Starting phenix.real_space_refine on Mon Nov 18 07:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyk_28691/11_2024/8eyk_28691_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= 0.000 sd= 0.176 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 58 5.16 5 C 9777 2.51 5 N 2704 2.21 5 O 2835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15386 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "F" Number of atoms: 7949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 7949 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 188 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.13, per 1000 atoms: 0.59 Number of scatterers: 15386 At special positions: 0 Unit cell: (90.64, 195.7, 90.64, 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 58 16.00 P 12 15.00 O 2835 8.00 N 2704 7.00 C 9777 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: 4.43 Conformation dependent library (CDL) restraints added in 2.0 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 37.6% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'E' and resid 872 through 876 Processing helix chain 'E' and resid 887 through 903 Processing helix chain 'E' and resid 906 through 910 Processing helix chain 'E' and resid 965 through 970 removed outlier: 3.532A pdb=" N ASP E 970 " --> pdb=" O ARG E 967 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 998 Processing helix chain 'E' and resid 1003 through 1006 Processing helix chain 'E' and resid 1025 through 1040 removed outlier: 4.134A pdb=" N GLY E1040 " --> pdb=" O MET E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1058 through 1066 removed outlier: 3.589A pdb=" N GLN E1064 " --> pdb=" O ALA E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1423 through 1434 removed outlier: 4.314A pdb=" N SER E1427 " --> pdb=" O ARG E1423 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E1434 " --> pdb=" O GLY E1430 " (cutoff:3.500A) Processing helix chain 'E' and resid 1453 through 1463 removed outlier: 3.839A pdb=" N ARG E1462 " --> pdb=" O ASN E1458 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU E1463 " --> pdb=" O CYS E1459 " (cutoff:3.500A) Processing helix chain 'E' and resid 1465 through 1470 Processing helix chain 'E' and resid 1490 through 1500 removed outlier: 3.639A 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 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 1647 through 1661 removed outlier: 4.288A pdb=" N VAL E1651 " --> pdb=" O SER E1647 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E1653 " --> pdb=" O PRO E1649 " (cutoff:3.500A) 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 1726 through 1736 removed outlier: 4.216A pdb=" N GLN E1730 " --> pdb=" O THR E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1750 through 1759 removed outlier: 3.564A pdb=" N SER E1756 " --> pdb=" O LYS E1752 " (cutoff:3.500A) Processing helix chain 'E' and resid 1771 through 1776 Processing helix chain 'E' and resid 1783 through 1788 Processing helix chain 'E' and resid 1795 through 1797 No H-bonds generated for 'chain 'E' and resid 1795 through 1797' Processing helix chain 'E' and resid 1798 through 1803 removed outlier: 4.288A pdb=" N GLU E1802 " --> pdb=" O ALA E1798 " (cutoff:3.500A) Processing helix chain 'E' and resid 1804 through 1820 removed outlier: 3.678A pdb=" N VAL E1810 " --> pdb=" O ASP E1806 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1846 removed outlier: 3.535A pdb=" N GLN E1845 " --> pdb=" O ARG E1841 " (cutoff:3.500A) removed outlier: 3.798A 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 1936 Processing helix chain 'E' and resid 1948 through 1963 removed outlier: 3.586A pdb=" N LEU E1962 " --> pdb=" O GLU E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1984 through 1993 Processing helix chain 'E' and resid 1995 through 2010 Processing helix chain 'E' and resid 2022 through 2026 Processing helix chain 'E' and resid 2031 through 2051 Processing helix chain 'E' and resid 2067 through 2072 removed outlier: 3.796A pdb=" N GLU E2071 " --> pdb=" O GLY E2067 " (cutoff:3.500A) Processing helix chain 'E' and resid 2087 through 2100 removed outlier: 3.777A pdb=" N ASN E2100 " --> pdb=" O ASP E2096 " (cutoff:3.500A) Processing helix chain 'F' and resid 873 through 876 Processing helix chain 'F' and resid 887 through 904 removed outlier: 3.552A pdb=" N TYR F 891 " --> pdb=" O PRO F 887 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 892 " --> pdb=" O ALA F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 910 Processing helix chain 'F' and resid 987 through 997 Processing helix chain 'F' and resid 1003 through 1006 Processing helix chain 'F' and resid 1025 through 1040 removed outlier: 3.571A pdb=" N PHE F1029 " --> pdb=" O ASN F1025 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET F1030 " --> pdb=" O TRP F1026 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY F1040 " --> pdb=" O MET F1036 " (cutoff:3.500A) Processing helix chain 'F' and resid 1058 through 1065 removed outlier: 3.687A pdb=" N GLN F1064 " --> pdb=" O ALA F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1221 through 1234 removed outlier: 3.913A pdb=" N LYS F1225 " --> pdb=" O SER F1221 " (cutoff:3.500A) Processing helix chain 'F' and resid 1251 through 1254 removed outlier: 4.029A pdb=" N SER F1254 " --> pdb=" O HIS F1251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1251 through 1254' Processing helix chain 'F' and resid 1255 through 1261 Processing helix chain 'F' and resid 1326 through 1336 Processing helix chain 'F' and resid 1376 through 1384 Processing helix chain 'F' and resid 1423 through 1433 removed outlier: 4.130A pdb=" N SER F1427 " --> pdb=" O ARG F1423 " (cutoff:3.500A) Processing helix chain 'F' and resid 1452 through 1462 removed outlier: 4.268A 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 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 1643 through 1646 Processing helix chain 'F' and resid 1647 through 1660 removed outlier: 4.214A pdb=" N VAL F1651 " --> pdb=" O SER F1647 " (cutoff:3.500A) 