Starting phenix.real_space_refine on Sat Mar 16 18:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bao_12126/03_2024/7bao_12126.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 74 5.16 5 C 9635 2.51 5 N 2640 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 15093 Classifications: {'peptide': 1904} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 74, 'TRANS': 1829} Chain breaks: 4 Chain: "B" 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: "C" 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: "D" 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: "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: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 101 Unusual residues: {' CA': 3, 'NAG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.51, per 1000 atoms: 0.56 Number of scatterers: 15306 At special positions: 0 Unit cell: (120.406, 147.35, 121.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 74 16.00 O 2954 8.00 N 2640 7.00 C 9635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 857 " distance=2.04 Simple disulfide: pdb=" SG CYS A 852 " - pdb=" SG CYS A 863 " distance=2.04 Simple disulfide: pdb=" SG CYS A 858 " - pdb=" SG CYS A 869 " distance=2.04 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1145 " distance=2.02 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A2524 " distance=2.04 Simple disulfide: pdb=" SG CYS A1217 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1237 " - pdb=" SG CYS A1545 " distance=2.04 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1336 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1448 " distance=2.03 Simple disulfide: pdb=" SG CYS A1513 " - pdb=" SG CYS A1521 " distance=2.03 Simple disulfide: pdb=" SG CYS A1515 " - pdb=" SG CYS A1523 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2801 " - " ASN A1705 " " NAG A2802 " - " ASN A1799 " " NAG A2803 " - " ASN A1884 " " NAG A2804 " - " ASN A1259 " " NAG A2805 " - " ASN A1741 " " NAG A2806 " - " ASN A1985 " " NAG A2807 " - " ASN A2188 " " NAG B 1 " - " ASN A1609 " " NAG C 1 " - " ASN A2328 " " NAG D 1 " - " ASN A2646 " " NAG E 1 " - " ASN A 940 " Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 2.7 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3508 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 23 sheets defined 9.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 850 through 860 Proline residue: A 855 - end of helix removed outlier: 3.706A pdb=" N LEU A 859 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 removed outlier: 3.819A pdb=" N GLU A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.634A pdb=" N ILE A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1271 through 1280 removed outlier: 4.358A pdb=" N HIS A1275 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Proline residue: A1277 - end of helix Processing helix chain 'A' and resid 1402 through 1404 No H-bonds generated for 'chain 'A' and resid 1402 through 1404' Processing helix chain 'A' and resid 2401 through 2405 Processing helix chain 'A' and resid 2434 through 2438 Processing helix chain 'A' and resid 2452 through 2456 Processing helix chain 'A' and resid 2465 through 2470 removed outlier: 3.752A pdb=" N THR A2469 " --> pdb=" O LYS A2465 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2465 through 2470' Processing helix chain 'A' and resid 2471 through 2479 removed outlier: 3.505A pdb=" N THR A2477 " --> pdb=" O SER A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2485 Processing helix chain 'A' and resid 2500 through 2506 Processing helix chain 'A' and resid 2506 through 2511 removed outlier: 4.060A pdb=" N GLN A2511 " --> pdb=" O GLN A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.706A pdb=" N CYS A2524 " --> pdb=" O LEU A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2539 through 2543 Processing helix chain 'A' and resid 2590 through 2599 Processing helix chain 'A' and resid 2625 through 2633 removed outlier: 3.517A pdb=" N ILE A2631 " --> pdb=" O GLY A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2682 through 2712 removed outlier: 3.547A pdb=" N LYS A2687 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A2712 " --> pdb=" O GLN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2732 removed outlier: 3.521A pdb=" N GLN A2726 " --> pdb=" O GLU A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2748 through 2752 Processing helix chain 'A' and resid 2754 through 2756 No H-bonds generated for 'chain 'A' and resid 2754 through 2756' Processing sheet with id=AA1, first strand: chain 'A' and resid 959 through 965 removed outlier: 8.251A pdb=" N PHE A 994 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 923 " --> pdb=" O PHE A 994 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 959 through 965 Processing sheet with id=AA3, first strand: chain 'A' and resid 951 through 953 removed outlier: 3.701A pdb=" N GLU A 975 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1022 through 1025 Processing