Starting phenix.real_space_refine on Sat Jun 14 23:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyi_28690/06_2025/8eyi_28690_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.150 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 63 5.16 5 C 10307 2.51 5 N 2865 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 16252 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 7150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7150 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 47, 'TRANS': 913} Chain breaks: 2 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "F" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 8910 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 64, 'TRANS': 1146} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 249 Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.13, per 1000 atoms: 0.56 Number of scatterers: 16252 At special positions: 0 Unit cell: (161.71, 105.06, 156.56, 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 63 16.00 P 12 15.00 O 3005 8.00 N 2865 7.00 C 10307 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: 4.00 Conformation dependent library (CDL) restraints added in 2.1 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3986 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 22 sheets defined 38.5% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'E' and resid 872 through 876 Processing helix chain 'E' and resid 887 through 904 Processing helix chain 'E' and resid 906 through 910 Processing helix chain 'E' and resid 965 through 970 Processing helix chain 'E' and resid 987 through 998 Processing helix chain 'E' and resid 1025 through 1040 removed outlier: 4.098A pdb=" N GLY E1040 " --> pdb=" O MET E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1066 removed outlier: 3.660A pdb=" N GLN E1064 " --> pdb=" O ALA E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1423 through 1434 removed outlier: 4.180A pdb=" N SER E1427 " --> pdb=" O ARG E1423 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP E1434 " --> pdb=" O GLY E1430 " (cutoff:3.500A) Processing helix chain 'E' and resid 1453 through 1463 removed outlier: 3.718A pdb=" N ARG E1462 " --> pdb=" O ASN E1458 " (cutoff:3.500A) Processing helix chain 'E' and resid 1465 through 1470 Processing helix chain 'E' and resid 1490 through 1500 removed outlier: 3.700A pdb=" N GLN E1494 " --> pdb=" O SER E1490 " (cutoff:3.500A) Processing helix chain 'E' and resid 1540 through 1542 No H-bonds generated for 'chain 'E' and resid 1540 through 1542' Processing helix chain 'E' and resid 1549 through 1554 removed outlier: 4.170A pdb=" N HIS E1553 " --> pdb=" O SER E1549 " (cutoff:3.500A) Processing helix chain 'E' and resid 1572 through 1580 Processing helix chain 'E' and resid 1584 through 1588 Processing helix chain 'E' and resid 1629 through 1631 No H-bonds generated for 'chain 'E' and resid 1629 through 1631' Processing helix chain 'E' and resid 1641 through 1646 Processing helix chain 'E' and resid 1648 through 1660 Processing helix chain 'E' and resid 1678 through 1691 Processing helix chain 'E' and resid 1701 through 1712 Processing helix chain 'E' and resid 1716 through 1718 No H-bonds generated for 'chain 'E' and resid 1716 through 1718' Processing helix chain 'E' and resid 1727 through 1736 Processing helix chain 'E' and resid 1750 through 1759 Processing helix chain 'E' and resid 1771 through 1777 Processing helix chain 'E' and resid 1783 through 1788 Processing helix chain 'E' and resid 1796 through 1800 Processing helix chain 'E' and resid 1804 through 1820 removed outlier: 3.616A pdb=" N VAL E1810 " --> pdb=" O ASP E1806 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1846 removed outlier: 3.681A pdb=" N GLY E1846 " --> pdb=" O TYR E1842 " (cutoff:3.500A) Processing helix chain 'E' and resid 1894 through 1907 Processing helix chain 'E' and resid 1922 through 1935 Processing helix chain 'E' and resid 1948 through 1963 removed outlier: 3.539A pdb=" N LEU E1962 " --> pdb=" O GLU E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1984 through 2010 Proline residue: E1994 - end of helix removed outlier: 3.898A pdb=" N SER E1997 " --> pdb=" O LYS E1993 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E1998 " --> pdb=" O PRO E1994 " (cutoff:3.500A) Processing helix chain 'E' and resid 2022 through 2026 Processing helix chain 'E' and resid 2031 through 2052 Processing helix chain 'E' and resid 2087 through 2099 Processing helix chain 'F' and resid 873 through 876 Processing helix chain 'F' and resid 887 through 904 removed outlier: 3.598A pdb=" N LEU F 892 " --> pdb=" O ALA F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 965 through 970 Processing helix chain 'F' and resid 987 through 998 Processing helix chain 'F' and resid 1003 through 1006 Processing helix chain 'F' and resid 1025 through 1040 removed outlier: 4.030A pdb=" N GLY F1040 " --> pdb=" O MET F1036 " (cutoff:3.500A) Processing helix chain 'F' and resid 1058 through 1065 removed outlier: 3.667A pdb=" N GLN F1064 " --> pdb=" O ALA F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1150 Processing helix chain 'F' and resid 1176 through 1188 Processing helix chain 'F' and resid 1200 through 1206 Processing helix chain 'F' and resid 1221 through 1234 removed outlier: 3.876A pdb=" N LYS F1225 " --> pdb=" O SER F1221 " (cutoff:3.500A) Processing helix chain 'F' and resid 1246 through 1251 Processing helix chain 'F' and resid 1255 through 1261 Processing helix chain 'F' and resid 1276 through 1282 removed outlier: 4.407A pdb=" N ALA F1282 " --> pdb=" O ALA F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1283 through 1290 Processing helix chain 'F' and resid 1304 through 1308 Processing helix chain 'F' and resid 1324 through 1335 Processing helix chain 'F' and resid 1351 through 1362 Processing helix chain 'F' and resid 1373 through 1384 Processing helix chain 'F' and resid 1423 through 1433 removed outlier: 4.079A pdb=" N SER F1427 " --> pdb=" O ARG F1423 " (cutoff:3.500A) Processing helix chain 'F' and resid 1452 through 1462 removed outlier: 4.408A pdb=" N ARG F1462 " --> pdb=" O ASN F1458 " (cutoff:3.500A) Processing helix chain 'F' and resid 1490 through 1500 Processing helix chain 'F' and resid 1540 through 1542 No H-bonds generated for 'chain 'F' and resid 1540 through 1542' Processing helix chain 'F' and resid 1572 through 1580 removed outlier: 3.641A pdb=" N ILE F1576 " --> pdb=" O ASN F1572 " (cutoff:3.500A) Processing helix chain 'F' and resid 1584 through 1588 Processing helix chain 'F' and resid 1629 through 1631 No H-bonds generated for 'chain 'F' and resid 1629 through 1631' Processing helix chain 'F' and resid 1641 through 1646 Processing helix chain 'F' and resid 1648 through 1660 Processing helix chain 'F' and resid 1678 through 1691 Processing helix chain 'F' and resid 1701 through 1712 Processing helix chain 'F' and resid 1716 through 1718 No H-bonds generated for 'chain 'F' and resid 1716 through 1718' Processing helix chain 'F' and resid 1727 through 1736 Processing helix chain 'F' and resid 1750 through 1759 Processing helix chain 'F' and resid 1771 through 1776 Processing helix chain 'F' and resid 1783 through 1788 Processing helix chain 'F' and resid 1797 through 1801 Processing helix chain 'F' and resid 1806 through 1821 removed outlier: 3.884A pdb=" N VAL F1810 " --> pdb=" O ASP F1806 " (cutoff:3.500A) Processing helix chain 'F' and resid 1835 through 1843 Processing helix chain 'F' and resid 1894 through 1907 removed outlier: 3.538A pdb=" N GLU F1899 " --> pdb=" O GLY F1895 " (cutoff:3.500A) Processing helix chain 'F' and resid 1922 through 1935 Processing helix chain 'F' and resid 1948 through 1963 removed outlier: 3.536A pdb=" N LEU F1962 " --> pdb=" O GLU F1958 " (cutoff:3.500A) Processing helix chain 'F' and resid 1979 through 1983 Processing helix chain 'F' and resid 1984 through 2010 Proline residue: F1994 - end of helix removed outlier: 3.871A pdb=" N SER F1997 " --> pdb=" O LYS F1993 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY F1998 " --> pdb=" O PRO F1994 " (cutoff:3.500A) Processing helix chain 'F' and resid 2022 through 2026 Processing helix chain 'F' and resid 2031 through 2051 removed outlier: 3.648A pdb=" N GLY F2035 " --> pdb=" O GLN F2031 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F2051 " --> pdb=" O LYS F2047 " (cutoff:3.500A) Processing helix chain 'F' and resid 2068 through 2073 removed outlier: 3.612A pdb=" N MET F2073 " --> pdb=" O LEU F2069 " (cutoff:3.500A) Processing helix chain 'F' and resid 2087 through 2099 Processing sheet with id=AA1, first strand: chain 'E' and resid 860 through 865 removed outlier: 6.877A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS E 957 " --> pdb=" O ASP E 916 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP E 916 " --> pdb=" O LYS E 957 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR E 959 " --> pdb=" O PHE E 914 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE E 914 " --> pdb=" O TYR E 959 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU E1010 " --> pdb=" O ARG E1019 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E1021 " --> pdb=" O ILE E1008 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E1008 " --> pdb=" O LEU E1021 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 860 through 865 removed outlier: 6.877A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS E 957 " --> pdb=" O ASP E 916 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP E 916 " --> pdb=" O LYS E 957 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR E 959 " --> pdb=" O PHE E 914 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE E 914 " --> pdb=" O TYR E 959 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 878 through 880 removed outlier: 3.866A pdb=" N THR E 879 " --> pdb=" O ASP E1000 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 3.693A pdb=" N VAL E1472 " --> pdb=" O VAL E1441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE E2016 " --> pdb=" O LEU E2056 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E2058 " --> pdb=" O PHE E2016 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E2018 " --> pdb=" O VAL E2058 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP E2060 " --> pdb=" O VAL E2018 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER E2020 " --> pdb=" O TRP E2060 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N SER E1886 " --> pdb=" O VAL E1965 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E1967 " --> pdb=" O SER E1886 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 3.693A pdb=" N VAL E1472 " --> pdb=" O VAL E1441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL E2110 " --> pdb=" O LEU E2084 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 1525 through 1528 Processing sheet with id=AA7, first strand: chain 'E' and resid 1531 through 1535 Processing sheet with id=AA8, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 5.297A pdb=" N VAL E1566 " --> pdb=" O ARG E1606 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG E1606 " --> pdb=" O VAL E1566 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU E1602 " --> pdb=" O SER E1570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 4.617A pdb=" N VAL E1852 " --> pdb=" O LEU E1571 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR E1829 " --> pdb=" O VAL E1853 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN E1855 " --> pdb=" O THR E1829 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE E1831 " --> pdb=" O GLN E1855 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1720 through 1722 removed outlier: 6.535A pdb=" N ASP E1742 " --> pdb=" O ARG E1765 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU E1767 " --> pdb=" O ASP E1742 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL E1744 " --> pdb=" O LEU E1767 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR E1790 " --> pdb=" O THR E1762 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY E1764 " --> pdb=" O THR E1790 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N HIS E1792 " --> pdb=" O GLY E1764 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE E1766 " --> pdb=" O HIS E1792 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR F1790 " --> pdb=" O THR F1762 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY F1764 " --> pdb=" O THR F1790 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N HIS F1792 " --> pdb=" O GLY F1764 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE F1766 " --> pdb=" O HIS F1792 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP F1742 " --> pdb=" O ARG F1765 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU F1767 " --> pdb=" O ASP F1742 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL F1744 " --> pdb=" O LEU F1767 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F1670 " --> pdb=" O LEU F1743 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU F1745 " --> pdb=" O THR F1670 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU F1672 " --> pdb=" O LEU F1745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1779 through 1781 Processing sheet with id=AB3, first strand: chain 'F' and resid 860 through 864 removed outlier: 3.535A pdb=" N GLY F 956 " --> pdb=" O PHE F 944 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS F 957 " --> pdb=" O ASP F 916 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP F 916 " --> pdb=" O LYS F 957 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR F 959 " --> pdb=" O PHE F 914 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE F 914 " --> pdb=" O TYR F 959 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 913 " --> pdb=" O HIS F1056 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS F1056 " --> pdb=" O VAL F 913 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU F 915 " --> pdb=" O ALA F1054 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA F1054 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N THR F1050 " --> pdb=" O LEU F 919 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 985 through 986 removed outlier: 6.056A pdb=" N ILE F1008 " --> pdb=" O LEU F1021 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU F1021 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU F1010 " --> pdb=" O ARG F1019 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU F1100 " --> pdb=" O PRO F1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 883 through 884 removed outlier: 3.735A pdb=" N THR F 879 " --> pdb=" O ASP F1000 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 1475 through 1476 removed outlier: 6.891A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE F2016 " --> pdb=" O LEU F2056 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL F2058 " --> pdb=" O PHE F2016 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F2018 " --> pdb=" O VAL F2058 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP F2060 " --> pdb=" O VAL F2018 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER F2020 " --> pdb=" O TRP F2060 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER F1886 " --> pdb=" O VAL F1965 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY F1967 " --> pdb=" O SER F1886 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU F1912 " --> pdb=" O GLN F1940 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER F1942 " --> pdb=" O LEU F1912 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F1914 " --> pdb=" O SER F1942 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 1475 through 1476 removed outlier: 6.891A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL F2110 " --> pdb=" O LEU F2084 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 1123 through 1127 removed outlier: 6.798A pdb=" N LEU F1402 " --> pdb=" O VAL F1389 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU F1391 " --> pdb=" O LEU F1400 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU F1400 " --> pdb=" O LEU F1391 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS F1393 " --> pdb=" O SER F1398 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER