Starting phenix.real_space_refine on Fri May 16 23:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182.map" model { file = "/net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gkc_40182/05_2025/8gkc_40182_neut.cif" } resolution = 2.45 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= -0.001 sd= 0.520 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 P 12 5.49 5 S 52 5.16 5 C 9280 2.51 5 N 2574 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "D" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.92, per 1000 atoms: 0.54 Number of scatterers: 14616 At special positions: 0 Unit cell: (120.51, 169.95, 87.55, 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) S 52 16.00 P 12 15.00 O 2698 8.00 N 2574 7.00 C 9280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 38.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 887 through 903 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 965 through 970 removed outlier: 3.544A pdb=" N ASP A 970 " --> pdb=" O ARG A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 998 Processing helix chain 'A' and resid 1003 through 1006 Processing helix chain 'A' and resid 1025 through 1040 removed outlier: 4.007A pdb=" N GLY A1040 " --> pdb=" O MET A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.513A pdb=" N GLN A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1434 removed outlier: 4.064A pdb=" N SER A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A1434 " --> pdb=" O GLY A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1461 removed outlier: 4.271A pdb=" N LEU A1456 " --> pdb=" O GLY A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1470 Processing helix chain 'A' and resid 1490 through 1500 removed outlier: 3.776A pdb=" N GLN A1494 " --> pdb=" O SER A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1542 No H-bonds generated for 'chain 'A' and resid 1540 through 1542' Processing helix chain 'A' and resid 1549 through 1554 removed outlier: 4.003A pdb=" N HIS A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1580 Processing helix chain 'A' and resid 1584 through 1588 Processing helix chain 'A' and resid 1629 through 1631 No H-bonds generated for 'chain 'A' and resid 1629 through 1631' Processing helix chain 'A' and resid 1641 through 1646 Processing helix chain 'A' and resid 1648 through 1660 Processing helix chain 'A' and resid 1678 through 1691 Processing helix chain 'A' and resid 1701 through 1712 Processing helix chain 'A' and resid 1716 through 1718 No H-bonds generated for 'chain 'A' and resid 1716 through 1718' Processing helix chain 'A' and resid 1727 through 1736 Processing helix chain 'A' and resid 1750 through 1759 Processing helix chain 'A' and resid 1771 through 1776 Processing helix chain 'A' and resid 1783 through 1788 Processing helix chain 'A' and resid 1795 through 1801 removed outlier: 3.542A pdb=" N PHE A1800 " --> pdb=" O ASP A1797 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1801 " --> pdb=" O ALA A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1820 removed outlier: 3.665A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1846 removed outlier: 3.994A pdb=" N ALA A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A1845 " --> pdb=" O ARG A1841 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A1846 " --> pdb=" O TYR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1907 Processing helix chain 'A' and resid 1922 through 1936 Processing helix chain 'A' and resid 1948 through 1963 removed outlier: 3.632A pdb=" N LEU A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2010 Proline residue: A1994 - end of helix removed outlier: 3.643A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1998 " --> pdb=" O PRO A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2026 Processing helix chain 'A' and resid 2031 through 2051 Processing helix chain 'A' and resid 2067 through 2072 Processing helix chain 'A' and resid 2087 through 2099 Processing helix chain 'D' and resid 872 through 876 Processing helix chain 'D' and resid 887 through 903 Processing helix chain 'D' and resid 906 through 910 Processing helix chain 'D' and resid 965 through 970 removed outlier: 3.544A pdb=" N ASP D 970 " --> pdb=" O ARG D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 998 Processing helix chain 'D' and resid 1003 through 1006 Processing helix chain 'D' and resid 1025 through 1040 removed outlier: 4.006A pdb=" N GLY D1040 " --> pdb=" O MET D1036 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1066 removed outlier: 3.513A pdb=" N GLN D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1434 removed outlier: 4.064A pdb=" N SER D1427 " --> pdb=" O ARG D1423 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D1434 " --> pdb=" O GLY D1430 " (cutoff:3.500A) Processing helix chain 'D' and resid 1452 through 1461 removed outlier: 4.271A pdb=" N LEU D1456 " --> pdb=" O GLY D1452 " (cutoff:3.500A) Processing helix chain 'D' and resid 1465 through 1470 Processing helix chain 'D' and resid 1490 through 1500 removed outlier: 3.776A pdb=" N GLN D1494 " --> pdb=" O SER D1490 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1542 No H-bonds generated for 'chain 'D' and resid 1540 through 1542' Processing helix chain 'D' and resid 1549 through 1554 removed outlier: 4.003A pdb=" N HIS D1553 " --> pdb=" O SER D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1572 through 1580 Processing helix chain 'D' and resid 1584 through 1588 Processing helix chain 'D' and resid 1629 through 1631 No H-bonds generated for 'chain 'D' and resid 1629 through 1631' Processing helix chain 'D' and resid 1641 through 1646 Processing helix chain 'D' and resid 1648 through 1660 Processing helix chain 'D' and resid 1678 through 1691 Processing helix chain 'D' and resid 1701 through 1712 Processing helix chain 'D' and resid 1716 through 1718 No H-bonds generated for 'chain 'D' and resid 1716 through 1718' Processing helix chain 'D' and resid 1727 through 1736 Processing helix chain 'D' and resid 1750 through 1759 Processing helix chain 'D' and resid 1771 through 1776 Processing helix chain 'D' and resid 1783 through 1788 Processing helix chain 'D' and resid 1795 through 1801 removed outlier: 3.542A pdb=" N PHE D1800 " --> pdb=" O ASP D1797 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN D1801 " --> pdb=" O ALA D1798 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1820 removed outlier: 3.666A pdb=" N VAL D1810 " --> pdb=" O ASP