Starting phenix.real_space_refine on Fri Jun 13 11:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gkc_40182/06_2025/8gkc_40182_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gkc_40182/06_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_40182/06_2025/8gkc_40182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gkc_40182/06_2025/8gkc_40182.map" model { file = "/net/cci-nas-00/data/ceres_data/8gkc_40182/06_2025/8gkc_40182_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gkc_40182/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.11, per 1000 atoms: 0.62 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: 4.07 Conformation dependent library (CDL) restraints added in 2.1 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: 2.82 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: 7.86 Time building geometry restraints manager: 4.70 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: 0.08 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.000 ------------------------------------------------------------------------------- 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 : 1.528 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: 1.5014 time to fit residues: 270.0848 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 : 1.484 ------------------------------------------------------------------------------- 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 = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136497 restraints weight = 14738.205| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.46 r_work: 0.3416 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 1.689 Fit side-chains REVERT: A 1644 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7174 (mt-10) REVERT: A 1819 ARG cc_start: 0.7335 (ptt-90) cc_final: 0.6797 (ptt-90) REVERT: A 1843 MET cc_start: 0.8347 (ttt) cc_final: 0.8070 (ttm) REVERT: A 2104 MET cc_start: 0.8066 (mpp) cc_final: 0.7753 (mpt) REVERT: D 1644 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7239 (mt-10) REVERT: D 1819 ARG cc_start: 0.7263 (ptt-90) cc_final: 0.6699 (ptt-90) REVERT: D 1843 MET cc_start: 0.8317 (ttt) cc_final: 0.8025 (ttm) REVERT: D 2104 MET cc_start: 0.8032 (mpp) cc_final: 0.7747 (mpt) outliers start: 37 outliers final: 11 residues processed: 190 average time/residue: 1.4082 time to fit residues: 292.4892 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 : 1.625 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 188 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133325 restraints weight = 14729.565| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.70 r_work: 0.3355 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14970 Z= 0.222 Angle : 0.619 6.885 20456 Z= 0.315 Chirality : 0.045 0.197 2332 Planarity : 0.004 0.063 2628 Dihedral : 8.963 170.801 2170 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.03 % Allowed : 17.32 % 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: -0.48 (0.19), residues: 1920 helix: 0.41 (0.20), residues: 684 sheet: -1.35 (0.27), residues: 322 loop : -0.35 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1807 HIS 0.004 0.001 HIS D 920 PHE 0.014 0.002 PHE A1005 TYR 0.033 0.002 TYR D 991 ARG 0.005 0.001 ARG D2007 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 654) hydrogen bonds : angle 5.12876 ( 2052) covalent geometry : bond 0.00527 (14970) covalent geometry : angle 0.61870 (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 229 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.659 Fit side-chains REVERT: A 1085 ARG cc_start: 0.8006 (mpt-90) cc_final: 0.7716 (mpp80) REVERT: A 1614 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8507 (ptt) REVERT: A 1644 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 1865 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6296 (tt) REVERT: A 2104 MET cc_start: 0.8146 (mpp) cc_final: 0.7841 (mpt) REVERT: D 1085 ARG cc_start: 0.7992 (mpt-90) cc_final: 0.7704 (mpp80) REVERT: D 1614 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8509 (ptt) REVERT: D 1644 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 1801 ASN cc_start: 0.6617 (m110) cc_final: 0.6417 (m110) REVERT: D 2104 MET cc_start: 0.8100 (mpp) cc_final: 0.7819 (mpt) outliers start: 58 outliers final: 23 residues processed: 211 average time/residue: 1.2278 time to fit residues: 285.6693 Evaluate side-chains 186 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 931 VAL 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 1614 MET 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 1118 CYS 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: 1.9990 chunk 12 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 86 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 133 optimal weight: 0.0980 chunk 189 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1458 ASN A1835 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1458 ASN D1835 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 = 0.3960 r_free = 0.3960 target = 0.176703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139678 restraints weight = 14751.804| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.71 r_work: 0.3425 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1460 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= 0.115 Angle : 0.525 6.626 20456 Z= 0.264 Chirality : 0.041 0.144 2332 Planarity : 0.003 0.054 2628 Dihedral : 8.442 173.384 2170 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.16 % Allowed : 19.19 % 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: 0.75 (0.20), residues: 682 sheet: -1.28 (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 D1664 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 654) hydrogen bonds : angle 4.62585 ( 2052) covalent geometry : bond 0.00270 (14970) covalent