F1398 " --> pdb=" O LYS F1393 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP F1311 " --> pdb=" O PHE F1341 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU F1343 " --> pdb=" O ASP F1311 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU F1313 " --> pdb=" O LEU F1343 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N HIS F1345 " --> pdb=" O LEU F1313 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS F1315 " --> pdb=" O HIS F1345 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N LEU F1347 " --> pdb=" O CYS F1315 " (cutoff:3.500A) removed outlier: 11.642A pdb=" N LYS F1239 " --> pdb=" O ALA F1310 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU F1312 " --> pdb=" O LYS F1239 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS F1241 " --> pdb=" O LEU F1312 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL F1314 " --> pdb=" O LYS F1241 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL F1243 " --> pdb=" O VAL F1314 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN F1316 " --> pdb=" O VAL F1243 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F1245 " --> pdb=" O ASN F1316 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET F1240 " --> pdb=" O SER F1269 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR F1271 " --> pdb=" O MET F1240 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F1242 " --> pdb=" O THR F1271 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR F1273 " --> pdb=" O VAL F1242 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU F1244 " --> pdb=" O THR F1273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 1413 through 1416 removed outlier: 6.082A pdb=" N ILE F1413 " --> pdb=" O TRP F1442 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS F1444 " --> pdb=" O ILE F1413 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU F1415 " --> pdb=" O LYS F1444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1525 through 1528 Processing sheet with id=AC2, first strand: chain 'F' and resid 1531 through 1535 Processing sheet with id=AC3, first strand: chain 'F' and resid 1625 through 1628 removed outlier: 3.754A pdb=" N SER F1570 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLU F1602 " --> pdb=" O SER F1570 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1625 through 1628 removed outlier: 4.651A pdb=" N VAL F1852 " --> pdb=" O LEU F1571 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR F1829 " --> pdb=" O VAL F1853 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN F1855 " --> pdb=" O THR F1829 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE F1831 " --> pdb=" O GLN F1855 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2244 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: 8.69 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.52: 11618 1.52 - 1.88: 5011 1.88 - 2.24: 0 2.24 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 16630 Sorted by residual: bond pdb=" C GLU F1802 " pdb=" N ALA F1805 " ideal model delta sigma weight residual 1.332 2.969 -1.637 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C1B NDP F3002 " pdb=" C2B NDP F3002 " ideal model delta sigma weight residual 1.575 1.256 0.319 3.70e-02 7.30e+02 7.45e+01 bond pdb=" C1B NDP E3002 " pdb=" C2B NDP E3002 " ideal model delta sigma weight residual 1.575 1.256 0.319 3.70e-02 7.30e+02 7.43e+01 bond pdb=" C2D NDP F3002 " pdb=" C3D NDP F3002 " ideal model delta sigma weight residual 1.545 1.244 0.301 3.60e-02 7.72e+02 7.00e+01 bond pdb=" C1B NDP E3001 " pdb=" C2B NDP E3001 " ideal model delta sigma weight residual 1.575 1.268 0.307 3.70e-02 7.30e+02 6.90e+01 ... (remaining 16625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.18: 22698 12.18 - 24.37: 19 24.37 - 36.55: 0 36.55 - 48.73: 0 48.73 - 60.92: 1 Bond angle restraints: 22718 Sorted by residual: angle pdb=" O GLU F1802 " pdb=" C GLU F1802 " pdb=" N ALA F1805 " ideal model delta sigma weight residual 122.59 61.67 60.92 1.33e+00 5.65e-01 2.10e+03 angle pdb=" PA NDP F3001 " pdb=" O3 NDP F3001 " pdb=" PN NDP F3001 " ideal model delta sigma weight residual 107.74 128.89 -21.15 1.95e+00 2.62e-01 1.17e+02 angle pdb=" PA NDP F3002 " pdb=" O3 NDP F3002 " pdb=" PN NDP F3002 " ideal model delta sigma weight residual 107.74 126.90 -19.16 1.95e+00 2.62e-01 9.61e+01 angle pdb=" C5B NDP F3002 " pdb=" O5B NDP F3002 " pdb=" PA NDP F3002 " ideal model delta sigma weight residual 103.84 120.19 -16.35 1.91e+00 2.73e-01 7.29e+01 angle pdb=" O1X NDP F3002 " pdb=" P2B NDP F3002 " pdb=" O3X NDP F3002 " ideal model delta sigma weight residual 117.46 107.79 9.67 1.17e+00 7.36e-01 6.88e+01 ... (remaining 22713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 9384 33.22 - 66.44: 324 66.44 - 99.66: 20 99.66 - 132.87: 0 132.87 - 166.09: 2 Dihedral angle restraints: 9730 sinusoidal: 3533 harmonic: 6197 Sorted by residual: dihedral pdb=" CA MET F1332 " pdb=" C MET F1332 " pdb=" N VAL F1333 " pdb=" CA VAL F1333 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C5B NDP F3001 " pdb=" O5B NDP F3001 " pdb=" PA NDP F3001 " pdb=" O3 NDP F3001 " ideal model delta sinusoidal sigma weight residual 175.04 8.95 166.09 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C5B NDP E3001 " pdb=" O5B NDP E3001 " pdb=" PA NDP E3001 " pdb=" O3 NDP E3001 " ideal model delta sinusoidal sigma weight residual 175.04 19.32 155.72 