D1806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1835 through 1846 removed outlier: 3.995A pdb=" N ALA D1839 " --> pdb=" O GLN D1835 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D1845 " --> pdb=" O ARG D1841 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D1846 " --> pdb=" O TYR D1842 " (cutoff:3.500A) Processing helix chain 'D' and resid 1894 through 1907 Processing helix chain 'D' and resid 1922 through 1936 Processing helix chain 'D' and resid 1948 through 1963 removed outlier: 3.632A pdb=" N LEU D1962 " --> pdb=" O GLU D1958 " (cutoff:3.500A) Processing helix chain 'D' and resid 1984 through 2010 Proline residue: D1994 - end of helix removed outlier: 3.643A pdb=" N SER D1997 " --> pdb=" O LYS D1993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D1998 " --> pdb=" O PRO D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2026 Processing helix chain 'D' and resid 2031 through 2051 Processing helix chain 'D' and resid 2067 through 2072 Processing helix chain 'D' and resid 2087 through 2099 Processing sheet with id=AA1, first strand: chain 'A' and resid 860 through 864 removed outlier: 6.666A pdb=" N PHE A 944 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 955 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 946 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL A 953 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU A 919 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER A 955 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 917 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 913 " --> pdb=" O HIS A1056 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS A1056 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A 915 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A1054 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR A1050 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU A1100 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY A1096 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A1055 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A1094 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A1057 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A1092 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER A1017 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1010 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1021 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1008 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 860 through 864 removed outlier: 6.666A pdb=" N PHE A 944 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 955 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 946 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL A 953 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU A 919 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER A 955 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 917 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 913 " --> pdb=" O HIS A1056 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS A1056 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU A 915 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A1054 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR A1050 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU A1100 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY A1096 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A1055 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A1094 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A1057 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A1092 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 883 through 884 removed outlier: 3.808A pdb=" N THR A 879 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 6.100A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU A1473 " --> pdb=" O ASN A1504 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR A1506 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A1475 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET A1503 " --> pdb=" O PHE A1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A1514 " --> pdb=" O MET A1503 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1515 " --> pdb=" O CYS A1118 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A1118 " --> pdb=" O ARG A1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE A2016 " --> pdb=" O LEU A2056 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A2058 " --> pdb=" O PHE A2016 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A2018 " --> pdb=" O VAL A2058 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TRP A2060 " --> pdb=" O VAL A2018 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A2020 " --> pdb=" O TRP A2060 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER A1886 " --> pdb=" O VAL A1965 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A1967 " --> pdb=" O SER A1886 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A1912 " --> pdb=" O GLN A1940 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER A1942 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A1914 " --> pdb=" O SER A1942 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 6.100A pdb=" N ILE A1413 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS A1444 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A1415 " --> pdb=" O LYS A1444 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU A1473 " --> pdb=" O ASN A1504 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR A1506 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER A1475 " --> pdb=" O TYR A1506 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET A1503 " --> pdb=" O PHE A1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A1514 " --> pdb=" O MET A1503 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1515 " --> pdb=" O CYS A1118 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A1118 " --> pdb=" O ARG A1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A2110 " --> pdb=" O LEU A2084 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1525 through 1528 Processing sheet with id=AA7, first strand: chain 'A' and resid 1531 through 1535 Processing sheet with id=AA8, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 5.377A pdb=" N VAL A1566 " --> pdb=" O ARG A1606 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A1606 " --> pdb=" O VAL A1566 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A1602 " --> pdb=" O SER A1570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 