sheet with id=AA5, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AA6, first strand: chain 'A' and resid 1100 through 1107 Processing sheet with id=AA7, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1203 removed outlier: 3.625A pdb=" N ARG A1559 " --> pdb=" O ASP A1554 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1541 " --> pdb=" O ALA A1553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1222 through 1223 removed outlier: 6.635A pdb=" N ILE A1251 " --> pdb=" O ILE A1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1283 through 1285 removed outlier: 4.212A pdb=" N VAL A1292 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1294 " --> pdb=" O PHE A1303 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1322 " --> pdb=" O VAL A1302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1350 through 1355 removed outlier: 4.936A pdb=" N GLY A1352 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1399 through 1400 removed outlier: 7.110A pdb=" N VAL A1429 " --> pdb=" O VAL A1441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1423 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A1411 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1470 through 1475 removed outlier: 6.485A pdb=" N ALA A1484 " --> pdb=" O THR A1471 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1473 " --> pdb=" O TYR A1482 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A1482 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A1494 " --> pdb=" O VAL A1506 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1569 through 1570 removed outlier: 3.872A pdb=" N PHE A1569 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1586 " --> pdb=" O THR A1598 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A1598 " --> pdb=" O LEU A1586 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A1588 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU A1596 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN A1609 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A1598 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN A1609 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1617 " --> pdb=" O THR A1613 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ASP A1617 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ARG A1633 " --> pdb=" O ASP A1617 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR A1619 " --> pdb=" O VAL A1631 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A1630 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A1642 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A1632 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A1640 " --> pdb=" O VAL A1652 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A1651 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A1663 " --> pdb=" O TRP A1651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A1653 " --> pdb=" O LYS A1661 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1671 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N MET A1672 " --> pdb=" O LYS A1685 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A1685 " --> pdb=" O MET A1672 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A1674 " --> pdb=" O ALA A1683 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A1681 " --> pdb=" O HIS A1676 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N LEU A1681 " --> pdb=" O TYR A1697 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR A1697 " --> pdb=" O LEU A1681 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR A1704 " --> pdb=" O PHE A1716 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A1719 " --> pdb=" O HIS A1725 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A1724 " --> pdb=" O THR A1740 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1740 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1828 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1826 " --> pdb=" O GLU A1818 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1839 " --> pdb=" O LEU A1831 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A1833 " --> pdb=" O ASN A1837 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN A1837 " --> pdb=" O VAL A1833 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1782 through 1784 Processing sheet with id=AB7, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.718A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG A2009 " --> pdb=" O TYR A2025 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR A2025 " --> pdb=" O ARG A2009 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A2029 " --> pdb=" O LEU A2046 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2046 " --> pdb=" O LYS A2029 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A2031 " --> pdb=" O ILE A2044 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A2044 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A2033 " --> pdb=" O LYS A2042 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.718A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG A2009 " --> pdb=" O TYR A2025 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR A2025 " --> pdb=" O ARG A2009 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A2029 " --> pdb=" O LEU A2046 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2046 " --> pdb=" O LYS A2029 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A2031 " --> pdb=" O ILE A2044 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A2044 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A2033 " --> pdb=" O LYS A2042 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A2092 " --> pdb=" O TYR A2108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A2107 " --> pdb=" O PHE A2120 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A2120 " --> pdb=" O LEU A2107 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG A2109 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A2118 " --> pdb=" O VAL A2125 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A2132 " --> pdb=" O LYS A2143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A2153 " --> pdb=" O HIS A2144 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A2152 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A2164 " --> pdb=" O TYR A2156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A2158 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A2162 " --> pdb=" O ILE A2158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A2178 " --> pdb=" O GLN A2169 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL A2177 " --> pdb=" O TYR A2194 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A2191 " --> pdb=" O ILE A2207 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A2207 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A2193 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A2205 " --> pdb=" O SER A2193 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A2195 " --> pdb=" O GLN A2203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A2207 " --> pdb=" O PRO A2211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 6.657A pdb=" N SER A2216 " --> pdb=" O HIS A2224 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS A2224 " --> pdb=" O LEU A2237 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A2248 " --> pdb=" O PRO A2236 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG A2238 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A2246 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A2252 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A2264 " --> pdb=" O GLN A2252 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS A2254 " --> pdb=" O ARG A2262 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG A2262 " --> pdb=" O PHE A2269 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A2279 " --> pdb=" O GLU A2270 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE A2278 " --> pdb=" O TYR A2291 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A2288 " --> pdb=" O SER A2304 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A2304 " --> pdb=" O SER A2288 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A2290 " --> pdb=" O SER A2302 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A2302 " --> pdb=" O ARG A2290 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A2292 " --> pdb=" O VAL A2300 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A2300 " --> pdb=" O PHE A2312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A2325 " --> pdb=" O PHE A2313 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2333 " --> pdb=" O ASN A2328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A2347 " --> pdb=" O TYR A2338 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A2346 " --> pdb=" O ILE A2358 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A2355 " --> pdb=" O SER A2371 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER A2371 " --> pdb=" O GLU A2355 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A2357 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A2369 " --> pdb=" O TYR A2357 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A2359 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU A2367 " --> pdb=" O GLN A2379 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN A2379 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A2369 " --> pdb=" O ILE A2377 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A2390 " --> pdb=" O LEU A2381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2406 through 2408 removed outlier: 4.064A pdb=" N LEU A2413 " --> pdb=" O ASP A2408 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2570 through 2574 Processing sheet with id=AC3, first strand: chain 'A' and resid 2602 through 2603 Processing sheet with id=AC4, first strand: chain 'A' and resid 2602 through 2603 removed outlier: 6.165A pdb=" N ASP A2615 " --> pdb=" O CYS A2674 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN A2676 " --> pdb=" O ASP A2615 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS A2617 " --> pdb=" O ASN A2676 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ARG A2678 " --> pdb=" O HIS A2617 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A2619 " --> pdb=" O ARG A2678 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2737 through 2741 546 hydrogen bonds defined for protein. 