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2546 0.107 - 0.214: 58 0.214 - 0.320: 7 0.320 - 0.427: 5 0.427 - 0.534: 2 Chirality restraints: 2618 Sorted by residual: chirality pdb=" C2B NDP F3002 " pdb=" C1B NDP F3002 " pdb=" C3B NDP F3002 " pdb=" O2B NDP F3002 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C3D NDP E3001 " pdb=" C2D NDP E3001 " pdb=" C4D NDP E3001 " pdb=" O3D NDP E3001 " both_signs ideal model delta sigma weight residual False -2.71 -2.22 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1D NDP F3001 " pdb=" C2D NDP F3001 " pdb=" N1N NDP F3001 " pdb=" O4D NDP F3001 " both_signs ideal model delta sigma weight residual False 2.60 2.20 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 2615 not shown) Planarity restraints: 2925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F1802 " -0.190 2.00e-02 2.50e+03 2.73e-01 7.43e+02 pdb=" C GLU F1802 " 0.447 2.00e-02 2.50e+03 pdb=" O GLU F1802 " -0.248 2.00e-02 2.50e+03 pdb=" N ALA F1805 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 976 " -0.060 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO F 977 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO F 977 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 977 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F1328 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA F1328 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA F1328 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU F1329 " -0.010 2.00e-02 2.50e+03 ... (remaining 2922 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1629 2.74 - 3.28: 16052 3.28 - 3.82: 29505 3.82 - 4.36: 34693 4.36 - 4.90: 59089 Nonbonded interactions: 140968 Sorted by model distance: nonbonded pdb=" OH TYR E 891 " pdb=" OG1 THR E 923 " model vdw 2.204 3.040 nonbonded pdb=" O PRO F1649 " pdb=" OG SER F1653 " model vdw 2.207 3.040 nonbonded pdb=" NE2 HIS F1674 " pdb=" OG SER F1756 " model vdw 2.218 3.120 nonbonded pdb=" N GLU E2012 " pdb=" OE1 GLU E2012 " model vdw 2.229 3.120 nonbonded pdb=" O LYS E1995 " pdb=" OG1 THR E1999 " model vdw 2.235 3.040 ... (remaining 140963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.560 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.017 1.637 16630 Z= 0.982 Angle : 0.980 60.916 22718 Z= 0.526 Chirality : 0.050 0.534 2618 Planarity : 0.006 0.273 2925 Dihedral : 16.317 166.093 5744 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 2.06 % Allowed : 23.38 % Favored : 74.56 % 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: 0.27 (0.19), residues: 2154 helix: 0.84 (0.20), residues: 756 sheet: -0.45 (0.26), residues: 425 loop : 0.13 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F1442 HIS 0.004 0.001 HIS E1674 PHE 0.025 0.001 PHE E2109 TYR 0.022 0.001 TYR F 991 ARG 0.006 0.000 ARG E1545 Details of bonding type rmsd hydrogen bonds : bond 0.14549 ( 738) hydrogen bonds : angle 6.20547 ( 2244) covalent geometry : bond 0.01736 (16630) covalent geometry : angle 0.97978 (22718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: E 1010 GLU cc_start: 0.7973 (tt0) cc_final: 0.7742 (tt0) REVERT: F 1294 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7741 (mm-40) outliers start: 33 outliers final: 30 residues processed: 110 average time/residue: 0.9918 time to fit residues: 126.4227 Evaluate side-chains 106 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 930 THR Chi-restraints excluded: chain E residue 939 GLU Chi-restraints excluded: chain E residue 1000 ASP Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1480 THR Chi-restraints excluded: chain E residue 1584 SER Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1584 SER Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1915 THR Chi-restraints excluded: chain F residue 1991 VAL Chi-restraints excluded: chain F residue 2022 VAL Chi-restraints excluded: chain F residue 2024 CYS Chi-restraints excluded: chain F residue 2032 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1848 HIS F1940 GLN F1970 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.120605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079657 restraints weight = 26722.095| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.59 r_work: 0.3028 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16630 Z= 0.132 Angle : 0.548 12.178 22718 Z= 0.273 Chirality : 0.042 0.223 2618 Planarity : 0.004 0.037 2925 Dihedral : 7.381 154.846 2408 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 2.74 % Allowed : 21.07 % Favored : 76.18 % 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: 0.42 (0.19), residues: 2156 helix: 1.18 (0.20), residues: 774 sheet: -0.64 (0.25), residues: 421 loop : 0.13 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1807 HIS 0.007 0.001 HIS E1674 PHE 0.011 0.001 PHE F1117 TYR 0.022 0.001 TYR E 991 ARG 0.005 0.000 ARG F1724 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 738) hydrogen bonds : angle 4.57941 ( 2244) covalent geometry : bond 0.00315 (16630) covalent geometry : angle 0.54768 (22718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 1.752 Fit side-chains REVERT: E 1071 ASP cc_start: 0.9153 (m-30) cc_final: 0.8694 (t0) REVERT: E 1782 MET cc_start: 0.9050 (mtp) cc_final: 0.8783 (mtm) REVERT: F 1294 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: F 1442 TRP cc_start: 0.7868 (m-90) cc_final: 0.7251 (m-90) outliers start: 