5.958A pdb=" N THR A1829 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLN A1855 " --> pdb=" O THR A1829 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A1831 " --> pdb=" O GLN A1855 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1720 through 1722 removed outlier: 6.324A pdb=" N LEU A1671 " --> pdb=" O PHE A1696 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR A1698 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A1673 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP A1742 " --> pdb=" O ARG A1765 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A1767 " --> pdb=" O ASP A1742 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL A1744 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP D1742 " --> pdb=" O ARG D1765 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU D1767 " --> pdb=" O ASP D1742 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL D1744 " --> pdb=" O LEU D1767 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D1671 " --> pdb=" O PHE D1696 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR D1698 " --> pdb=" O LEU D1671 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D1673 " --> pdb=" O THR D1698 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1779 through 1781 Processing sheet with id=AB3, first strand: chain 'D' and resid 860 through 864 removed outlier: 6.666A pdb=" N PHE D 944 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER D 955 " --> pdb=" O PHE D 944 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 946 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL D 953 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU D 919 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 955 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 917 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 913 " --> pdb=" O HIS D1056 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS D1056 " --> pdb=" O VAL D 913 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU D 915 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D1054 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR D1050 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU D1100 " --> pdb=" O PRO D1049 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY D1096 " --> pdb=" O THR D1053 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE D1055 " --> pdb=" O ILE D1094 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D1094 " --> pdb=" O ILE D1055 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE D1057 " --> pdb=" O VAL D1092 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D1092 " --> pdb=" O ILE D1057 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER D1017 " --> pdb=" O SER D1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D1010 " --> pdb=" O ARG D1019 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D1021 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE D1008 " --> pdb=" O LEU D1021 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 860 through 864 removed outlier: 6.666A pdb=" N PHE D 944 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER D 955 " --> pdb=" O PHE D 944 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 946 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL D 953 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU D 919 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D 955 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 917 " --> pdb=" O SER D 955 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 913 " --> pdb=" O HIS D1056 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS D1056 " --> pdb=" O VAL D 913 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU D 915 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D1054 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N THR D1050 " --> pdb=" O LEU D 919 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU D1100 " --> pdb=" O PRO D1049 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY D1096 " --> pdb=" O THR D1053 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE D1055 " --> pdb=" O ILE D1094 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D1094 " --> pdb=" O ILE D1055 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE D1057 " --> pdb=" O VAL D1092 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D1092 " --> pdb=" O ILE D1057 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 883 through 884 removed outlier: 3.807A pdb=" N THR D 879 " --> pdb=" O ASP D1000 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1413 through 1416 removed outlier: 6.099A pdb=" N ILE D1413 " --> pdb=" O TRP D1442 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS D1444 " --> pdb=" O ILE D1413 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D1415 " --> pdb=" O LYS D1444 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU D1473 " --> pdb=" O ASN D1504 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR D1506 " --> pdb=" O LEU D1473 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER D1475 " --> pdb=" O TYR D1506 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET D1503 " --> pdb=" O PHE D1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D1514 " --> pdb=" O MET D1503 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D1515 " --> pdb=" O CYS D1118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D1118 " --> pdb=" O ARG D1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D2105 " --> pdb=" O PHE D1117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE D2016 " --> pdb=" O LEU D2056 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL D2058 " --> pdb=" O PHE D2016 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D2018 " --> pdb=" O VAL D2058 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TRP D2060 " --> pdb=" O VAL D2018 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER D2020 " --> pdb=" O TRP D2060 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D1886 " --> pdb=" O VAL D1965 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D1967 " --> pdb=" O SER D1886 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D1912 " --> pdb=" O GLN D1940 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER D1942 " --> pdb=" O LEU D1912 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D1914 " --> pdb=" O SER D1942 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1413 through 1416 removed outlier: 6.099A pdb=" N ILE D1413 " --> pdb=" O TRP D1442 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS D1444 " --> pdb=" O ILE D1413 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D1415 " --> pdb=" O LYS D1444 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU D1473 " --> pdb=" O ASN D1504 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR D1506 " --> pdb=" O LEU D1473 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER D1475 " --> pdb=" O TYR D1506 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET D1503 " --> pdb=" O PHE D1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D1514 " --> pdb=" O MET D1503 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D1515 " --> pdb=" O CYS D1118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D1118 " --> pdb=" O ARG D1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D2105 " --> pdb=" O PHE D1117 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D2110 " --> pdb=" O LEU D2084 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1525 through 1528 Processing sheet with id=AB9, first strand: chain 'D' and resid 1531 through 1535 Processing sheet with id=AC1, first strand: chain 'D' and resid 1625 through 1628 removed outlier: 5.377A pdb=" N VAL D1566 " --> pdb=" O ARG D1606 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG D1606 " --> pdb=" O VAL D1566 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU D1602 " --> pdb=" O SER D1570 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1625 through 1628 removed outlier: 5.958A pdb=" N THR D1829 " --> pdb=" O VAL D1853 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLN D1855 " --> pdb=" O THR D1829 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE D1831 " --> pdb=" O GLN D1855 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2052 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: 6.94 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2370 1.27 - 1.41: 3817 1.41 - 1.55: 8649 1.55 - 1.68: 58 1.68 - 1.82: 76 Bond restraints: 14970 Sorted by residual: bond pdb=" C1B NDP A2603 " pdb=" C2B NDP A2603 " ideal model delta sigma weight residual 1.575 1.286 0.289 3.70e-02 7.30e+02 6.10e+01 bond pdb=" C1B NDP D2603 " pdb=" C2B NDP D2603 " ideal model delta sigma weight residual 1.575 1.287 0.288 3.70e-02 7.30e+02 6.06e+01 bond pdb=" C2D NDP A2603 " pdb=" C3D NDP A2603 " ideal model delta sigma weight residual 1.545 1.265 0.280 3.60e-02 7.72e+02 6.05e+01 bond pdb=" C2D NDP D2603 " pdb=" C3D NDP D2603 " ideal model delta sigma weight residual 1.545 1.265 0.280 3.60e-02 7.72e+02 6.05e+01 bond pdb=" C2D NDP A2602 " pdb=" C3D NDP A2602 " ideal model delta sigma weight residual 1.545 1.268 0.277 3.60e-02 7.72e+02 5.92e+01 ... (remaining 14965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.14: 20368 6.14 - 12.28: 68 12.28 - 18.41: 16 18.41 - 24.55: 2 24.55 - 30.69: 2 Bond angle restraints: 20456 Sorted by residual: angle pdb=" C12 X5O D2601 " pdb=" C13 X5O D2601 " pdb=" C16 X5O D2601 " ideal model delta sigma weight residual 112.89 82.20 30.69 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C12 X5O A2601 " pdb=" C13 X5O A2601 " pdb=" C16 X5O A2601 " ideal model delta sigma weight residual 112.89 82.22 30.67 3.00e+00 1.11e-01 1.05e+02 angle pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " pdb=" PN NDP A2602 " ideal model delta sigma weight residual 107.74 124.36 -16.62 1.95e+00 2.62e-01 7.23e+01 angle pdb=" PA NDP D2602 " pdb=" O3 NDP D2602 " pdb=" PN NDP D2602 " ideal model delta sigma weight residual 107.74 124.34 -16.60 1.95e+00 2.62e-01 7.22e+01 angle pdb=" C14 X5O A2601 " pdb=" C13 X5O A2601 " pdb=" C16 X5O A2601 " ideal model delta sigma weight residual 112.13 133.18 -21.05 3.00e+00 1.11e-01 4.92e+01 ... (remaining 20451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 8454 35.94 - 71.88: 250 71.88 - 107.82: 24 107.82 - 143.76: 0 143.76 - 179.70: 2 Dihedral angle restraints: 8730 sinusoidal: 3224 harmonic: 5506 Sorted by residual: dihedral pdb=" C5B NDP D2602 " pdb=" O5B NDP D2602 " pdb=" PA NDP D2602 " pdb=" O3 NDP D2602 " ideal model delta sinusoidal sigma weight residual 175.04 -5.26 -179.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5B NDP A2602 " pdb=" O5B NDP A2602 " pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " ideal model delta sinusoidal sigma weight residual 175.04 -2.05 177.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA VAL D1973 " pdb=" C VAL D1973 " pdb=" N VAL D1974 " pdb=" CA VAL D1974 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2106 0.081 - 0.163: 208 0.163 - 0.244: 7 0.244 - 0.326: 1 0.326 - 0.407: 10 Chirality restraints: 2332 Sorted by residual: chirality pdb=" C2D NDP D2603 " pdb=" C1D NDP D2603 " pdb=" C3D NDP D2603 " pdb=" O2D NDP D2603 " both_signs ideal model delta sigma weight residual False -2.71 -2.30 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C2D NDP A2603 " pdb=" C1D NDP A2603 " pdb=" C3D NDP A2603 " pdb=" O2D NDP A2603 " both_signs ideal model delta sigma weight residual False -2.71 -2.31 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C3D NDP D2603 " pdb=" C2D NDP D2603 " pdb=" C4D NDP D2603 " pdb=" O3D NDP D2603 " both_signs ideal model delta sigma weight residual False -2.71 -2.31 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 2329 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1120 " -0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO D1121 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO D1121 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D1121 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1120 " 0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A1121 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A1121 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1121 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 991 " -0.020 2.00e-02 2.50e+03 1.23e-02 3.02e+00 pdb=" CG TYR A 991 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 991 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 991 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 991 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 991 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 991 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 991 " -0.002 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 527 2.71 - 3.26: 14661 3.26 - 3.80: 26628 3.80 - 4.35: 34067 4.35 - 4.90: 55454 Nonbonded interactions: 131337 Sorted by model distance: nonbonded pdb=" OE2 GLU D2042 " pdb=" NE2 GLN D2059 " model vdw 2.160 3.120 nonbonded pdb=" OE2 GLU A2042 " pdb=" NE2 GLN A2059 " model