1401 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: 10.86 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4945 1.33 - 1.46: 3725 1.46 - 1.58: 6846 1.58 - 1.71: 0 1.71 - 1.84: 119 Bond restraints: 15635 Sorted by residual: bond pdb=" CG1 ILE A1989 " pdb=" CD1 ILE A1989 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" N LEU A 862 " pdb=" CA LEU A 862 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.93e+00 bond pdb=" CG ARG A1976 " pdb=" CD ARG A1976 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 bond pdb=" CB VAL A2423 " pdb=" CG2 VAL A2423 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB ARG A2008 " pdb=" CG ARG A2008 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.00e+00 ... (remaining 15630 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.77: 298 105.77 - 112.86: 8183 112.86 - 119.95: 5372 119.95 - 127.04: 7187 127.04 - 134.13: 159 Bond angle restraints: 21199 Sorted by residual: angle pdb=" C ASN A 874 " pdb=" N PRO A 875 " pdb=" CA PRO A 875 " ideal model delta sigma weight residual 119.56 115.12 4.44 1.02e+00 9.61e-01 1.90e+01 angle pdb=" N VAL A1321 " pdb=" CA VAL A1321 " pdb=" C VAL A1321 " ideal model delta sigma weight residual 113.42 108.52 4.90 1.17e+00 7.31e-01 1.75e+01 angle pdb=" CB ARG A2244 " pdb=" CG ARG A2244 " pdb=" CD ARG A2244 " ideal model delta sigma weight residual 111.30 101.77 9.53 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA ASP A 847 " pdb=" CB ASP A 847 " pdb=" CG ASP A 847 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N GLN A1823 " pdb=" CA GLN A1823 " pdb=" C GLN A1823 " ideal model delta sigma weight residual 108.34 113.39 -5.05 1.31e+00 5.83e-01 1.48e+01 ... (remaining 21194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 8741 17.75 - 35.50: 648 35.50 - 53.25: 90 53.25 - 71.00: 26 71.00 - 88.76: 15 Dihedral angle restraints: 9520 sinusoidal: 4020 harmonic: 5500 Sorted by residual: dihedral pdb=" CA TYR A2025 " pdb=" C TYR A2025 " pdb=" N ASP A2026 " pdb=" CA ASP A2026 " ideal model delta harmonic sigma weight residual -180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA ASN A1557 " pdb=" C ASN A1557 " pdb=" N ILE A1558 " pdb=" CA ILE A1558 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASN A2657 " pdb=" C ASN A2657 " pdb=" N GLY A2658 " pdb=" CA GLY A2658 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 9517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2201 0.112 - 0.223: 164 0.223 - 0.335: 6 0.335 - 0.446: 1 0.446 - 0.558: 1 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CB ILE A1989 " pdb=" CA ILE A1989 " pdb=" CG1 ILE A1989 " pdb=" CG2 ILE A1989 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CB VAL A2534 " pdb=" CA VAL A2534 " pdb=" CG1 VAL A2534 " pdb=" CG2 VAL A2534 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 940 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2370 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1865 " 0.020 2.00e-02 2.50e+03 2.15e-02 9.27e+00 pdb=" CG TYR A1865 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A1865 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A1865 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A1865 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A1865 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1865 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1865 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A1145 " -0.048 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A1146 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A1146 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1146 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2085 " -0.013 2.00e-02 2.50e+03 1.98e-02 7.86e+00 pdb=" CG TYR A2085 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A2085 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A2085 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A2085 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A2085 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A2085 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A2085 " 0.003 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 194 2.64 - 3.20: 13259 3.20 - 3.77: 21581 3.77 - 4.33: 31837 4.33 - 4.90: 54680 Nonbonded interactions: 121551 Sorted by model distance: nonbonded pdb=" NH1 ARG A1300 " pdb=" OD1 ASN A1349 " model vdw 2.075 2.520 nonbonded pdb=" NH1 ARG A1300 " pdb=" O THR A1348 " model vdw 2.124 2.520 nonbonded pdb=" OG1 THR A2006 " pdb=" OD2 ASP A2258 " model vdw 2.141 2.440 nonbonded pdb=" OG SER A2744 " pdb=" OE1 GLN A2747 " model vdw 2.146 2.440 nonbonded pdb=" NE2 GLN A2119 " pdb=" O GLY A2121 " model vdw 2.168 2.520 ... (remaining 121546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.530 