686) link_ALPHA1-4 : bond 0.00407 ( 1) link_ALPHA1-4 : angle 2.29369 ( 3) link_BETA1-4 : bond 0.01193 ( 6) link_BETA1-4 : angle 3.31049 ( 18) link_NAG-ASN : bond 0.00586 ( 8) link_NAG-ASN : angle 3.28721 ( 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: 29 poor density : 128 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8821 (tpp) REVERT: A 1096 MET cc_start: 0.6912 (ttt) cc_final: 0.6649 (ttt) REVERT: A 1161 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7561 (p-80) REVERT: A 1186 ARG cc_start: 0.6601 (tmm-80) cc_final: 0.6285 (tmm-80) REVERT: A 1394 CYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6688 (t) REVERT: A 1554 MET cc_start: 0.9117 (mpp) cc_final: 0.8800 (mpt) REVERT: A 1994 ASP cc_start: 0.9094 (t0) cc_final: 0.8747 (t70) REVERT: A 2056 MET cc_start: 0.8994 (mmm) cc_final: 0.8697 (mmt) REVERT: A 2411 PHE cc_start: 0.8976 (t80) cc_final: 0.8702 (t80) REVERT: A 2415 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8544 (mp0) REVERT: A 2472 SER cc_start: 0.9434 (t) cc_final: 0.9141 (p) REVERT: A 2546 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 2620 TYR cc_start: 0.8703 (m-80) cc_final: 0.8208 (m-80) REVERT: B 52 MET cc_start: 0.8683 (ppp) cc_final: 0.8401 (ppp) REVERT: B 79 TYR cc_start: 0.7801 (m-80) cc_final: 0.7234 (m-80) REVERT: B 92 ASN cc_start: 0.8103 (m110) cc_final: 0.7733 (m110) REVERT: B 115 LYS cc_start: 0.6727 (ptmm) cc_final: 0.6357 (ptmm) REVERT: B 120 GLN cc_start: 0.6437 (tt0) cc_final: 0.5781 (tm-30) outliers start: 29 outliers final: 17 residues processed: 148 average time/residue: 0.4796 time to fit residues: 79.6324 Evaluate side-chains 141 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 1242 LEU Chi-restraints excluded: chain A residue 1356 ILE 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 1857 ILE Chi-restraints excluded: chain A residue 2018 THR 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 2368 ILE 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 B residue 73 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** A2527 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.111036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076932 restraints weight = 35015.072| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.78 r_work: 0.3069 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3323 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= 0.169 Angle : 0.676 9.933 19803 Z= 0.332 Chirality : 0.047 0.331 2272 Planarity : 0.004 0.054 2520 Dihedral : 7.278 59.834 2334 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.10 % Allowed : 18.88 % Favored : 79.03 % 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: -0.57 (0.20), residues: 1813 helix: 1.13 (0.53), residues: 117 sheet: 0.12 (0.21), residues: 639 loop : -0.86 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2406 TYR 0.020 0.001 TYR B 121 PHE 0.011 0.001 PHE B 106 TRP 0.014 0.001 TRP A1572 HIS 0.003 0.001 HIS A1738 Details of bonding type rmsd covalent geometry : bond 0.00382 (14522) covalent geometry : angle 0.65838 (19742) SS BOND : bond 0.00177 ( 8) SS BOND : angle 1.00150 ( 16) hydrogen bonds : bond 0.03137 ( 486) hydrogen bonds : angle 4.89832 ( 1686) link_ALPHA1-4 : bond 0.00274 ( 1) link_ALPHA1-4 : angle 2.31894 ( 3) link_BETA1-4 : bond 0.01171 ( 6) link_BETA1-4 : angle 3.30113 ( 18) link_NAG-ASN : bond 0.00529 ( 8) link_NAG-ASN : angle 3.25652 ( 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 149 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8775 (tpp) REVERT: A 1161 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7602 (p-80) REVERT: A 1394 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6709 (t) REVERT: A 1554 MET cc_start: 0.9127 (mpp) cc_final: 0.8807 (mpt) REVERT: A 2056 MET cc_start: 0.9014 (mmm) cc_final: 0.8737 (mmm) REVERT: A 2411 PHE cc_start: 0.9023 (t80) cc_final: 0.8721 (t80) REVERT: A 2429 GLU cc_start: 0.8531 (pm20) cc_final: 0.8222 (mp0) REVERT: A 2447 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8619 (tpp) REVERT: A 2472 SER cc_start: 0.9455 (t) cc_final: 0.9159 (p) REVERT: A 2546 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 2620 TYR cc_start: 0.8765 (m-80) cc_final: 0.8287 (m-80) REVERT: B 31 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7227 (mtm-85) REVERT: B 52 MET cc_start: 0.8742 (ppp) cc_final: 0.8471 (ppp) REVERT: B 79 TYR cc_start: 0.7948 (m-80) cc_final: 0.7337 (m-80) REVERT: B 92 ASN cc_start: 0.8109 (m110) cc_final: 0.7695 (m110) REVERT: B 115 LYS cc_start: 0.7079 (ptmm) cc_final: 0.6738 (ptmm) outliers start: 31 outliers final: 20 residues processed: 137 average time/residue: 0.4883 time to fit residues: 75.1602 Evaluate side-chains 139 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 1242 LEU Chi-restraints excluded: chain A residue 1301 ASN 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 2018 THR 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 2359 MET 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 A