vdw 2.161 3.120 nonbonded pdb=" OH TYR A 891 " pdb=" OG1 THR A 923 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR D 891 " pdb=" OG1 THR D 923 " model vdw 2.163 3.040 nonbonded pdb=" OD2 ASP A1716 " pdb=" OG1 THR A1718 " model vdw 2.228 3.040 ... (remaining 131332 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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: 1.140 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.013 0.289 14970 Z= 0.423 Angle : 1.001 30.690 20456 Z= 0.473 Chirality : 0.052 0.407 2332 Planarity : 0.005 0.097 2628 Dihedral : 16.904 179.697 5194 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 22.53 % Favored : 77.47 % 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: -1.15 (0.18), residues: 1920 helix: -0.54 (0.19), residues: 666 sheet: -1.20 (0.27), residues: 342 loop : -0.59 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1807 HIS 0.006 0.001 HIS D1735 PHE 0.011 0.002 PHE D1005 TYR 0.027 0.002 TYR A 991 ARG 0.004 0.001 ARG A1538 Details of bonding type rmsd hydrogen bonds : bond 0.12907 ( 654) hydrogen bonds : angle 6.71979 ( 2052) covalent geometry : bond 0.01253 (14970) covalent geometry : angle 1.00142 (20456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.572 Fit side-chains REVERT: A 1644 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 1819 ARG cc_start: 0.7199 (ptt-90) cc_final: 0.6735 (ptt-90) REVERT: A 2051 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 1644 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 1819 ARG cc_start: 0.7187 (ptt-90) cc_final: 0.6731 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.4336 time to fit residues: 258.4878 Evaluate side-chains 145 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN A2059 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136505 restraints weight = 14738.204| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.46 r_work: 0.3417 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14970 Z= 0.130 Angle : 0.559 8.804 20456 Z= 0.278 Chirality : 0.042 0.155 2332 Planarity : 0.004 0.073 2628 Dihedral : 9.215 179.261 2170 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.57 % Allowed : 18.57 % Favored : 78.86 % 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: -0.52 (0.19), residues: 1920 helix: 0.37 (0.20), residues: 680 sheet: -1.35 (0.25), residues: 362 loop : -0.29 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1807 HIS 0.005 0.001 HIS A1674 PHE 0.008 0.001 PHE A1696 TYR 0.024 0.002 TYR A 991 ARG 0.004 0.000 ARG D2007 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 654) hydrogen bonds : angle 4.95627 ( 2052) covalent geometry : bond 0.00303 (14970) covalent geometry : angle 0.55916 (20456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.615 Fit side-chains REVERT: A 1644 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 1819 ARG cc_start: 0.7334 (ptt-90) cc_final: 0.6796 (ptt-90) REVERT: A 1843 MET cc_start: 0.8348 (ttt) cc_final: 0.8070 (ttm) REVERT: A 2104 MET cc_start: 0.8063 (mpp) cc_final: 0.7749 (mpt) REVERT: D 1644 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7238 (mt-10) REVERT: D 1819 ARG cc_start: 0.7263 (ptt-90) cc_final: 0.6698 (ptt-90) REVERT: D 1843 MET cc_start: 0.8315 (ttt) cc_final: 0.8024 (ttm) REVERT: D 2104 MET cc_start: 0.8029 (mpp) cc_final: 0.7744 (mpt) outliers start: 37 outliers final: 11 residues processed: 190 average time/residue: 1.3547 time to fit residues: 281.7862 Evaluate side-chains 158 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1609 SER Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1609 SER Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2070 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 188 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1902 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN D1902 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.171813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133807 restraints weight = 14729.591| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.63 r_work: 0.3362 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14970 Z= 0.216 Angle : 0.610 6.998 20456 Z= 0.310 Chirality : 0.045 0.191 2332 Planarity : 0.004 0.063 2628 Dihedral : 8.994 172.379 2170 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.82 % Allowed : 17.87 % Favored : 78.30 % 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: -0.45 (0.19), residues: 1920 helix: 0.45 (0.20), residues: 678 sheet: -1.34 (0.27), residues: 322 loop : -0.33 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1807 HIS 0.004 0.001 HIS D 920 PHE 0.013 0.002 PHE D1005 TYR 0.032 0.002 TYR A 991 ARG 0.004 0.001 ARG D2007 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 654) hydrogen bonds : angle 5.09966 ( 2052) covalent geometry : bond 0.00512 (14970) covalent geometry : angle 0.61017 (20456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.552 Fit side-chains REVERT: A 1085 ARG cc_start: 0.8007 (mpt-90) cc_final: 0.7717 (mpp80) REVERT: A 1644 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 1865 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6323 (tt) REVERT: A 2104 MET cc_start: 0.8131 (mpp) cc_final: 0.7819 (mpt) REVERT: D 1085 ARG cc_start: 0.8002 (mpt-90) cc_final: 0.7707 (mpp80) REVERT: D 1614 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8520 (ptt) REVERT: D 1644 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7306 (mt-10) REVERT: D 1801 ASN cc_start: 0.6649 (m110) cc_final: 0.6427 (m110) REVERT: D 2104 MET cc_start: 0.8085 (mpp) cc_final: 0.7799 (mpt) outliers start: 55 outliers final: 21 residues processed: 207 average time/residue: 1.2323 time to fit residues: 282.4445 Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1118 CYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 931 VAL Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1614 MET Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2070 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 164 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 133 optimal weight: 0.0670 chunk 189 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1458 ASN A1835 GLN A1902 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1458 ASN D1835 GLN D1902 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.176920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139985 restraints weight = 14743.724| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.68 r_work: 0.3422 