Starting phenix.real_space_refine on Fri Nov 17 01:02:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/11_2023/7kog_22975.pdb" } resolution = 4.25 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 10520 2.51 5 N 3228 2.21 5 O 3610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 861": "OE1" <-> "OE2" Residue "B GLU 872": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 891": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 938": "OE1" <-> "OE2" Residue "B GLU 954": "OE1" <-> "OE2" Residue "B ASP 964": "OD1" <-> "OD2" Residue "B GLU 1003": "OE1" <-> "OE2" Residue "B GLU 1009": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1022": "OE1" <-> "OE2" Residue "B GLU 1036": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1047": "OE1" <-> "OE2" Residue "B GLU 1049": "OE1" <-> "OE2" Residue "B GLU 1064": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1085": "OE1" <-> "OE2" Residue "B GLU 1103": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B GLU 1118": "OE1" <-> "OE2" Residue "B GLU 1125": "OE1" <-> "OE2" Residue "B GLU 1127": "OE1" <-> "OE2" Residue "B GLU 1128": "OE1" <-> "OE2" Residue "B GLU 1131": "OE1" <-> "OE2" Residue "B GLU 1141": "OE1" <-> "OE2" Residue "B GLU 1170": "OE1" <-> "OE2" Residue "B GLU 1178": "OE1" <-> "OE2" Residue "B GLU 1187": "OE1" <-> "OE2" Residue "B GLU 1194": "OE1" <-> "OE2" Residue "B GLU 1213": "OE1" <-> "OE2" Residue "B ARG 1229": "NH1" <-> "NH2" Residue "B GLU 1254": "OE1" <-> "OE2" Residue "B GLU 1329": "OE1" <-> "OE2" Residue "B ARG 1342": "NH1" <-> "NH2" Residue "B GLU 1356": "OE1" <-> "OE2" Residue "B GLU 1358": "OE1" <-> "OE2" Residue "B ARG 1380": "NH1" <-> "NH2" Residue "B GLU 1386": "OE1" <-> "OE2" Residue "B GLU 1393": "OE1" <-> "OE2" Residue "B GLU 1410": "OE1" <-> "OE2" Residue "B GLU 1413": "OE1" <-> "OE2" Residue "B GLU 1432": "OE1" <-> "OE2" Residue "B GLU 1434": "OE1" <-> "OE2" Residue "B GLU 1439": "OE1" <-> "OE2" Residue "B GLU 1481": "OE1" <-> "OE2" Residue "B GLU 1498": "OE1" <-> "OE2" Residue "B GLU 1504": "OE1" <-> "OE2" Residue "B GLU 1516": "OE1" <-> "OE2" Residue "B GLU 1533": "OE1" <-> "OE2" Residue "B GLU 1542": "OE1" <-> "OE2" Residue "B GLU 1547": "OE1" <-> "OE2" Residue "B GLU 1554": "OE1" <-> "OE2" Residue "B GLU 1556": "OE1" <-> "OE2" Residue "B GLU 1562": "OE1" <-> "OE2" Residue "B ASP 1581": "OD1" <-> "OD2" Residue "B GLU 1586": "OE1" <-> "OE2" Residue "B GLU 1588": "OE1" <-> "OE2" Residue "B GLU 1590": "OE1" <-> "OE2" Residue "B GLU 1610": "OE1" <-> "OE2" Residue "B GLU 1627": "OE1" <-> "OE2" Residue "B GLU 1632": "OE1" <-> "OE2" Residue "B GLU 1634": "OE1" <-> "OE2" Residue "B GLU 1677": "OE1" <-> "OE2" Residue "B GLU 1694": "OE1" <-> "OE2" Residue "B GLU 1713": "OE1" <-> "OE2" Residue "B GLU 1719": "OE1" <-> "OE2" Residue "B GLU 1761": "OE1" <-> "OE2" Residue "B GLU 1776": "OE1" <-> "OE2" Residue "B GLU 1780": "OE1" <-> "OE2" Residue "B GLU 1788": "OE1" <-> "OE2" Residue "B GLU 1807": "OE1" <-> "OE2" Residue "B GLU 1824": "OE1" <-> "OE2" Residue "B GLU 1833": "OE1" <-> "OE2" Residue "B GLU 1837": "OE1" <-> "OE2" Residue "B GLU 1857": "OE1" <-> "OE2" Residue "B GLU 1910": "OE1" <-> "OE2" Residue "B ARG 1929": "NH1" <-> "NH2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A GLU 1118": "OE1" <-> "OE2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A GLU 1129": "OE1" <-> "OE2" Residue "A GLU 1141": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1159": "OE1" <-> "OE2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A GLU 1210": "OE1" <-> "OE2" Residue "A GLU 1226": "OE1" <-> "OE2" Residue "A ARG 1229": "NH1" <-> "NH2" Residue "A GLU 1249": "OE1" <-> "OE2" Residue "A GLU 1266": "OE1" <-> "OE2" Residue "A GLU 1300": "OE1" <-> "OE2" Residue "A ARG 1332": "NH1" <-> "NH2" Residue "A GLU 1345": "OE1" <-> "OE2" Residue "A GLU 1356": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A GLU 1360": "OE1" <-> "OE2" Residue "A GLU 1375": "OE1" <-> "OE2" Residue "A GLU 1386": "OE1" <-> "OE2" Residue "A GLU 1395": "OE1" <-> "OE2" Residue "A GLU 1423": "OE1" <-> "OE2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A GLU 1488": "OE1" <-> "OE2" Residue "A GLU 1501": "OE1" <-> "OE2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A GLU 1556": "OE1" <-> "OE2" Residue "A GLU 1560": "OE1" <-> "OE2" Residue "A GLU 1562": "OE1" <-> "OE2" Residue "A GLU 1563": "OE1" <-> "OE2" Residue "A GLU 1572": "OE1" <-> "OE2" Residue "A GLU 1579": "OE1" <-> "OE2" Residue "A GLU 1590": "OE1" <-> "OE2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A GLU 1618": "OE1" <-> "OE2" Residue "A ARG 1621": "NH1" <-> "NH2" Residue "A GLU 1627": "OE1" <-> "OE2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A GLU 1646": "OE1" <-> "OE2" Residue "A GLU 1666": "OE1" <-> "OE2" Residue "A GLU 1683": "OE1" <-> "OE2" Residue "A GLU 1695": "OE1" <-> "OE2" Residue "A GLU 1701": "OE1" <-> "OE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A GLU 1719": "OE1" <-> "OE2" Residue "A GLU 1723": "OE1" <-> "OE2" Residue "A GLU 1739": "OE1" <-> "OE2" Residue "A GLU 1751": "OE1" <-> "OE2" Residue "A GLU 1760": "OE1" <-> "OE2" Residue "A GLU 1761": "OE1" <-> "OE2" Residue "A GLU 1780": "OE1" <-> "OE2" Residue "A GLU 1788": "OE1" <-> "OE2" Residue "A GLU 1800": "OE1" <-> "OE2" Residue "A ARG 1828": "NH1" <-> "NH2" Residue "A GLU 1829": "OE1" <-> "OE2" Residue "A GLU 1831": "OE1" <-> "OE2" Residue "A GLU 1852": "OE1" <-> "OE2" Residue "A GLU 1857": "OE1" <-> "OE2" Residue "A GLU 1864": "OE1" <-> "OE2" Residue "A GLU 1870": "OE1" <-> "OE2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A GLU 1915": "OE1" <-> "OE2" Residue "A GLU 1916": "OE1" <-> "OE2" Residue "A GLU 1922": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17384 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8692 Classifications: {'peptide': 1077} Link IDs: {'TRANS': 1076} Chain: "A" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8692 Classifications: {'peptide': 1077} Link IDs: {'TRANS': 1076} Time building chain proxies: 8.80, per 1000 atoms: 0.51 Number of scatterers: 17384 At special positions: 0 Unit cell: (89.18, 95.06, 1599.