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 1820 removed outlier: 4.124A pdb=" N VAL F1810 " --> pdb=" O ASP F1806 " (cutoff:3.500A) Processing helix chain 'F' and resid 1835 through 1844 Processing helix chain 'F' and resid 1894 through 1907 removed outlier: 3.543A 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: 3.629A 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: 4.124A pdb=" N SER F1997 " --> pdb=" O LYS F1993 " (cutoff:3.500A) removed outlier: 4.465A 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: 3.671A pdb=" N GLY F2035 " --> pdb=" O GLN F2031 " (cutoff:3.500A) Processing helix chain 'F' and resid 2068 through 2073 Processing helix chain 'F' and resid 2087 through 2099 Processing sheet with id=AA1, first strand: chain 'E' and resid 860 through 864 removed outlier: 6.848A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL E 953 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 919 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 955 " --> pdb=" O VAL E 917 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 917 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E1010 " --> pdb=" O ARG E1019 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E1021 " --> pdb=" O ILE E1008 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE E1008 " --> pdb=" O LEU E1021 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 860 through 864 removed outlier: 6.848A pdb=" N PHE E 944 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER E 955 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL E 946 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL E 953 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 919 " --> pdb=" O VAL E 953 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 955 " --> pdb=" O VAL E 917 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 917 " --> pdb=" O SER E 955 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 913 " --> pdb=" O HIS E1056 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS E1056 " --> pdb=" O VAL E 913 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU E 915 " --> pdb=" O ALA E1054 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA E1054 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR E1050 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E1100 " --> pdb=" O PRO E1049 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY E1096 " --> pdb=" O THR E1053 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE E1055 " --> pdb=" O ILE E1094 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE E1094 " --> pdb=" O ILE E1055 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E1057 " --> pdb=" O VAL E1092 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E1092 " --> pdb=" O ILE E1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 883 through 884 removed outlier: 3.604A 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: 5.979A pdb=" N ILE E1413 " --> pdb=" O TRP E1442 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS E1444 " --> pdb=" O ILE E1413 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E1415 " --> pdb=" O LYS E1444 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E1515 " --> pdb=" O CYS E1118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS E1118 " --> pdb=" O ARG E1515 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER E1886 " --> pdb=" O VAL E1965 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY E1967 " --> pdb=" O SER E1886 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E1912 " --> pdb=" O GLN E1940 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER E1942 " --> pdb=" O LEU E1912 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E1914 " --> pdb=" O SER E1942 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 5.979A pdb=" N ILE E1413 " --> pdb=" O TRP E1442 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS E1444 " --> pdb=" O ILE E1413 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E1415 " --> pdb=" O LYS E1444 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E1473 " --> pdb=" O ASN E1504 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR E1506 " --> pdb=" O LEU E1473 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER E1475 " --> pdb=" O TYR E1506 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E1515 " --> pdb=" O CYS E1118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS E1118 " --> pdb=" O ARG E1515 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 4.374A 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: 6.755A pdb=" N SER E1604 " --> pdb=" O TYR E1567 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA E1569 " --> pdb=" O GLU E1602 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU E1602 " --> pdb=" O ALA E1569 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 4.527A pdb=" N VAL E1852 " --> pdb=" O LEU E1571 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR E1829 " --> pdb=" O VAL E1853 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN E1855 " --> pdb=" O THR E1829 " (cutoff:3.500A) removed outlier: 6.695A 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: 7.802A pdb=" N ALA E1721 " --> pdb=" O VAL E1695 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR E1697 " --> pdb=" O ALA E1721 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP E1742 " --> pdb=" O ARG E1765 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU E1767 " --> pdb=" O ASP E1742 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E1744 " --> pdb=" O LEU E1767 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR E1790 " --> pdb=" O THR E1762 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY E1764 " --> pdb=" O THR E1790 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N HIS E1792 " --> pdb=" O GLY E1764 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE E1766 " --> pdb=" O HIS E1792 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR F1790 " --> pdb=" O THR F1762 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY F1764 " --> pdb=" O THR F1790 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS F1792 " --> pdb=" O GLY F1764 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE F1766 " --> pdb=" O HIS F1792 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP F1742 " --> pdb=" O ARG F1765 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU F1767 " --> pdb=" O ASP F1742 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL F1744 " --> pdb=" O LEU F1767 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR F1670 " --> pdb=" O LEU F1743 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU F1745 " --> pdb=" O THR F1670 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU F1672 " --> pdb=" O LEU F1745 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F1671 " --> pdb=" O PHE F1696 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR F1698 " --> pdb=" O LEU F1671 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE F1673 " --> pdb=" O THR F1698 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA F1721 " --> pdb=" O VAL F1695 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR F1697 " --> pdb=" O ALA F1721 " (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: 6.787A pdb=" N PHE F 944 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER F 955 " --> pdb=" O PHE F 944 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 946 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL F 953 " --> pdb=" O LEU F 919 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU F 919 " --> pdb=" O VAL F 953 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER F 955 " --> pdb=" O VAL F 917 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL F 917 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 913 " --> pdb=" O HIS F1056 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS F1056 " --> pdb=" O VAL F 913 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU F 915 " --> pdb=" O ALA F1054 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA F1054 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 5.475A 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: 6.233A pdb=" N ILE F1008 " --> pdb=" O LEU F1021 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F1021 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F1010 " --> pdb=" O ARG F1019 " (cutoff:3.500A) removed outlier: 5.853A 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: 3.749A 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: 6.711A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F1510 " --> pdb=" O ARG F1507 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY F1966 " --> pdb=" O TYR F2015 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL F2017 " --> pdb=" O GLY F1966 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL F1968 " --> pdb=" O VAL F2017 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE F2019 " --> pdb=" O VAL F1968 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN F1970 " --> pdb=" O PHE F2019 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N SER F2021 " --> pdb=" O ASN F1970 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER F1886 " --> pdb=" O VAL F1965 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F1967 " --> pdb=" O SER F1886 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F1912 " --> pdb=" O GLN F1940 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER F1942 " --> pdb=" O LEU F1912 " (cutoff:3.500A) removed outlier: 6.262A 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: 6.711A pdb=" N SER F1475 " --> pdb=" O TYR F1506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F1510 " --> pdb=" O ARG F1507 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL F2110 " --> pdb=" O LEU F2084 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 1123 through 1124 removed outlier: 6.872A pdb=" N LEU F1402 " --> pdb=" O VAL F1389 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F1313 " --> pdb=" O LEU F1343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 1239 through 1243 removed outlier: 6.117A pdb=" N MET F1240 " --> pdb=" O SER F1269 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR F1271 " --> pdb=" O MET F1240 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F1242 " --> pdb=" O THR F1271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 1413 through 1416 removed outlier: 5.787A pdb=" N ILE F1413 " --> pdb=" O TRP F1442 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS F1444 " --> pdb=" O ILE F1413 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU F1415 " --> pdb=" O LYS F1444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1525 through 1528 Processing sheet with id=AC3, first strand: chain 'F' and resid 1531 through 1535 Processing sheet with id=AC4, first strand: chain 'F' and resid 1625 through 1627 removed outlier: 3.663A pdb=" N SER F1570 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU F1602 " --> pdb=" O SER F1570 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F1614 " --> pdb=" O TRP F1634 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 1625 through 1627 removed outlier: 4.590A pdb=" N VAL F1852 " --> pdb=" O LEU F1571 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR F1829 " --> pdb=" O VAL F1853 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN F1855 " --> pdb=" O THR F1829 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE F1831 " --> pdb=" O GLN F1855 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2013 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: 8.44 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2509 1.27 - 1.41: 3953 1.41 - 1.55: 9149 1.55 - 1.68: 50 1.68 - 1.82: 84 Bond restraints: 15745 Sorted by residual: bond pdb=" C1B NDP F2603 " pdb=" C2B NDP F2603 " ideal model delta sigma weight residual 1.575 1.252 0.323 3.70e-02 7.30e+02 7.64e+01 bond pdb=" C1B NDP E2602 " pdb=" C2B NDP E2602 " ideal model delta sigma weight residual 1.575 1.252 0.323 3.70e-02 7.30e+02 7.64e+01 bond pdb=" C2D NDP F2602 " pdb=" C3D NDP F2602 " ideal model delta sigma weight residual 1.545 1.233 0.312 3.60e-02 7.72e+02 7.50e+01 bond pdb=" C1B NDP F2602 " pdb=" C2B NDP F2602 " ideal