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14970 Z= 0.114 Angle : 0.524 6.768 20456 Z= 0.264 Chirality : 0.041 0.149 2332 Planarity : 0.003 0.054 2628 Dihedral : 8.458 173.013 2170 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.29 % Allowed : 19.19 % Favored : 78.51 % 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: -0.20 (0.19), residues: 1920 helix: 0.75 (0.20), residues: 682 sheet: -1.27 (0.26), residues: 362 loop : -0.17 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1807 HIS 0.004 0.001 HIS A1674 PHE 0.010 0.001 PHE D2109 TYR 0.024 0.002 TYR D 991 ARG 0.002 0.000 ARG D1051 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 654) hydrogen bonds : angle 4.61279 ( 2052) covalent geometry : bond 0.00271 (14970) covalent geometry : angle 0.52406 (20456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.565 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7978 (mpt-90) cc_final: 0.7674 (mpp80) REVERT: A 1644 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 1819 ARG cc_start: 0.7381 (ptt-90) cc_final: 0.7063 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6236 (tt) REVERT: A 1940 GLN cc_start: 0.8081 (mt0) cc_final: 0.7825 (mt0) REVERT: A 1980 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7165 (tp) REVERT: A 2004 ARG cc_start: 0.7601 (ttt-90) cc_final: 0.7320 (ttt-90) REVERT: A 2051 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7558 (mp0) REVERT: A 2104 MET cc_start: 0.8077 (mpp) cc_final: 0.7787 (mpt) REVERT: D 1085 ARG cc_start: 0.7979 (mpt-90) cc_final: 0.7685 (mpp80) REVERT: D 1644 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7062 (mt-10) REVERT: D 1819 ARG cc_start: 0.7234 (ptt-90) cc_final: 0.6912 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6247 (tt) REVERT: D 1980 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7173 (tp) REVERT: D 2004 ARG cc_start: 0.7696 (ttt-90) cc_final: 0.7311 (ttt-90) REVERT: D 2104 MET cc_start: 0.8020 (mpp) cc_final: 0.7714 (mpt) outliers start: 33 outliers final: 9 residues processed: 189 average time/residue: 1.3164 time to fit residues: 272.8546 Evaluate side-chains 161 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 152 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1746 ASN A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1746 ASN D1835 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.173847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137137 restraints weight = 14713.942| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.53 r_work: 0.3374 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14970 Z= 0.160 Angle : 0.558 7.224 20456 Z= 0.282 Chirality : 0.043 0.161 2332 Planarity : 0.004 0.050 2628 Dihedral : 8.306 169.266 2170 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.13 % Allowed : 18.22 % Favored : 78.65 % 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: -0.20 (0.19), residues: 1920 helix: 0.71 (0.20), residues: 688 sheet: -1.18 (0.27), residues: 338 loop : -0.22 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1807 HIS 0.003 0.001 HIS D1516 PHE 0.011 0.001 PHE A1005 TYR 0.030 0.002 TYR A 991 ARG 0.002 0.000 ARG A1664 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 654) hydrogen bonds : angle 4.74771 ( 2052) covalent geometry : bond 0.00379 (14970) covalent geometry : angle 0.55769 (20456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.615 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7994 (mpt-90) cc_final: 0.7671 (mpp80) REVERT: A 1644 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 1819 ARG cc_start: 0.7434 (ptt-90) cc_final: 0.7090 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6225 (tt) REVERT: A 1931 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7098 (ttp-110) REVERT: A 1980 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7213 (tp) REVERT: A 2004 ARG cc_start: 0.7656 (ttt-90) cc_final: 0.7359 (ttt-90) REVERT: A 2051 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7496 (mp0) REVERT: A 2104 MET cc_start: 0.8135 (mpp) cc_final: 0.7842 (mpt) REVERT: D 1085 ARG cc_start: 0.7994 (mpt-90) cc_final: 0.7676 (mpp80) REVERT: D 1644 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7199 (mt-10) REVERT: D 1819 ARG cc_start: 0.7443 (ptt-90) cc_final: 0.7107 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6220 (tt) REVERT: D 1931 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7082 (ttp-110) REVERT: D 1980 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7190 (tp) REVERT: D 2104 MET cc_start: 0.8078 (mpp) cc_final: 0.7789 (mpt) outliers start: 45 outliers final: 21 residues processed: 191 average time/residue: 1.3252 time to fit residues: 277.6710 Evaluate side-chains 176 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1523 LYS Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 189 optimal weight: 0.0970 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 171 optimal weight: 0.0010 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.178583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142565 restraints weight = 14908.379| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.55 r_work: 0.3447 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14970 Z= 0.106 Angle : 0.513 7.821 20456 Z= 0.258 Chirality : 0.041 0.155 2332 Planarity : 0.003 0.046 2628 Dihedral : 7.955 175.817 2170 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.71 % Allowed : 18.78 % Favored : 78.51 % 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: -0.01 (0.20), residues: 1920 helix: 0.89 (0.21), residues: 682 sheet: -1.13 (0.26), residues: 362 loop : -0.05 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1424 HIS 0.003 0.001 HIS D1674 PHE 0.010 0.001 PHE D2109 TYR 0.022 0.001 TYR D 991 ARG 0.003 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 654) hydrogen bonds : angle 4.43691 ( 2052) covalent geometry : bond 0.00253 (14970) covalent geometry : angle 0.51341 (20456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.650 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7917 (mpt-90) cc_final: 0.7629 (mpp80) REVERT: A 1644 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6917 (mt-10) REVERT: A 1739 LYS cc_start: 0.7438 (mmtm) cc_final: 0.7230 (mttp) REVERT: A 1819 ARG cc_start: 0.7397 (ptt-90) cc_final: 0.7052 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6051 (tp) REVERT: A 1940 GLN cc_start: 0.8072 (mt0) cc_final: 0.7807 (mt0) REVERT: A 1980 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 2004 