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: 0.020 Extract box with map and model: 10.130 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 47.810 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.011 0.139 15635 Z= 0.721 Angle : 1.002 12.898 21199 Z= 0.550 Chirality : 0.064 0.558 2373 Planarity : 0.006 0.074 2737 Dihedral : 13.014 88.755 5979 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 1894 helix: -2.35 (0.41), residues: 109 sheet: -0.14 (0.21), residues: 601 loop : -1.70 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 990 HIS 0.015 0.003 HIS A2000 PHE 0.045 0.003 PHE A2069 TYR 0.052 0.003 TYR A1865 ARG 0.014 0.002 ARG A2427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 945 ASN cc_start: 0.8281 (p0) cc_final: 0.8072 (p0) REVERT: A 1363 PHE cc_start: 0.8961 (p90) cc_final: 0.8692 (p90) REVERT: A 1440 ILE cc_start: 0.8668 (mm) cc_final: 0.8195 (tt) REVERT: A 1673 MET cc_start: 0.9015 (mpp) cc_final: 0.8664 (mpp) REVERT: A 1748 PHE cc_start: 0.7767 (t80) cc_final: 0.7423 (t80) REVERT: A 1905 MET cc_start: 0.8078 (mpp) cc_final: 0.7673 (mpt) outliers start: 1 outliers final: 2 residues processed: 181 average time/residue: 1.3911 time to fit residues: 275.5473 Evaluate side-chains 135 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 896 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1427 ASN ** A1792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN A2095 GLN A2252 GLN A2403 HIS A2588 ASN A2651 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15635 Z= 0.185 Angle : 0.655 9.482 21199 Z= 0.342 Chirality : 0.047 0.291 2373 Planarity : 0.005 0.052 2737 Dihedral : 6.811 102.039 2425 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.80 % Allowed : 7.04 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1894 helix: -0.49 (0.48), residues: 109 sheet: 0.18 (0.21), residues: 617 loop : -1.30 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1874 HIS 0.005 0.001 HIS A2000 PHE 0.012 0.001 PHE A 974 TYR 0.018 0.001 TYR A2025 ARG 0.010 0.000 ARG A1371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.726 Fit side-chains REVERT: A 853 MET cc_start: 0.7718 (mmp) cc_final: 0.7311 (mtm) REVERT: A 945 ASN cc_start: 0.7986 (p0) cc_final: 0.7566 (p0) REVERT: A 1425 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7682 (p0) REVERT: A 1440 ILE cc_start: 0.8483 (mm) cc_final: 0.8257 (tt) REVERT: A 1748 PHE cc_start: 0.7708 (t80) cc_final: 0.7500 (t80) REVERT: A 1905 MET cc_start: 0.7955 (mpp) cc_final: 0.7604 (mpt) REVERT: A 2470 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7105 (t0) outliers start: 30 outliers final: 8 residues processed: 174 average time/residue: 1.1521 time to fit residues: 224.7100 Evaluate side-chains 141 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1425 ASP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2470 ASP Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 ASN ** A1298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1496 GLN A1571 ASN A1668 HIS ** A1792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN A2608 HIS A2676 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15635 Z= 0.206 Angle : 0.622 9.640 21199 Z= 0.321 Chirality : 0.047 0.295 2373 Planarity : 0.005 0.050 2737 Dihedral : 5.994 56.688 2421 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.22 % Allowed : 10.46 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1894 helix: 0.49 (0.52), residues: 103 sheet: 0.47 (0.21), residues: 619 loop : -1.12 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1874 HIS 0.006 0.001 HIS A 984 PHE 0.011 0.001 PHE A2069 TYR 0.016 0.001 TYR A2025 ARG 0.007 0.000 ARG A1371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.726 Fit side-chains REVERT: A 853 MET cc_start: 0.7780 (mmp) cc_final: 0.7444 (mtm) REVERT: A 1060 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7448 (mtp85) REVERT: A 1748 PHE cc_start: 0.7695 (t80) cc_final: 0.7493 (t80) REVERT: A 1905 MET cc_start: 0.7965 (mpp) cc_final: 0.7480 (mpt) REVERT: A 2106 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (m-30) outliers start: 37 outliers final: 11 residues processed: 172 average time/residue: 1.1492 time to fit residues: 221.3791 Evaluate side-chains 139 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 2106 ASP Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 ASN A1419 ASN A1668 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15635 Z= 0.248 Angle : 0.626 9.812 21199 Z= 0.324 Chirality : 0.047 0.267 2373 Planarity : 0.004 0.047 2737 Dihedral : 5.796 57.560 2421 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.35 % Allowed : 12.21 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1894 helix: 0.94 (0.52), residues: 103 sheet: 0.64 (0.21), residues: 609 loop : -1.06 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2165 HIS 0.006 0.001 HIS A2438 PHE 0.012 0.001 PHE A2120 TYR 0.017 0.001 TYR A1865 ARG 0.006 0.000 ARG A2160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.839 Fit side-chains