model delta sigma weight residual 1.575 1.258 0.317 3.70e-02 7.30e+02 7.36e+01 bond pdb=" C2D NDP F2603 " pdb=" C3D NDP F2603 " ideal model delta sigma weight residual 1.545 1.237 0.308 3.60e-02 7.72e+02 7.32e+01 ... (remaining 15740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.34: 21410 6.34 - 12.69: 70 12.69 - 19.03: 17 19.03 - 25.37: 3 25.37 - 31.72: 2 Bond angle restraints: 21502 Sorted by residual: angle pdb=" PA NDP F2602 " pdb=" O3 NDP F2602 " pdb=" PN NDP F2602 " ideal model delta sigma weight residual 107.74 130.81 -23.07 1.95e+00 2.62e-01 1.39e+02 angle pdb=" C12 X5O E2601 " pdb=" C13 X5O E2601 " pdb=" C16 X5O E2601 " ideal model delta sigma weight residual 112.89 81.17 31.72 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C12 X5O F2601 " pdb=" C13 X5O F2601 " pdb=" C16 X5O F2601 " ideal model delta sigma weight residual 112.89 82.95 29.94 3.00e+00 1.11e-01 9.96e+01 angle pdb=" PA NDP E2602 " pdb=" O3 NDP E2602 " pdb=" PN NDP E2602 " ideal model delta sigma weight residual 107.74 125.10 -17.36 1.95e+00 2.62e-01 7.89e+01 angle pdb=" C14 X5O F2601 " pdb=" C13 X5O F2601 " pdb=" C16 X5O F2601 " ideal model delta sigma weight residual 112.13 135.00 -22.87 3.00e+00 1.11e-01 5.81e+01 ... (remaining 21497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 8921 35.56 - 71.12: 271 71.12 - 106.68: 19 106.68 - 142.24: 1 142.24 - 177.80: 3 Dihedral angle restraints: 9215 sinusoidal: 3409 harmonic: 5806 Sorted by residual: dihedral pdb=" C5B NDP F2602 " pdb=" O5B NDP F2602 " pdb=" PA NDP F2602 " pdb=" O3 NDP F2602 " ideal model delta sinusoidal sigma weight residual 175.04 -2.76 177.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5B NDP E2602 " pdb=" O5B NDP E2602 " pdb=" PA NDP E2602 " pdb=" O3 NDP E2602 " ideal model delta sinusoidal sigma weight residual 175.04 -26.89 -158.07 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C5B NDP F2603 " pdb=" O5B NDP F2603 " pdb=" PA NDP F2603 " pdb=" O3 NDP F2603 " ideal model delta sinusoidal sigma weight residual 175.04 23.03 152.01 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 9212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2447 0.144 - 0.288: 16 0.288 - 0.431: 4 0.431 - 0.575: 1 0.575 - 0.719: 2 Chirality restraints: 2470 Sorted by residual: chirality pdb=" C1B NDP E2602 " pdb=" C2B NDP E2602 " pdb=" N9A NDP E2602 " pdb=" O4B NDP E2602 " both_signs ideal model delta sigma weight residual False 2.59 1.87 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1B NDP F2602 " pdb=" C2B NDP F2602 " pdb=" N9A NDP F2602 " pdb=" O4B NDP F2602 " both_signs ideal model delta sigma weight residual False 2.59 2.00 0.59 2.00e-01 2.50e+01 8.78e+00 chirality pdb=" C3D NDP E2603 " pdb=" C2D NDP E2603 " pdb=" C4D NDP E2603 " pdb=" O3D NDP E2603 " both_signs ideal model delta sigma weight residual False -2.71 -2.27 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2467 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F1558 " 0.065 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO F1559 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO F1559 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO F1559 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F1405 " 0.034 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO F1406 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F1406 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F1406 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E1657 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C TYR E1657 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR E1657 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA E1658 " -0.011 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 719 2.72 - 3.26: 15374 3.26 - 3.81: 27793 3.81 - 4.35: 34031 4.35 - 4.90: 57158 Nonbonded interactions: 135075 Sorted by model distance: nonbonded pdb=" N GLU F1950 " pdb=" OE1 GLU F1950 " model vdw 2.171 3.120 nonbonded pdb=" O GLU F1233 " pdb=" NH1 ARG F1461 " model vdw 2.181 3.120 nonbonded pdb=" OD1 ASP F1716 " pdb=" N SER F1717 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR E 891 " pdb=" OG1 THR E 923 " model vdw 2.213 3.040 nonbonded pdb=" O VAL F1732 " pdb=" OG1 THR F1736 " model vdw 2.214 3.040 ... (remaining 135070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 858 through 871 or (resid 872 and (name N or name CA or na \ me C or name O or name CB )) or resid 873 through 947 or (resid 948 and (name N \ or name CA or name C or name O or name CB )) or resid 949 through 962 or (resid \ 963 and (name N or name CA or name C or name O or name CB )) or resid 964 throug \ h 1067 or (resid 1068 and (name N or name CA or name C or name O or name CB )) o \ r resid 1069 or (resid 1070 and (name N or name CA or name C or name O or name C \ B )) or resid 1071 through 1104 or (resid 1105 through 1109 and (name N or name \ CA or name C or name O or name CB )) or resid 1110 through 1418 or (resid 1419 t \ hrough 1421 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 22 through 1503 or (resid 1504 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1505 through 1522 or (resid 1523 and (name N or name CA or name \ C or name O or name CB )) or resid 1524 through 1554 or (resid 1555 and (name N \ or name CA or name C or name O or name CB )) or resid 1556 or (resid 1557 throu \ gh 1558 and (name N or name CA or name C or name O or name CB )) or resid 1559 t \ hrough 1802 or resid 1805 through 1866 or resid 1871 through 1933 or (resid 1934 \ and (name N or name CA or name C or name O or name CB )) or resid 1935 through \ 1960 or (resid 1961 and (name N or name CA or name C or name O or name CB )) or \ resid 1962 through 2080 or (resid 2081 and (name N or name CA or name C or name \ O or name CB )) or resid 2082 through 2112 or resid 2601 through 2603)) selection = (chain 'F' and (resid 858 through 866 or (resid 867 through 869 and (name N or n \ ame CA or name C or name O or name CB )) or resid 870 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 966 or (resid 967 and (name N or name CA or name C or