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7386 (ttt-90) REVERT: A 2051 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7468 (mp0) REVERT: A 2104 MET cc_start: 0.7984 (mpp) cc_final: 0.7712 (mpt) REVERT: D 1085 ARG cc_start: 0.7938 (mpt-90) cc_final: 0.7645 (mpp80) REVERT: D 1644 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6938 (mt-10) REVERT: D 1819 ARG cc_start: 0.7282 (ptt-90) cc_final: 0.6936 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6198 (tp) REVERT: D 1940 GLN cc_start: 0.8076 (mt0) cc_final: 0.7818 (mt0) REVERT: D 1980 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7257 (tp) REVERT: D 2004 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.7289 (ttt-90) REVERT: D 2104 MET cc_start: 0.7905 (mpp) cc_final: 0.7620 (mpt) outliers start: 39 outliers final: 23 residues processed: 197 average time/residue: 1.2545 time to fit residues: 272.4178 Evaluate side-chains 176 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1523 LYS Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 131 optimal weight: 20.0000 chunk 64 optimal weight: 0.0970 chunk 173 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1746 ASN A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1746 ASN ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137404 restraints weight = 14952.563| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.50 r_work: 0.3395 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14970 Z= 0.149 Angle : 0.552 8.036 20456 Z= 0.277 Chirality : 0.043 0.160 2332 Planarity : 0.004 0.044 2628 Dihedral : 7.825 173.523 2170 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.78 % Allowed : 18.85 % Favored : 78.37 % 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: 0.05 (0.19), residues: 1920 helix: 0.95 (0.21), residues: 672 sheet: -1.20 (0.26), residues: 362 loop : 0.03 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1424 HIS 0.004 0.001 HIS A1516 PHE 0.010 0.001 PHE A1005 TYR 0.029 0.002 TYR D 991 ARG 0.003 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 654) hydrogen bonds : angle 4.61322 ( 2052) covalent geometry : bond 0.00354 (14970) covalent geometry : angle 0.55156 (20456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.460 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7960 (mpt-90) cc_final: 0.7628 (mpp80) REVERT: A 1097 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8372 (tp) REVERT: A 1644 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 1767 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8446 (mt) REVERT: A 1819 ARG cc_start: 0.7265 (ptt-90) cc_final: 0.6914 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6162 (tt) REVERT: A 1931 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7277 (ttp-110) REVERT: A 1980 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7233 (tp) REVERT: A 2051 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7506 (mp0) REVERT: A 2104 MET cc_start: 0.8036 (mpp) cc_final: 0.7765 (mpt) REVERT: D 1085 ARG cc_start: 0.7961 (mpt-90) cc_final: 0.7635 (mpp80) REVERT: D 1097 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8382 (tp) REVERT: D 1644 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7088 (mt-10) REVERT: D 1819 ARG cc_start: 0.7266 (ptt-90) cc_final: 0.6924 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6172 (tt) REVERT: D 1931 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7264 (ttp-110) REVERT: D 1980 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7226 (tp) REVERT: D 2004 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.7187 (ttt-90) REVERT: D 2104 MET cc_start: 0.7988 (mpp) cc_final: 0.7718 (mpt) outliers start: 40 outliers final: 23 residues processed: 184 average time/residue: 1.2590 time to fit residues: 255.1599 Evaluate side-chains 176 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1523 LYS Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.172105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133984 restraints weight = 14705.611| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.80 r_work: 0.3350 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14970 Z= 0.199 Angle : 0.601 8.181 20456 Z= 0.303 Chirality : 0.044 0.176 2332 Planarity : 0.004 0.044 2628 Dihedral : 7.995 172.896 2170 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.99 % Allowed : 18.64 % Favored : 78.37 % 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: -0.06 (0.19), residues: 1920 helix: 0.80 (0.20), residues: 670 sheet: -1.23 (0.26), residues: 362 loop : -0.00 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1424 HIS 0.004 0.001 HIS A1516 PHE 0.012 0.002 PHE D1005 TYR 0.031 0.002 TYR A 991 ARG 0.004 0.000 ARG D1082 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 654) hydrogen bonds : angle 4.86186 ( 2052) covalent geometry : bond 0.00469 (14970) covalent geometry : angle 0.60103 (20456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.590 Fit side-chains REVERT: A 1097 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 1644 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 1767 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 1865 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6294 (tt) REVERT: A 1980 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7247 (tp) REVERT: A 2004 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.7310 (ttt-90) REVERT: A 2051 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7398 (mp0) REVERT: A 2104 MET cc_start: 0.8186 (mpp) cc_final: 0.7914 (mpt) REVERT: D 1097 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 1865 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6294 (tt) REVERT: D 1980 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7230 (tp) REVERT: D 1996 TYR cc_start: 0.7853 (t80) cc_final: 0.7612 (t80) REVERT: D 2004 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7253 (ttt-90) outliers start: 43 outliers final: 29 residues processed: 189 average time/residue: 1.2526 time to fit residues: 261.2144 Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1523 LYS Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1601 MET Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2000 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 171 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 86 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.176419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139399 restraints weight = 14765.512| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.63 r_work: 