REVERT: A 853 MET cc_start: 0.7908 (mmp) cc_final: 0.7568 (mtm) REVERT: A 1905 MET cc_start: 0.7913 (mpp) cc_final: 0.7503 (mpt) REVERT: A 2106 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: A 2163 MET cc_start: 0.8641 (mmm) cc_final: 0.8398 (mmt) REVERT: A 2355 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7328 (mm-30) outliers start: 39 outliers final: 21 residues processed: 170 average time/residue: 1.1344 time to fit residues: 216.8297 Evaluate side-chains 154 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1721 ASP Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2106 ASP Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1668 HIS ** A1792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15635 Z= 0.185 Angle : 0.594 9.631 21199 Z= 0.305 Chirality : 0.045 0.267 2373 Planarity : 0.004 0.049 2737 Dihedral : 5.551 56.284 2421 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.98 % Allowed : 13.41 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1894 helix: 1.17 (0.53), residues: 103 sheet: 0.72 (0.21), residues: 614 loop : -0.98 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1874 HIS 0.007 0.001 HIS A2438 PHE 0.009 0.001 PHE A2120 TYR 0.016 0.001 TYR A2025 ARG 0.006 0.000 ARG A2160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.7882 (mmp) cc_final: 0.7535 (mtm) REVERT: A 1060 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7422 (mtm180) REVERT: A 1905 MET cc_start: 0.7876 (mpp) cc_final: 0.7379 (mpt) REVERT: A 2163 MET cc_start: 0.8625 (mmm) cc_final: 0.8381 (mmt) REVERT: A 2355 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: A 2588 ASN cc_start: 0.7601 (t0) cc_final: 0.7058 (p0) outliers start: 33 outliers final: 17 residues processed: 173 average time/residue: 1.1402 time to fit residues: 221.6224 Evaluate side-chains 154 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 1835 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1427 ASN A1431 GLN A1668 HIS A2087 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15635 Z= 0.186 Angle : 0.587 9.576 21199 Z= 0.303 Chirality : 0.045 0.264 2373 Planarity : 0.004 0.050 2737 Dihedral : 5.381 56.330 2421 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.35 % Allowed : 13.83 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1894 helix: 1.39 (0.53), residues: 103 sheet: 0.75 (0.21), residues: 623 loop : -0.93 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2165 HIS 0.007 0.001 HIS A2438 PHE 0.021 0.001 PHE A 974 TYR 0.015 0.001 TYR A2025 ARG 0.006 0.000 ARG A2160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.7898 (mmp) cc_final: 0.7525 (mtt) REVERT: A 1060 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7357 (mtm180) REVERT: A 1905 MET cc_start: 0.7865 (mpp) cc_final: 0.7376 (mpt) REVERT: A 2163 MET cc_start: 0.8612 (mmm) cc_final: 0.8383 (mmt) REVERT: A 2355 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: A 2588 ASN cc_start: 0.7589 (t0) cc_final: 0.7042 (p0) REVERT: A 2701 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (mt0) outliers start: 39 outliers final: 22 residues processed: 172 average time/residue: 1.1252 time to fit residues: 219.7226 Evaluate side-chains 160 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1613 THR Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1835 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2642 GLU Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1427 ASN A2132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15635 Z= 0.172 Angle : 0.578 9.497 21199 Z= 0.299 Chirality : 0.045 0.264 2373 Planarity : 0.004 0.050 2737 Dihedral : 5.121 56.915 2421 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.29 % Allowed : 14.49 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1894 helix: 1.42 (0.53), residues: 105 sheet: 0.82 (0.21), residues: 624 loop : -0.86 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1874 HIS 0.007 0.001 HIS A2438 PHE 0.016 0.001 PHE A 974 TYR 0.013 0.001 TYR A2025 ARG 0.007 0.000 ARG A2160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.7945 (mmp) cc_final: 0.7543 (mtt) REVERT: A 1060 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7413 (mtm180) REVERT: A 1713 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 1905 MET cc_start: 0.7846 (mpp) cc_final: 0.7379 (mpt) REVERT: A 2163 MET cc_start: 0.8595 (mmm) cc_final: 0.8300 (mmt) REVERT: A 2355 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: A 2588 ASN cc_start: 0.7523 (t0) cc_final: 0.7040 (p0) REVERT: A 2701 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7888 (mt0) outliers start: 38 outliers final: 18 residues processed: 182 average time/residue: 1.1503 time to fit residues: 234.9418 Evaluate side-chains 161 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1668 HIS A1725 HIS A2087 ASN A2523 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15635 Z= 0.258 Angle : 0.614 9.779 21199 Z= 0.316 Chirality : 0.046 0.260 2373 Planarity : 0.004 0.049 2737 Dihedral : 5.173 56.690 2421 