44 outliers final: 18 residues processed: 123 average time/residue: 0.9482 time to fit residues: 135.7567 Evaluate side-chains 102 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1865 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.118845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077563 restraints weight = 26673.815| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.59 r_work: 0.2989 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16630 Z= 0.180 Angle : 0.544 11.250 22718 Z= 0.273 Chirality : 0.042 0.228 2618 Planarity : 0.003 0.032 2925 Dihedral : 7.031 150.558 2378 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 21.45 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2156 helix: 1.22 (0.19), residues: 777 sheet: -0.72 (0.25), residues: 422 loop : 0.10 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1807 HIS 0.005 0.001 HIS E1674 PHE 0.014 0.001 PHE E2109 TYR 0.026 0.002 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 738) hydrogen bonds : angle 4.44141 ( 2244) covalent geometry : bond 0.00428 (16630) covalent geometry : angle 0.54443 (22718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 1.552 Fit side-chains REVERT: E 1071 ASP cc_start: 0.9147 (m-30) cc_final: 0.8692 (t0) REVERT: E 1767 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8774 (mt) REVERT: E 1782 MET cc_start: 0.9260 (mtp) cc_final: 0.9044 (mtm) REVERT: F 1442 TRP cc_start: 0.7900 (m-90) cc_final: 0.7348 (m-90) REVERT: F 2041 MET cc_start: 0.8968 (mtm) cc_final: 0.8727 (mtm) outliers start: 43 outliers final: 20 residues processed: 123 average time/residue: 1.3006 time to fit residues: 184.8789 Evaluate side-chains 104 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 205 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078122 restraints weight = 26614.508| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.63 r_work: 0.3000 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16630 Z= 0.155 Angle : 0.536 12.396 22718 Z= 0.267 Chirality : 0.042 0.217 2618 Planarity : 0.003 0.034 2925 Dihedral : 6.757 145.954 2375 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.93 % Allowed : 21.70 % Favored : 75.37 % 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: 0.48 (0.19), residues: 2156 helix: 1.37 (0.20), residues: 767 sheet: -0.81 (0.24), residues: 439 loop : 0.17 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1807 HIS 0.005 0.001 HIS E1674 PHE 0.010 0.001 PHE F1117 TYR 0.024 0.001 TYR E 991 ARG 0.004 0.000 ARG F1439 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 738) hydrogen bonds : angle 4.33589 ( 2244) covalent geometry : bond 0.00372 (16630) covalent geometry : angle 0.53559 (22718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 1.736 Fit side-chains REVERT: E 1071 ASP cc_start: 0.9134 (m-30) cc_final: 0.8692 (t0) REVERT: E 1538 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8115 (mmp80) REVERT: E 1767 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8748 (mt) REVERT: E 1782 MET cc_start: 0.9264 (mtp) cc_final: 0.9016 (mtm) REVERT: F 1332 MET cc_start: 0.9475 (pmm) cc_final: 0.9204 (pmm) REVERT: F 2041 MET cc_start: 0.8960 (mtm) cc_final: 0.8732 (mtm) outliers start: 47 outliers final: 23 residues processed: 128 average time/residue: 0.9693 time to fit residues: 143.9001 Evaluate side-chains 109 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1865 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 211 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.120321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079150 restraints weight = 26785.807| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.67 r_work: 0.3021 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16630 Z= 0.125 Angle : 0.511 11.298 22718 Z= 0.255 Chirality : 0.041 0.206 2618 Planarity : 0.003 0.034 2925 Dihedral : 6.489 137.079 2375 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.93 % Allowed : 21.57 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 2156 helix: 1.48 (0.20), residues: 767 sheet: -0.85 (0.24), residues: 443 loop : 0.22 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.016 0.001 PHE E2109 TYR 0.022 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 738) hydrogen bonds : angle 4.18671 ( 2244) covalent geometry : bond 0.00301 (16630) covalent geometry : angle 0.51136 (22718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: E 881 ASP cc_start: 0.8475 (t70) cc_final: 0.8239 (t70) REVERT: E 1071 ASP cc_start: 0.9114 (m-30) cc_final: 0.8661 (t0) REVERT: E 1767 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8702 (mt) REVERT: E 1782 MET cc_start: 0.9223 (mtp) cc_final: 0.8959 (mtm) REVERT: F 2041 MET cc_start: 0.8940 (mtm) cc_final: 0.8690 (mtm) outliers start: 47 outliers final: 30 residues processed: 128 average time/residue: 1.1140 time to fit residues: 166.1246 Evaluate side-chains 119 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1454 VAL Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1802 GLU Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1980 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 90 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN F1345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078104 restraints weight = 26683.747| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.62 r_work: 0.3001 