0.3425 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14970 Z= 0.118 Angle : 0.539 8.716 20456 Z= 0.270 Chirality : 0.042 0.163 2332 Planarity : 0.003 0.043 2628 Dihedral : 7.770 178.412 2170 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.43 % Allowed : 19.05 % Favored : 78.51 % 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 (0.20), residues: 1920 helix: 0.97 (0.21), residues: 672 sheet: -1.14 (0.27), residues: 362 loop : 0.06 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1807 HIS 0.004 0.001 HIS A1516 PHE 0.007 0.001 PHE D1791 TYR 0.025 0.002 TYR A 991 ARG 0.002 0.000 ARG A1664 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 654) hydrogen bonds : angle 4.52088 ( 2052) covalent geometry : bond 0.00282 (14970) covalent geometry : angle 0.53863 (20456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.484 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7494 (mpp80) REVERT: A 1097 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 1644 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7055 (mt-10) REVERT: A 1819 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.6914 (ptt-90) REVERT: A 1843 MET cc_start: 0.8304 (ttt) cc_final: 0.7991 (ttm) REVERT: A 1865 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6157 (tt) REVERT: A 1980 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7250 (tp) REVERT: A 1989 GLN cc_start: 0.6687 (mt0) cc_final: 0.6369 (mt0) REVERT: A 2004 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7310 (ttt-90) REVERT: A 2051 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7286 (mp0) REVERT: A 2104 MET cc_start: 0.8045 (mpp) cc_final: 0.7773 (mpt) REVERT: D 1085 ARG cc_start: 0.7825 (mpt-90) cc_final: 0.7560 (mpp80) REVERT: D 1097 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8341 (tp) REVERT: D 1644 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6965 (mt-10) REVERT: D 1819 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.7040 (ptt-90) REVERT: D 1843 MET cc_start: 0.8328 (ttt) cc_final: 0.8027 (ttm) REVERT: D 1865 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6121 (tt) REVERT: D 1940 GLN cc_start: 0.8191 (mt0) cc_final: 0.7933 (mt0) REVERT: D 2004 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7175 (ttt-90) outliers start: 35 outliers final: 22 residues processed: 185 average time/residue: 1.2195 time to fit residues: 248.9497 Evaluate side-chains 179 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1085 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2000 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 175 optimal weight: 8.9990 chunk 168 optimal weight: 0.1980 chunk 41 optimal weight: 0.0070 chunk 26 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 0.0000 chunk 10 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1746 ASN A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1746 ASN D1835 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144934 restraints weight = 14871.431| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.79 r_work: 0.3490 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14970 Z= 0.099 Angle : 0.521 8.607 20456 Z= 0.262 Chirality : 0.041 0.154 2332 Planarity : 0.003 0.043 2628 Dihedral : 7.456 172.311 2170 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.81 % Allowed : 20.24 % Favored : 77.96 % 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: 0.15 (0.20), residues: 1920 helix: 0.97 (0.21), residues: 686 sheet: -0.96 (0.27), residues: 362 loop : 0.04 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1807 HIS 0.004 0.001 HIS D1674 PHE 0.008 0.001 PHE A1791 TYR 0.021 0.001 TYR D 991 ARG 0.002 0.000 ARG D1953 Details of bonding type rmsd hydrogen bonds : bond 0.02676 ( 654) hydrogen bonds : angle 4.26536 ( 2052) covalent geometry : bond 0.00236 (14970) covalent geometry : angle 0.52067 (20456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.436 Fit side-chains REVERT: A 881 ASP cc_start: 0.8202 (t0) cc_final: 0.7965 (t70) REVERT: A 1085 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7502 (mpp80) REVERT: A 1819 ARG cc_start: 0.7364 (ptt-90) cc_final: 0.7018 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.6032 (tp) REVERT: A 1940 GLN cc_start: 0.8117 (mt0) cc_final: 0.7820 (mt0) REVERT: A 1980 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7239 (tp) REVERT: A 1989 GLN cc_start: 0.6671 (mt0) cc_final: 0.6301 (mt0) REVERT: A 2004 ARG cc_start: 0.7581 (ttt-90) cc_final: 0.7230 (ttt-90) REVERT: A 2104 MET cc_start: 0.7833 (mpp) cc_final: 0.7558 (mpt) REVERT: D 881 ASP cc_start: 0.8214 (t0) cc_final: 0.7979 (t70) REVERT: D 1085 ARG cc_start: 0.7706 (mpt-90) cc_final: 0.7485 (mpp80) REVERT: D 1819 ARG cc_start: 0.7292 (ptt-90) cc_final: 0.6937 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6019 (tp) REVERT: D 1940 GLN cc_start: 0.8131 (mt0) cc_final: 0.7828 (mt0) REVERT: D 1989 GLN cc_start: 0.6678 (mt0) cc_final: 0.6302 (mt0) REVERT: D 2093 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7964 (mt-10) outliers start: 26 outliers final: 18 residues processed: 178 average time/residue: 1.2370 time to fit residues: 242.4922 Evaluate side-chains 174 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1085 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2000 LEU Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 49 optimal weight: 0.3980 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.176181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138533 restraints weight = 14840.984| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.81 r_work: 0.3416 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14970 Z= 0.137 Angle : 0.554 8.317 20456 Z= 0.280 Chirality : 0.042 0.168 2332 Planarity : 0.004 0.044 2628 Dihedral : 7.634 173.454 2170 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.81 % Allowed : 20.38 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.20), residues: 1920 helix: 1.05 (0.21), residues: 672 sheet: -1.03 (0.27), residues: 362 loop : 0.13 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1807 HIS 0.005 0.001 HIS A1516 PHE 0.009 0.001 PHE D1005 TYR 0.028 0.002 TYR A 991 ARG 0.004 0.000 ARG A1931 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 654) hydrogen bonds : angle 4.45742 ( 2052) covalent geometry : bond 0.00325 (14970) covalent geometry : angle 0.55396 (20456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12060.70 seconds wall clock time: 207 minutes 40.32 seconds (12460.32 seconds total)