geometry : angle 0.52468 (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 194 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.873 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7962 (mpt-90) cc_final: 0.7656 (mpp80) REVERT: A 1644 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7117 (mt-10) REVERT: A 1819 ARG cc_start: 0.7235 (ptt-90) cc_final: 0.6901 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6273 (tt) REVERT: A 1940 GLN cc_start: 0.8077 (mt0) cc_final: 0.7823 (mt0) REVERT: A 1980 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7163 (tp) REVERT: A 2051 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7560 (mp0) REVERT: A 2104 MET cc_start: 0.8089 (mpp) cc_final: 0.7802 (mpt) REVERT: D 1085 ARG cc_start: 0.7977 (mpt-90) cc_final: 0.7684 (mpp80) REVERT: D 1644 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7075 (mt-10) REVERT: D 1819 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.6905 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6255 (tt) REVERT: D 1980 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7175 (tp) REVERT: D 2004 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.7343 (ttt-90) REVERT: D 2104 MET cc_start: 0.8018 (mpp) cc_final: 0.7708 (mpt) outliers start: 31 outliers final: 9 residues processed: 187 average time/residue: 2.1517 time to fit residues: 442.4304 Evaluate side-chains 162 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 9.9990 chunk 114 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 131 optimal weight: 50.0000 chunk 156 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1746 ASN A1835 GLN A1902 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1746 ASN D1835 GLN D1902 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137632 restraints weight = 14746.912| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.70 r_work: 0.3409 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1504 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= 0.138 Angle : 0.538 7.245 20456 Z= 0.272 Chirality : 0.042 0.157 2332 Planarity : 0.004 0.049 2628 Dihedral : 8.226 170.597 2170 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.13 % Allowed : 18.08 % Favored : 78.79 % 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 (0.19), residues: 1920 helix: 0.76 (0.20), residues: 688 sheet: -1.26 (0.26), residues: 362 loop : -0.12 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1807 HIS 0.003 0.001 HIS A1735 PHE 0.009 0.001 PHE A1005 TYR 0.028 0.002 TYR A 991 ARG 0.002 0.000 ARG D1664 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 654) hydrogen bonds : angle 4.64886 ( 2052) covalent geometry : bond 0.00328 (14970) covalent geometry : angle 0.53822 (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 203 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.700 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7952 (mpt-90) cc_final: 0.7640 (mpp80) REVERT: A 1644 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7137 (mt-10) REVERT: A 1819 ARG cc_start: 0.7391 (ptt-90) cc_final: 0.7052 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6216 (tt) REVERT: A 1940 GLN cc_start: 0.8063 (mt0) cc_final: 0.7801 (mt0) REVERT: A 1980 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7174 (tp) REVERT: A 2104 MET cc_start: 0.8069 (mpp) cc_final: 0.7769 (mpt) REVERT: D 1085 ARG cc_start: 0.7965 (mpt-90) cc_final: 0.7665 (mpp80) REVERT: D 1644 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7117 (mt-10) REVERT: D 1865 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6210 (tt) REVERT: D 1980 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7204 (tp) REVERT: D 2104 MET cc_start: 0.8010 (mpp) cc_final: 0.7712 (mpt) outliers start: 45 outliers final: 20 residues processed: 194 average time/residue: 1.3381 time to fit residues: 284.6540 Evaluate side-chains 171 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 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 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 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: 0.0370 chunk 66 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 171 optimal weight: 0.5980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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** ** A2103 HIS ** 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 = 0.3973 r_free = 0.3973 target = 0.178096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142056 restraints weight = 14914.712| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.54 r_work: 0.3440 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1692 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= 0.108 Angle : 0.517 7.783 20456 Z= 0.259 Chirality : 0.041 0.154 2332 Planarity : 0.003 0.046 2628 Dihedral : 7.912 174.597 2170 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.64 % Allowed : 19.05 % 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: 0.01 (0.20), residues: 1920 helix: 0.91 (0.21), residues: 682 sheet: -1.15 (0.26), residues: 362 loop : -0.04 (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 0.009 0.001 PHE D2109 TYR 0.023 0.002 TYR A 991 ARG 0.003 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 654) hydrogen bonds : angle 4.42999 ( 2052) covalent geometry : bond 0.00259 (14970) covalent geometry : angle 0.51669 (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 200 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 1085 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7641 (mpp80) REVERT: A 1644 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 1739 LYS cc_start: 0.7449 (mmtm) cc_final: 0.7237 (mttp) REVERT: A 1819 ARG cc_start: 0.7286 (ptt-90) cc_final: 0.6923 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6064 (tp) REVERT: A 1931 