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16630 Z= 0.162 Angle : 0.544 12.707 22718 Z= 0.268 Chirality : 0.042 0.220 2618 Planarity : 0.003 0.033 2925 Dihedral : 6.604 136.136 2375 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.87 % Allowed : 21.70 % Favored : 75.44 % 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: 0.54 (0.19), residues: 2156 helix: 1.48 (0.20), residues: 767 sheet: -0.85 (0.24), residues: 450 loop : 0.21 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F1442 HIS 0.004 0.001 HIS E1674 PHE 0.020 0.001 PHE E2109 TYR 0.024 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 738) hydrogen bonds : angle 4.22255 ( 2244) covalent geometry : bond 0.00391 (16630) covalent geometry : angle 0.54410 (22718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 1.914 Fit side-chains REVERT: E 881 ASP cc_start: 0.8537 (t70) cc_final: 0.8249 (t70) REVERT: E 1071 ASP cc_start: 0.9119 (m-30) cc_final: 0.8742 (t0) REVERT: E 1538 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8140 (mmp80) REVERT: E 1767 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8759 (mt) REVERT: F 2041 MET cc_start: 0.8948 (mtm) cc_final: 0.8690 (mtm) REVERT: F 2056 LEU cc_start: 0.8568 (tt) cc_final: 0.8181 (tm) outliers start: 46 outliers final: 25 residues processed: 125 average time/residue: 0.9371 time to fit residues: 136.8901 Evaluate side-chains 110 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1980 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.119562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078210 restraints weight = 26698.983| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.68 r_work: 0.3004 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16630 Z= 0.152 Angle : 0.545 11.315 22718 Z= 0.270 Chirality : 0.042 0.215 2618 Planarity : 0.003 0.033 2925 Dihedral : 6.362 134.852 2373 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.81 % Allowed : 21.57 % Favored : 75.62 % 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: 2156 helix: 1.41 (0.20), residues: 775 sheet: -0.92 (0.24), residues: 459 loop : 0.29 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.021 0.001 PHE E2109 TYR 0.022 0.001 TYR F 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 738) hydrogen bonds : angle 4.20771 ( 2244) covalent geometry : bond 0.00366 (16630) covalent geometry : angle 0.54507 (22718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 87 time to evaluate : 1.769 Fit side-chains revert: symmetry clash REVERT: E 881 ASP cc_start: 0.8538 (t70) cc_final: 0.8214 (t70) REVERT: E 1071 ASP cc_start: 0.9117 (m-30) cc_final: 0.8750 (t0) REVERT: E 1538 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (mmp80) REVERT: E 1552 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7156 (ptm160) REVERT: E 1767 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8739 (mt) REVERT: E 1835 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: F 1666 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7419 (mmp80) REVERT: F 2041 MET cc_start: 0.8946 (mtm) cc_final: 0.8689 (mtm) REVERT: F 2056 LEU cc_start: 0.8509 (tt) cc_final: 0.8114 (tm) outliers start: 45 outliers final: 29 residues processed: 123 average time/residue: 0.9679 time to fit residues: 138.2331 Evaluate side-chains 117 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1552 ARG Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1796 LEU Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1802 GLU Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1980 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.117077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075420 restraints weight = 26752.968| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.62 r_work: 0.2945 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16630 Z= 0.256 Angle : 0.612 12.883 22718 Z= 0.304 Chirality : 0.044 0.248 2618 Planarity : 0.004 0.032 2925 Dihedral : 6.540 143.103 2371 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.05 % Allowed : 21.76 % Favored : 75.19 % 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: 0.38 (0.19), residues: 2156 helix: 1.24 (0.20), residues: 775 sheet: -0.93 (0.24), residues: 459 loop : 0.22 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F1442 HIS 0.004 0.001 HIS E1062 PHE 0.024 0.002 PHE E2109 TYR 0.030 0.002 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 738) hydrogen bonds : angle 4.43232 ( 2244) covalent geometry : bond 0.00607 (16630) covalent geometry : angle 0.61205 (22718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 1.894 Fit side-chains REVERT: E 881 ASP cc_start: 0.8528 (t70) cc_final: 0.8218 (t70) REVERT: E 1071 ASP cc_start: 0.9137 (m-30) cc_final: 0.8782 (t0) REVERT: E 1538 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8150 (mmp80) REVERT: E 1767 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8796 (mt) REVERT: E 1835 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: F 1046 LEU cc_start: 0.8865 (tp) cc_final: 0.8632 (mt) REVERT: F 1666 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7742 (mmp80) REVERT: F 2056 LEU cc_start: 0.8482 (tt) cc_final: 0.7879 (tm) outliers start: 49 outliers final: 27 residues processed: 125 average time/residue: 0.9434 time to fit residues: 137.0396 Evaluate side-chains 114 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1038 ILE Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1597 