name O or name C \ B )) or resid 968 through 969 or (resid 970 and (name N or name CA or name C or \ name O or name CB )) or resid 971 through 975 or (resid 976 and (name N or name \ CA or name C or name O or name CB )) or resid 977 through 980 or (resid 981 and \ (name N or name CA or name C or name O or name CB )) or resid 982 or (resid 983 \ and (name N or name CA or name C or name O or name CB )) or resid 984 through 10 \ 42 or (resid 1043 through 1044 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1045 through 1105 or (resid 1106 through 1109 and (name N or na \ me CA or name C or name O or name CB )) or resid 1110 or (resid 1111 and (name N \ or name CA or name C or name O or name CB )) or resid 1112 through 1122 or (res \ id 1410 through 1411 and (name N or name CA or name C or name O or name CB )) or \ resid 1412 or (resid 1413 and (name N or name CA or name C or name O or name CB \ )) or resid 1414 or (resid 1415 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1416 through 1427 or (resid 1428 through 1429 and (name N or \ name CA or name C or name O or name CB )) or resid 1430 or (resid 1431 through 1 \ 439 and (name N or name CA or name C or name O or name CB )) or resid 1440 throu \ gh 1443 or (resid 1444 through 1445 and (name N or name CA or name C or name O o \ r name CB )) or resid 1446 through 1459 or (resid 1460 through 1461 and (name N \ or name CA or name C or name O or name CB )) or resid 1462 through 1466 or (resi \ d 1467 through 1471 and (name N or name CA or name C or name O or name CB )) or \ resid 1472 through 1482 or (resid 1483 and (name N or name CA or name C or name \ O or name CB )) or resid 1484 through 1492 or (resid 1493 through 1498 and (name \ N or name CA or name C or name O or name CB )) or (resid 1499 through 1504 and \ (name N or name CA or name C or name O or name CB )) or resid 1505 through 1519 \ or (resid 1520 through 1523 and (name N or name CA or name C or name O or name C \ B )) or resid 1524 through 1557 or (resid 1558 and (name N or name CA or name C \ or name O or name CB )) or resid 1559 through 1585 or (resid 1586 through 1587 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1588 through 15 \ 92 or (resid 1593 and (name N or name CA or name C or name O or name CB )) or re \ sid 1594 or (resid 1595 and (name N or name CA or name C or name O or name CB )) \ or resid 1596 through 1861 or (resid 1862 through 1864 and (name N or name CA o \ r name C or name O or name CB )) or resid 1865 through 1980 or (resid 1981 and ( \ name N or name CA or name C or name O or name CB )) or resid 1982 through 2070 o \ r (resid 2071 and (name N or name CA or name C or name O or name CB )) or resid \ 2072 through 2074 or resid 2077 through 2112 or resid 2601 through 2603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 41.050 Find NCS groups from input model: 0.810 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.323 15745 Z= 0.818 Angle : 1.000 31.716 21502 Z= 0.461 Chirality : 0.051 0.719 2470 Planarity : 0.004 0.096 2754 Dihedral : 16.758 177.797 5479 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.25 % Allowed : 23.16 % Favored : 75.59 % 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: 0.16 (0.20), residues: 2012 helix: 0.72 (0.21), residues: 698 sheet: -0.47 (0.27), residues: 392 loop : 0.07 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E1442 HIS 0.003 0.001 HIS E1735 PHE 0.009 0.001 PHE E1728 TYR 0.024 0.001 TYR F 991 ARG 0.006 0.000 ARG F1461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9081 (t0) cc_final: 0.8754 (t0) REVERT: E 1458 ASN cc_start: 0.8831 (m-40) cc_final: 0.8348 (m110) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 1.2391 time to fit residues: 188.4810 Evaluate side-chains 133 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1473 LEU Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1789 VAL Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1065 LYS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1650 VAL Chi-restraints excluded: chain F residue 1651 VAL 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 1915 THR Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15745 Z= 0.244 Angle : 0.557 7.360 21502 Z= 0.280 Chirality : 0.042 0.182 2470 Planarity : 0.004 0.056 2754 Dihedral : 8.882 161.316 2299 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 19.61 % Favored : 76.97 % 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: 0.14 (0.20), residues: 2012 helix: 0.76 (0.21), residues: 712 sheet: -0.74 (0.27), residues: 398 loop : 0.13 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1442 HIS 0.006 0.001 HIS E1674 PHE 0.011 0.001 PHE F1791 TYR 0.022 0.001 TYR F 991 ARG 0.004 0.000 ARG F1921 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: E 915 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8731 (mt-10) REVERT: E 1071 ASP cc_start: 0.9062 (t0) cc_final: 0.8727 (t0) REVERT: E 1458 ASN cc_start: 0.8814 (m-40) cc_final: 0.8548 (m110) REVERT: E 1596 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: E 1614 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7086 (pp-130) REVERT: E 2012 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8349 (mp0) REVERT: F 862 TYR cc_start: 0.8850 (m-80) cc_final: 0.8565 (m-80) REVERT: F 915 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8819 (mt-10) REVERT: F 1023 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8507 (mtmm) REVERT: F 1989 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7120 (mp10) outliers start: 52 outliers final: 15 residues processed: 175 average time/residue: 1.2484 time to fit residues: 243.4466 Evaluate side-chains 139 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1583 LEU Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1601 MET Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN F2059 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15745 Z= 0.266 Angle : 0.547 10.393 21502 Z= 0.273 Chirality : 0.043 0.318 2470 Planarity : 0.003 0.049 2754 Dihedral : 8.057 155.147 2280 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.49 % Allowed : 20.00 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2012 helix: 0.78 (0.20), residues: 712 sheet: -0.84 (0.26), residues: 402 loop : 0.14 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.011 0.001 PHE F1791 TYR 0.024 0.002 TYR F 991 ARG 0.005 0.000 ARG F1461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9075 (t0) cc_final: 0.8745 (t0) REVERT: E 1458 ASN cc_start: 0.8876 (m-40) cc_final: 0.8593 (m110) REVERT: E 1614 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7134 (pp-130) REVERT: E 1725 ASP cc_start: 0.7899 (t70) cc_final: 0.7613 (m-30) REVERT: E 1797 ASP cc_start: 0.8697 (p0) cc_final: 0.8465 (p0) REVERT: E 2012 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8350 (mp0) REVERT: F 862 TYR cc_start: 0.8868 (m-80) cc_final: 0.8540 (m-80) REVERT: F 915 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8847 (mt-10) REVERT: F 1023 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8512 (mtmm) REVERT: F 1666 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7543 (mmp80) REVERT: F 1835 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7142 (mt0) REVERT: F 1989 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: F 2008 GLU cc_start: 0.7773 (pp20) cc_final: 0.7508 (pp20) outliers start: 53 outliers final: 18 residues processed: 172 average time/residue: 1.3536 time to fit residues: 257.8408 Evaluate side-chains 140 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1583 LEU Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1782 MET Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1824 ARG Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 185 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15745 Z= 0.254 Angle : 0.536 9.207 21502 Z= 0.268 Chirality : 0.042 0.184 2470 Planarity : 0.003 0.049 2754 Dihedral : 7.710 154.676 2280 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.55 % Allowed : 20.59 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 2012 helix: 0.81 (0.20), residues: 712 sheet: -0.86 (0.26), residues: 404 loop : 0.20 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.011 0.001 PHE F1791 TYR 0.023 0.002 TYR E 991 ARG 0.008 0.000 ARG F1515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9069 (t0) cc_final: 0.8759 (t0) REVERT: E 1458 ASN cc_start: 0.8928 (m-40) cc_final: 0.8622 (m110) REVERT: E 1518 LEU cc_start: 0.9075 (mt) cc_final: 0.8659 (tm) REVERT: E 1596 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: E 1614 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7099 (pp-130) REVERT: E 1725 ASP cc_start: 0.7891 (t70) cc_final: 0.7622 (m-30) REVERT: E 2012 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8347 (mp0) REVERT: F 862 TYR cc_start: 0.8877 (m-80) cc_final: 0.8523 (m-80) REVERT: F 915 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8780 (mt-10) REVERT: F 1023 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8512 (mtmm) REVERT: F 1432 LEU cc_start: 0.9317 (mm) cc_final: 0.9050 (mm) REVERT: F 1666 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7519 (mmp80) REVERT: F 1835 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7218 (mt0) REVERT: F 1989 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7098 (mp10) outliers start: 54 outliers final: 25 residues processed: 178 average time/residue: 1.3417 time to fit residues: 265.2091 Evaluate side-chains 147 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1853 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15745 Z= 0.251 Angle : 0.548 12.595 21502 Z= 0.272 Chirality : 0.042 0.350 2470 Planarity : 0.003 0.050 2754 Dihedral : 7.541 154.744 2280 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.42 % Allowed : 20.59 % Favored : 75.99 % 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: 0.14 (0.20), residues: 2012 helix: 0.83 (0.20), residues: 712 sheet: -0.86 (0.26), residues: 420 loop : 0.16 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.010 0.001 PHE F1791 TYR 0.023 0.001 TYR E 991 ARG 0.005 0.000 ARG F1515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9063 (t0) cc_final: 0.8796 (t0) REVERT: E 1458 ASN cc_start: 0.8943 (m-40) cc_final: 0.8624 (m110) REVERT: E 1518 LEU cc_start: 0.9140 (mt) cc_final: 0.8708 (tm) REVERT: E 1577 MET cc_start: 0.8240 (mmp) cc_final: 0.8037 (mmt) REVERT: E 1596 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: E 1614 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.7094 (pp-130) REVERT: E 1725 ASP cc_start: 0.7878 (t70) cc_final: 0.7634 (m-30) REVERT: E 2012 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8345 (mp0) REVERT: F 862 TYR cc_start: 0.8864 (m-80) cc_final: 0.8445 (m-80) REVERT: F 1023 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8510 (mtmm) REVERT: F 1432 LEU cc_start: 0.9306 (mm) cc_final: 0.8994 (mm) REVERT: F 1666 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7555 (mmp80) REVERT: F 1835 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7220 (mt0) REVERT: F 1989 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: F 2071 GLU cc_start: 0.7788 (pp20) cc_final: 0.7572 (pp20) outliers start: 52 outliers final: 28 residues processed: 172 average time/residue: 1.2984 time to fit residues: 248.3445 Evaluate side-chains 156 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1602 GLU Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1974 VAL Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1782 MET Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1853 VAL Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Chi-restraints excluded: chain F residue 2070 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1476 ASN F2031 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15745 Z= 0.215 Angle : 0.534 10.380 21502 Z= 0.265 Chirality : 0.042 0.253 2470 Planarity : 0.003 0.051 2754 Dihedral : 7.424 156.647 2280 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.49 % Allowed : 20.99 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 2012 helix: 0.85 (0.21), residues: 714 sheet: -0.80 (0.27), residues: 401 loop : 0.14 