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7164 (ttp-110) REVERT: A 1940 GLN cc_start: 0.8068 (mt0) cc_final: 0.7794 (mt0) REVERT: A 1980 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7235 (tp) REVERT: A 2093 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 2104 MET cc_start: 0.7985 (mpp) cc_final: 0.7715 (mpt) REVERT: D 1085 ARG cc_start: 0.7953 (mpt-90) cc_final: 0.7662 (mpp80) REVERT: D 1644 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 1865 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6210 (tp) REVERT: D 1931 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7156 (ttp-110) REVERT: D 1940 GLN cc_start: 0.8060 (mt0) cc_final: 0.7799 (mt0) REVERT: D 1980 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7240 (tp) REVERT: D 2004 ARG cc_start: 0.7642 (ttt-90) cc_final: 0.7292 (ttt-90) REVERT: D 2104 MET cc_start: 0.7913 (mpp) cc_final: 0.7626 (mpt) outliers start: 38 outliers final: 23 residues processed: 193 average time/residue: 1.3187 time to fit residues: 279.9773 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 : 1.646 ------------------------------------------------------------------------------- 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 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 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 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 1789 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: 0.9990 chunk 131 optimal weight: 20.0000 chunk 64 optimal weight: 0.4980 chunk 173 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 40.0000 chunk 95 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.173885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135960 restraints weight = 14925.858| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.77 r_work: 0.3380 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14970 Z= 0.164 Angle : 0.562 6.957 20456 Z= 0.284 Chirality : 0.043 0.164 2332 Planarity : 0.004 0.043 2628 Dihedral : 7.803 169.547 2170 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.06 % Allowed : 18.57 % 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: 0.02 (0.19), residues: 1920 helix: 0.92 (0.20), residues: 670 sheet: -1.13 (0.28), residues: 338 loop : -0.07 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1424 HIS 0.004 0.001 HIS A1516 PHE 0.011 0.001 PHE A1005 TYR 0.029 0.002 TYR A 991 ARG 0.004 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 654) hydrogen bonds : angle 4.67437 ( 2052) covalent geometry : bond 0.00389 (14970) covalent geometry : angle 0.56230 (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 192 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 1085 ARG cc_start: 0.7969 (mpt-90) cc_final: 0.7620 (mpp80) REVERT: A 1097 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 1644 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 1819 ARG cc_start: 0.7273 (ptt-90) cc_final: 0.6920 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6202 (tt) REVERT: A 1931 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7117 (ttp-110) REVERT: A 1980 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 2093 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 2104 MET cc_start: 0.8094 (mpp) cc_final: 0.7810 (mpt) REVERT: D 1085 ARG cc_start: 0.7971 (mpt-90) cc_final: 0.7634 (mpp80) REVERT: D 1097 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8370 (tp) REVERT: D 1644 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7140 (mt-10) REVERT: D 1865 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6210 (tt) REVERT: D 1931 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7091 (ttp-110) REVERT: D 1980 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7216 (tp) REVERT: D 2104 MET cc_start: 0.8057 (mpp) cc_final: 0.7785 (mpt) outliers start: 44 outliers final: 24 residues processed: 185 average time/residue: 1.3220 time to fit residues: 269.0752 Evaluate side-chains 172 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** ** A2103 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.172765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134818 restraints weight = 14698.061| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.76 r_work: 0.3370 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14970 Z= 0.186 Angle : 0.589 8.270 20456 Z= 0.297 Chirality : 0.044 0.168 2332 Planarity : 0.004 0.044 2628 Dihedral : 7.907 171.214 2170 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.13 % Allowed : 18.85 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.19), residues: 1920 helix: 0.82 (0.20), residues: 670 sheet: -1.13 (0.28), residues: 338 loop : -0.08 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1424 HIS 0.004 0.001 HIS A1516 PHE 0.011 0.002 PHE A1005 TYR 0.031 0.002 TYR D 991 ARG 0.003 0.000 ARG D1082 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 654) hydrogen bonds : angle 4.80988 ( 2052) covalent geometry : bond 0.00440 (14970) covalent geometry : angle 0.58866 (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 200 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.591 Fit side-chains REVERT: A 1097 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 1644 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 1739 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7673 (mmtm) REVERT: A 1767 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 1819 ARG cc_start: 0.7297 (ptt-90) cc_final: 0.7030 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6439 (tt) REVERT: A 1931 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7069 (ttp-110) REVERT: A 1980 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7251 (tp) REVERT: A 2051 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7611 (mp0) REVERT: A 2093 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 2104 MET