SER Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1991 VAL Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077844 restraints weight = 26482.729| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.68 r_work: 0.2997 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16630 Z= 0.145 Angle : 0.567 12.126 22718 Z= 0.280 Chirality : 0.042 0.211 2618 Planarity : 0.003 0.046 2925 Dihedral : 6.279 138.967 2369 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.31 % Allowed : 22.44 % Favored : 75.25 % 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: 0.47 (0.19), residues: 2156 helix: 1.39 (0.20), residues: 768 sheet: -0.96 (0.24), residues: 459 loop : 0.25 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.025 0.001 PHE E2109 TYR 0.022 0.001 TYR F 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 738) hydrogen bonds : angle 4.27721 ( 2244) covalent geometry : bond 0.00350 (16630) covalent geometry : angle 0.56733 (22718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.714 Fit side-chains REVERT: E 881 ASP cc_start: 0.8418 (t70) cc_final: 0.8071 (t70) REVERT: E 1071 ASP cc_start: 0.9116 (m-30) cc_final: 0.8757 (t0) REVERT: E 1538 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8104 (mmp80) REVERT: E 1767 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8721 (mt) REVERT: E 1835 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 1046 LEU cc_start: 0.8923 (tp) cc_final: 0.8718 (OUTLIER) REVERT: F 1462 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7765 (ptp-170) REVERT: F 1497 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (mm) REVERT: F 1666 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7389 (mmp80) outliers start: 37 outliers final: 24 residues processed: 114 average time/residue: 1.0202 time to fit residues: 134.2504 Evaluate side-chains 109 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1497 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 3 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN F1848 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.119215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077912 restraints weight = 26713.279| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.67 r_work: 0.2997 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16630 Z= 0.149 Angle : 0.566 12.402 22718 Z= 0.280 Chirality : 0.042 0.214 2618 Planarity : 0.003 0.040 2925 Dihedral : 6.211 135.113 2369 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.00 % Allowed : 23.00 % Favored : 75.00 % 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: 0.50 (0.19), residues: 2156 helix: 1.43 (0.20), residues: 768 sheet: -0.96 (0.24), residues: 459 loop : 0.27 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.011 0.001 PHE F2109 TYR 0.024 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 738) hydrogen bonds : angle 4.24002 ( 2244) covalent geometry : bond 0.00361 (16630) covalent geometry : angle 0.56579 (22718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 1.900 Fit side-chains REVERT: E 881 ASP cc_start: 0.8454 (t70) cc_final: 0.8107 (t70) REVERT: E 1071 ASP cc_start: 0.9109 (m-30) cc_final: 0.8762 (t0) REVERT: E 1538 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8103 (mmp80) REVERT: E 1739 LYS cc_start: 0.9069 (mttt) cc_final: 0.8655 (mmtm) REVERT: E 1767 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8730 (mt) REVERT: F 1046 LEU cc_start: 0.8911 (tp) cc_final: 0.8643 (mt) REVERT: F 1462 ARG cc_start: 0.8265 (ptp90) cc_final: 0.7739 (ptp-170) REVERT: F 1497 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8560 (mm) REVERT: F 1666 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7398 (mmp80) outliers start: 32 outliers final: 24 residues processed: 112 average time/residue: 1.0462 time to fit residues: 135.1270 Evaluate side-chains 111 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 989 GLU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1497 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1718 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1991 VAL Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 167 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 170 optimal weight: 0.0970 chunk 155 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.118508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077101 restraints weight = 26742.042| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.66 r_work: 0.2982 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16630 Z= 0.177 Angle : 0.582 12.530 22718 Z= 0.287 Chirality : 0.043 0.223 2618 Planarity : 0.003 0.036 2925 Dihedral : 6.260 136.342 2369 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.12 % Allowed : 22.82 % Favored : 75.06 % 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: 2156 helix: 1.42 (0.20), residues: 767 sheet: -0.97 (0.24), residues: 461 loop : 0.25 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F1442 HIS 0.004 0.001 HIS E1674 PHE 0.028 0.001 PHE E2109 TYR 0.025 0.002 TYR E 991 ARG 0.005 0.000 ARG F1462 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 738) hydrogen bonds : angle 4.29421 ( 2244) covalent geometry : bond 0.00426 (16630) covalent geometry : angle 0.58201 (22718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15274.95 seconds wall clock time: 264 minutes 39.49 seconds (15879.49 seconds total)