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 2.10 % Allowed : 14.97 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1894 helix: 1.40 (0.53), residues: 105 sheet: 0.80 (0.21), residues: 629 loop : -0.83 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 990 HIS 0.006 0.001 HIS A2438 PHE 0.015 0.001 PHE A 974 TYR 0.015 0.001 TYR A1865 ARG 0.008 0.000 ARG A2659 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.763 Fit side-chains REVERT: A 853 MET cc_start: 0.7909 (mmp) cc_final: 0.7561 (mtt) REVERT: A 1060 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7398 (mtm180) REVERT: A 1427 ASN cc_start: 0.8421 (m-40) cc_final: 0.8219 (m110) REVERT: A 1905 MET cc_start: 0.7874 (mpp) cc_final: 0.7487 (mpt) REVERT: A 2163 MET cc_start: 0.8613 (mmm) cc_final: 0.8384 (mmt) REVERT: A 2355 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: A 2588 ASN cc_start: 0.7599 (t0) cc_final: 0.7183 (p0) REVERT: A 2701 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7911 (mt0) outliers start: 35 outliers final: 27 residues processed: 166 average time/residue: 1.1050 time to fit residues: 207.1127 Evaluate side-chains 163 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1742 LEU Chi-restraints excluded: chain A residue 1748 PHE Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2132 GLN Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1725 HIS A2132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15635 Z= 0.180 Angle : 0.587 10.445 21199 Z= 0.302 Chirality : 0.047 0.632 2373 Planarity : 0.004 0.050 2737 Dihedral : 5.192 56.478 2421 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.98 % Allowed : 15.51 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1894 helix: 1.46 (0.53), residues: 105 sheet: 0.88 (0.21), residues: 624 loop : -0.78 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1874 HIS 0.007 0.001 HIS A2438 PHE 0.014 0.001 PHE A 974 TYR 0.014 0.001 TYR A2025 ARG 0.007 0.000 ARG A2160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.579 Fit side-chains REVERT: A 853 MET cc_start: 0.7951 (mmp) cc_final: 0.7581 (mtt) REVERT: A 1713 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8628 (t) REVERT: A 1905 MET cc_start: 0.7837 (mpp) cc_final: 0.7374 (mpt) REVERT: A 2163 MET cc_start: 0.8595 (mmm) cc_final: 0.8368 (mmt) REVERT: A 2355 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: A 2588 ASN cc_start: 0.7500 (t0) cc_final: 0.7157 (p0) REVERT: A 2701 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7883 (mt0) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 1.1266 time to fit residues: 209.2395 Evaluate side-chains 158 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1427 ASN A1725 HIS ** A2087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15635 Z= 0.263 Angle : 0.626 10.906 21199 Z= 0.321 Chirality : 0.047 0.435 2373 Planarity : 0.004 0.047 2737 Dihedral : 5.333 57.383 2421 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.74 % Allowed : 15.94 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1894 helix: 1.35 (0.52), residues: 105 sheet: 0.80 (0.20), residues: 634 loop : -0.80 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 990 HIS 0.007 0.001 HIS A2438 PHE 0.014 0.001 PHE A 974 TYR 0.013 0.001 TYR A1865 ARG 0.006 0.000 ARG A2160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.649 Fit side-chains REVERT: A 853 MET cc_start: 0.7942 (mmp) cc_final: 0.7581 (mtt) REVERT: A 1905 MET cc_start: 0.7857 (mpp) cc_final: 0.7468 (mpt) REVERT: A 2163 MET cc_start: 0.8623 (mmm) cc_final: 0.8390 (mmt) REVERT: A 2355 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: A 2588 ASN cc_start: 0.7615 (t0) cc_final: 0.7355 (p0) REVERT: A 2701 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7929 (mt0) outliers start: 29 outliers final: 21 residues processed: 164 average time/residue: 1.0717 time to fit residues: 198.3617 Evaluate side-chains 159 residues out of total 1663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 ASP Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1419 ASN A1725 HIS ** A2087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2132 GLN A2342 GLN A2403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102512 restraints weight = 21160.346| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.43 r_work: 0.3147 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15635 Z= 0.198 Angle : 0.603 10.566 21199 Z= 0.310 Chirality : 0.046 0.378 2373 Planarity : 0.004 0.048 2737 Dihedral : 5.136 56.339 2421 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.86 % Allowed : 16.24 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1894 helix: 1.41 (0.53), residues: 105 sheet: 0.90 (0.20), residues: 624 loop : -0.79 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 990 HIS 0.006 0.001 HIS A2438 PHE 0.013 0.001 PHE A 974 TYR 0.013 0.001 TYR A2025 ARG 0.007 0.000 ARG A2160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5042.06 seconds wall clock time: 90 minutes 3.60 seconds (5403.60 seconds total)