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.013 0.001 PHE F1514 TYR 0.022 0.001 TYR E 991 ARG 0.006 0.000 ARG F1515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9047 (t0) cc_final: 0.8818 (t0) REVERT: E 1458 ASN cc_start: 0.8921 (m-40) cc_final: 0.8622 (m110) REVERT: E 1515 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7592 (mmt-90) REVERT: E 1518 LEU cc_start: 0.9099 (mt) cc_final: 0.8678 (tm) REVERT: E 1596 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: E 1614 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7076 (pp-130) REVERT: E 1725 ASP cc_start: 0.7872 (t70) cc_final: 0.7613 (m-30) REVERT: E 1835 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: E 2012 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8341 (mp0) REVERT: F 862 TYR cc_start: 0.8844 (m-80) cc_final: 0.8470 (m-80) REVERT: F 915 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8775 (mt-10) REVERT: F 1023 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8504 (mtmm) REVERT: F 1432 LEU cc_start: 0.9330 (mm) cc_final: 0.9034 (mm) REVERT: F 1518 LEU cc_start: 0.9010 (tp) cc_final: 0.8755 (tm) REVERT: F 1520 GLU cc_start: 0.8670 (mp0) cc_final: 0.8466 (mp0) REVERT: F 1835 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7216 (mt0) REVERT: F 1989 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: F 2071 GLU cc_start: 0.7751 (pp20) cc_final: 0.7484 (pp20) outliers start: 53 outliers final: 29 residues processed: 185 average time/residue: 1.2581 time to fit residues: 259.8741 Evaluate side-chains 162 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1940 GLN Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1795 LEU Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1843 MET Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1922 THR Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1476 ASN ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15745 Z= 0.290 Angle : 0.566 10.066 21502 Z= 0.281 Chirality : 0.043 0.175 2470 Planarity : 0.003 0.052 2754 Dihedral : 7.436 157.345 2279 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.36 % Allowed : 20.92 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 2012 helix: 0.83 (0.21), residues: 712 sheet: -0.83 (0.26), residues: 403 loop : 0.14 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F1442 HIS 0.004 0.001 HIS E1674 PHE 0.017 0.001 PHE E2109 TYR 0.025 0.002 TYR E 991 ARG 0.007 0.000 ARG F1515 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9040 (t0) cc_final: 0.8801 (t0) REVERT: E 1458 ASN cc_start: 0.8942 (m-40) cc_final: 0.8622 (m110) REVERT: E 1515 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7581 (mmt-90) REVERT: E 1518 LEU cc_start: 0.9119 (mt) cc_final: 0.8693 (tm) REVERT: E 1596 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: E 1614 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7086 (pp-130) REVERT: E 1725 ASP cc_start: 0.7899 (t70) cc_final: 0.7647 (m-30) REVERT: E 1835 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: E 2012 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8329 (mp0) REVERT: F 1023 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8521 (mtmm) REVERT: F 1432 LEU cc_start: 0.9336 (mm) cc_final: 0.9076 (mm) REVERT: F 1835 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7252 (mt0) REVERT: F 1989 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: F 2071 GLU cc_start: 0.7759 (pp20) cc_final: 0.7462 (pp20) outliers start: 51 outliers final: 30 residues processed: 174 average time/residue: 1.2905 time to fit residues: 252.7087 Evaluate side-chains 161 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1542 SER Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1562 GLN Chi-restraints excluded: chain E residue 1596 ASP Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1782 MET Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1843 MET Chi-restraints excluded: chain F residue 1853 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1872 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1476 ASN ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15745 Z= 0.490 Angle : 0.651 10.432 21502 Z= 0.325 Chirality : 0.046 0.171 2470 Planarity : 0.004 0.051 2754 Dihedral : 7.700 155.059 2279 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.83 % Allowed : 21.91 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 2012 helix: 0.67 (0.20), residues: 703 sheet: -0.94 (0.26), residues: 421 loop : 0.12 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F1442 HIS 0.007 0.001 HIS F1553 PHE 0.019 0.002 PHE F1514 TYR 0.030 0.002 TYR F 991 ARG 0.015 0.001 ARG F1552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1071 ASP cc_start: 0.9064 (t0) cc_final: 0.8779 (t0) REVERT: E 1515 ARG cc_start: 0.7831 (mmm-85) cc_final: 0.7583 (mmt-90) REVERT: E 1614 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.7117 (pp-130) REVERT: E 1725 ASP cc_start: 0.7949 (t70) cc_final: 0.7708 (m-30) REVERT: E 1835 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: E 2012 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8328 (mp0) REVERT: F 1023 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8528 (mtmm) REVERT: F 1432 LEU cc_start: 0.9322 (mm) cc_final: 0.9091 (mm) REVERT: F 1666 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7591 (mmp80) REVERT: F 1835 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7356 (mt0) REVERT: F 1989 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: F 2012 GLU cc_start: 0.7578 (pm20) cc_final: 0.7212 (pm20) REVERT: F 2071 GLU cc_start: 0.7743 (pp20) cc_final: 0.7534 (pp20) outliers start: 43 outliers final: 27 residues processed: 162 average time/residue: 1.1713 time to fit residues: 212.7925 Evaluate side-chains 156 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1547 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1872 LEU Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain E residue 2070 VAL Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1052 VAL Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1789 VAL Chi-restraints excluded: chain F residue 1824 ARG Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1853 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1873 MET Chi-restraints excluded: chain F residue 1886 SER Chi-restraints excluded: chain F residue 1939 VAL Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 119 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1476 ASN ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15745 Z= 0.191 Angle : 0.566 9.912 21502 Z= 0.280 Chirality : 0.042 0.225 2470 Planarity : 0.003 0.052 2754 Dihedral : 7.477 164.794 2279 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 22.96 % 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: 0.10 (0.20), residues: 2012 helix: 0.82 (0.21), residues: 707 sheet: -0.82 (0.26), residues: 409 loop : 0.07 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F1442 HIS 0.006 0.001 HIS E1674 PHE 0.015 0.001 PHE F1514 TYR 0.019 0.001 TYR F 991 ARG 0.008 0.000 ARG F1552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: E 1458 ASN cc_start: 0.8945 (m-40) cc_final: 0.8619 (m110) REVERT: E 1515 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7447 (mmt-90) REVERT: E 1614 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7011 (pp-130) REVERT: E 1725 ASP cc_start: 0.7923 (t70) cc_final: 0.7652 (m-30) REVERT: E 1820 ASP cc_start: 0.8517 (m-30) cc_final: 0.8273 (m-30) REVERT: E 1835 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: E 2012 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8328 (mp0) REVERT: F 862 TYR cc_start: 0.8793 (m-80) cc_final: 0.8523 (m-80) REVERT: F 915 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8768 (mt-10) REVERT: F 1023 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8517 (mtmm) REVERT: F 1432 LEU cc_start: 0.9329 (mm) cc_final: 0.8884 (mm) REVERT: F 1666 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7540 (mmt180) REVERT: F 1835 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7113 (mt0) REVERT: F 1886 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8046 (p) REVERT: F 1989 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7048 (mp10) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 1.3009 time to fit residues: 229.6803 Evaluate side-chains 145 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1993 LYS Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1789 VAL 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 1886 SER Chi-restraints excluded: chain F residue 1974 VAL Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 98 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15745 Z= 0.307 Angle : 0.599 9.649 21502 Z= 0.299 Chirality : 0.044 0.218 2470 Planarity : 0.003 0.051 2754 Dihedral : 7.533 170.159 2279 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 23.29 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 2012 helix: 0.75 (0.21), residues: 710 sheet: -0.97 (0.26), residues: 416 loop : 0.18 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F1442 HIS 0.005 0.001 HIS F1553 PHE 0.020 0.001 PHE F1514 TYR 0.026 0.002 TYR F 991 ARG 0.010 0.000 ARG F1515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.981 Fit side-chains revert: symmetry clash REVERT: E 1458 ASN cc_start: 0.8952 (m-40) cc_final: 0.8601 (m110) REVERT: E 1515 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7562 (mmt-90) REVERT: E 1614 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.7103 (pp-130) REVERT: E 1725 ASP cc_start: 0.7935 (t70) cc_final: 0.7682 (m-30) REVERT: E 1835 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: E 2012 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8310 (mp0) REVERT: F 862 TYR cc_start: 0.8848 (m-80) cc_final: 0.8546 (m-80) REVERT: F 915 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8790 (mt-10) REVERT: F 1023 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8530 (mtmm) REVERT: F 1432 LEU cc_start: 0.9321 (mm) cc_final: 0.8860 (mm) REVERT: F 1666 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7656 (mmp80) REVERT: F 1835 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7242 (mt0) REVERT: F 1989 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7190 (mp10) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 1.2370 time to fit residues: 211.4568 Evaluate side-chains 148 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 1505 VAL Chi-restraints excluded: chain E residue 1557 THR Chi-restraints excluded: chain E residue 1614 MET Chi-restraints excluded: chain E residue 1677 SER Chi-restraints excluded: chain E residue 1697 THR Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain F residue 1044 HIS Chi-restraints excluded: chain F residue 1048 LEU Chi-restraints excluded: chain F residue 1052 VAL Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1428 LEU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1493 LEU Chi-restraints excluded: chain F residue 1563 LEU Chi-restraints excluded: chain F residue 1651 VAL Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1789 VAL 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 1974 VAL Chi-restraints excluded: chain F residue 1989 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 148 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.084931 restraints weight = 23811.541| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.45 r_work: 0.2920 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15745 Z= 0.237 Angle : 0.590 15.311 21502 Z= 0.290 Chirality : 0.043 0.327 2470 Planarity : 0.003 0.051 2754 Dihedral : 7.500 175.684 2279 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.84 % Allowed : 23.29 % Favored : 74.87 % 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: 0.08 (0.19), residues: 2012 helix: 0.77 (0.21), residues: 710 sheet: -0.93 (0.27), residues: 384 loop : 0.12 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F1442 HIS 0.005 0.001 HIS E1674 PHE 0.013 0.001 PHE E2109 TYR 0.022 0.001 TYR E 991 ARG 0.010 0.000 ARG F1515 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4988.29 seconds wall clock time: 90 minutes 43.86 seconds (5443.86 seconds total)