residue 2630 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1719 ASN 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077608 restraints weight = 34819.351| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.74 r_work: 0.3081 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14545 Z= 0.142 Angle : 0.677 10.899 19803 Z= 0.332 Chirality : 0.047 0.332 2272 Planarity : 0.004 0.054 2520 Dihedral : 7.186 58.472 2334 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.69 % Allowed : 19.49 % Favored : 78.82 % 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: -0.52 (0.20), residues: 1813 helix: 1.05 (0.52), residues: 117 sheet: 0.16 (0.21), residues: 628 loop : -0.81 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2406 TYR 0.022 0.001 TYR B 121 PHE 0.010 0.001 PHE B 106 TRP 0.014 0.001 TRP A1572 HIS 0.002 0.001 HIS A2227 Details of bonding type rmsd covalent geometry : bond 0.00322 (14522) covalent geometry : angle 0.66000 (19742) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.93352 ( 16) hydrogen bonds : bond 0.03072 ( 486) hydrogen bonds : angle 4.85684 ( 1686) link_ALPHA1-4 : bond 0.00256 ( 1) link_ALPHA1-4 : angle 2.31285 ( 3) link_BETA1-4 : bond 0.01190 ( 6) link_BETA1-4 : angle 3.29360 ( 18) link_NAG-ASN : bond 0.00525 ( 8) link_NAG-ASN : angle 3.17935 ( 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 150 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 MET cc_start: 0.9545 (mtm) cc_final: 0.9217 (mtm) REVERT: A 983 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8789 (tpp) REVERT: A 1096 MET cc_start: 0.6801 (ttt) cc_final: 0.6573 (ttt) REVERT: A 1161 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7611 (p-80) REVERT: A 1394 CYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6629 (t) REVERT: A 1554 MET cc_start: 0.9103 (mpp) cc_final: 0.8780 (mpt) REVERT: A 1994 ASP cc_start: 0.9094 (t0) cc_final: 0.8784 (t70) REVERT: A 2056 MET cc_start: 0.9028 (mmm) cc_final: 0.8728 (mmt) REVERT: A 2376 MET cc_start: 0.9128 (mtp) cc_final: 0.8775 (ptm) REVERT: A 2411 PHE cc_start: 0.9019 (t80) cc_final: 0.8723 (t80) REVERT: A 2415 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8642 (mp0) REVERT: A 2429 GLU cc_start: 0.8634 (pm20) cc_final: 0.8340 (mp0) REVERT: A 2447 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8522 (tmm) REVERT: A 2472 SER cc_start: 0.9455 (t) cc_final: 0.9161 (p) REVERT: A 2620 TYR cc_start: 0.8741 (m-80) cc_final: 0.8266 (m-80) REVERT: B 31 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7223 (mtm-85) REVERT: B 52 MET cc_start: 0.8691 (ppp) cc_final: 0.8422 (ppp) REVERT: B 79 TYR cc_start: 0.7871 (m-80) cc_final: 0.7267 (m-80) REVERT: B 92 ASN cc_start: 0.8096 (m110) cc_final: 0.7509 (m110) REVERT: B 115 LYS cc_start: 0.6829 (ptmm) cc_final: 0.6492 (ptmm) REVERT: B 120 GLN cc_start: 0.6416 (tt0) cc_final: 0.5743 (tm-30) outliers start: 25 outliers final: 20 residues processed: 141 average time/residue: 0.5259 time to fit residues: 82.9576 Evaluate side-chains 142 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 1242 LEU Chi-restraints excluded: chain A residue 1301 ASN 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 1934 SER 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 2359 MET Chi-restraints excluded: chain A residue 2447 MET Chi-restraints excluded: chain A residue 2496 VAL 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 61 THR Chi-restraints excluded: chain B residue 73 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 133 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1820 GLN A2084 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.113762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078966 restraints weight = 34639.743| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.90 r_work: 0.3082 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14545 Z= 0.141 Angle : 0.680 10.917 19803 Z= 0.332 Chirality : 0.047 0.330 2272 Planarity : 0.004 0.062 2520 Dihedral : 7.082 58.044 2334 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.76 % Allowed : 19.55 % Favored : 78.69 % 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: -0.48 (0.20), residues: 1813 helix: 1.06 (0.52), residues: 117 sheet: 0.21 (0.21), residues: 629 loop : -0.80 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2406 TYR 0.021 0.001 TYR B 121 PHE 0.010 0.001 PHE A1245 TRP 0.015 0.001 TRP A1572 HIS 0.002 0.001 HIS A2227 Details of bonding type rmsd covalent geometry : bond 0.00318 (14522) covalent geometry : angle 0.66356 (19742) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.99436 ( 16) hydrogen bonds : bond 0.03029 ( 486) hydrogen bonds : angle 4.80570 ( 1686) link_ALPHA1-4 : bond 0.00237 ( 1) link_ALPHA1-4 : angle 2.32887 ( 3) link_BETA1-4 : bond 0.01126 ( 6) link_BETA1-4 : angle 3.30934 ( 18) link_NAG-ASN : bond 0.00537 ( 8) link_NAG-ASN : angle 3.10373 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.77 seconds wall clock time: 77 minutes 39.20 seconds (4659.20 seconds total)