cc_start: 0.8171 (mpp) cc_final: 0.7896 (mpt) REVERT: D 1097 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8308 (tp) REVERT: D 1644 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7241 (mt-10) REVERT: D 1865 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6291 (tt) REVERT: D 1931 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7049 (ttp-110) REVERT: D 1980 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7276 (tp) REVERT: D 2004 ARG cc_start: 0.7619 (ttt-90) cc_final: 0.7360 (ttt-90) REVERT: D 2104 MET cc_start: 0.8144 (mpp) cc_final: 0.7869 (mpt) outliers start: 45 outliers final: 28 residues processed: 190 average time/residue: 1.3497 time to fit residues: 282.2042 Evaluate side-chains 185 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 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 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 1601 MET 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 1739 LYS 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 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 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: 0.8980 chunk 133 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** A2103 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137572 restraints weight = 14723.833| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.81 r_work: 0.3394 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1688 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 8.459 20456 Z= 0.278 Chirality : 0.042 0.165 2332 Planarity : 0.004 0.044 2628 Dihedral : 7.723 171.797 2170 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.78 % Allowed : 19.05 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1920 helix: 0.89 (0.20), residues: 672 sheet: -1.19 (0.26), residues: 362 loop : 0.04 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1807 HIS 0.004 0.001 HIS D1516 PHE 0.026 0.001 PHE D2109 TYR 0.028 0.002 TYR D 991 ARG 0.002 0.000 ARG D1953 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 654) hydrogen bonds : angle 4.63352 ( 2052) covalent geometry : bond 0.00327 (14970) covalent geometry : angle 0.55425 (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 193 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.672 Fit side-chains REVERT: A 881 ASP cc_start: 0.8326 (t0) cc_final: 0.8092 (t70) REVERT: A 1085 ARG cc_start: 0.7845 (mpt-90) cc_final: 0.7566 (mpp80) REVERT: A 1097 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 1644 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 1767 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 1819 ARG cc_start: 0.7274 (ptt-90) cc_final: 0.6922 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6200 (tt) REVERT: A 1931 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7112 (ttp-110) REVERT: A 1980 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7207 (tp) REVERT: A 2051 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7631 (mp0) REVERT: A 2093 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 2104 MET cc_start: 0.8103 (mpp) cc_final: 0.7834 (mpt) REVERT: A 2109 PHE cc_start: 0.8306 (p90) cc_final: 0.8104 (p90) REVERT: D 1085 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7573 (mpp80) REVERT: D 1097 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8326 (tp) REVERT: D 1644 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7156 (mt-10) REVERT: D 1865 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6160 (tt) REVERT: D 1931 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7096 (ttp-110) REVERT: D 2004 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7383 (ttt-90) REVERT: D 2051 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7565 (mp0) REVERT: D 2104 MET cc_start: 0.8073 (mpp) cc_final: 0.7819 (mpt) outliers start: 40 outliers final: 27 residues processed: 187 average time/residue: 1.3333 time to fit residues: 274.2165 Evaluate side-chains 182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 1767 LEU 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 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 1085 ARG 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 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0362 > 50: distance: 7 - 139: 7.383 distance: 10 - 136: 3.227 distance: 84 - 85: 7.844 distance: 85 - 86: 9.390 distance: 86 - 87: 9.820 distance: 86 - 89: 3.478 distance: 90 - 91: 7.680 distance: 90 - 93: 5.584 distance: 91 - 92: 9.562 distance: 91 - 97: 11.749 distance: 93 - 94: 7.671 distance: 94 - 95: 6.494 distance: 94 - 96: 11.605 distance: 97 - 98: 18.676 distance: 98 - 99: 8.027 distance: 98 - 101: 22.622 distance: 99 - 100: 13.591 distance: 99 - 102: 7.860 distance: 102 - 103: 30.622 distance: 103 - 104: 19.325 distance: 104 - 105: 16.702 distance: 106 - 107: 21.715 distance: 107 - 108: 25.159 distance: 107 - 110: 20.256 distance: 108 - 109: 4.446 distance: 108 - 111: 16.241 distance: 111 - 112: 15.921 distance: 112 - 113: 9.718 distance: 112 - 115: 18.722 distance: 113 - 114: 16.632 distance: 113 - 116: 6.032 distance: 116 - 117: 5.991 distance: 116 - 122: 13.235 distance: 117 - 118: 21.401 distance: 117 - 120: 12.385 distance: 118 - 119: 22.140 distance: 118 - 123: 27.831 distance: 120 - 121: 14.024 distance: 121 - 122: 15.915 distance: 123 - 124: 20.602 distance: 124 - 125: 12.178 distance: 124 - 127: 29.355 distance: 125 - 126: 7.740 distance: 125 - 128: 10.811 distance: 128 - 129: 9.442 distance: 129 - 130: 6.455 distance: 129 - 132: 10.679 distance: 130 - 131: 16.227 distance: 130 - 136: 9.094 distance: 132 - 133: 4.612 distance: 133 - 134: 9.002 distance: 133 - 135: 9.510 distance: 136 - 137: 3.849 distance: 137 - 140: 7.782 distance: 138 - 139: 3.809 distance: 138 - 144: 4.012 distance: 140 - 141: 6.905 distance: 141 - 142: 6.676 distance: 142 - 143: 6.593