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 3610 8.00 N 3228 7.00 C 10520 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 3.2 seconds 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 100.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 854 through 889 removed outlier: 3.562A pdb=" N LEU B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 862 " --> pdb=" O ARG B 858 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B 863 " --> pdb=" O LYS B 859 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 864 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 872 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 873 " --> pdb=" O ALA B 869 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 880 " --> pdb=" O LYS B 876 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 881 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 883 " --> pdb=" O LYS B 879 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 889 " --> pdb=" O ASN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 922 removed outlier: 3.792A pdb=" N LEU B 895 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 911 " --> pdb=" O SER B 907 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 912 " --> pdb=" O SER B 908 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 935 removed outlier: 3.545A pdb=" N ASP B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 950 removed outlier: 4.320A pdb=" N ASN B 940 " --> pdb=" O GLN B 936 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 945 " --> pdb=" O ARG B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 993 removed outlier: 3.544A pdb=" N LEU B 967 " --> pdb=" O GLU B 963 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1092 removed outlier: 3.511A pdb=" N ASN B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B1004 " --> pdb=" O LEU B1000 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B1010 " --> pdb=" O MET B1006 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B1012 " --> pdb=" O GLY B1008 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B1015 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B1037 " --> pdb=" O ALA B1033 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1038 " --> pdb=" O LYS B1034 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B1047 " --> pdb=" O GLU B1043 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B1052 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B1063 " --> pdb=" O ALA B1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B1072 " --> pdb=" O LYS B1068 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B1082 " --> pdb=" O GLU B1078 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B1083 " --> pdb=" O ARG B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1119 removed outlier: 3.982A pdb=" N ALA B1100 " --> pdb=" O ALA B1096 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1108 " --> pdb=" O ASP B1104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B1110 " --> pdb=" O GLN B1106 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B1117 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1184 removed outlier: 3.966A pdb=" N GLU B1125 " --> pdb=" O SER B1121 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B1132 " --> pdb=" O GLU B1128 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B1158 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU B1159 " --> pdb=" O GLY B1155 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B1173 " --> pdb=" O ILE B1169 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS B1174 " --> pdb=" O GLU B1170 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B1177 " --> pdb=" O LYS B1173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B1182 " --> pdb=" O GLU B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1185 through 1343 removed outlier: 3.875A pdb=" N GLN B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1200 " --> pdb=" O THR B1196 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1202 " --> pdb=" O ALA B1198 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B1203 " --> pdb=" O ASN B1199 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B1207 " --> pdb=" O LYS B1203 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B1208 " --> pdb=" O HIS B1204 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B1231 " --> pdb=" O HIS B1227 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B1233 " --> pdb=" O ARG B1229 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B1235 " --> pdb=" O HIS B1231 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B1244 " --> pdb=" O ARG B1240 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B1248 " --> pdb=" O ASP B1244 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B1251 " --> pdb=" O CYS B1247 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B1255 " --> pdb=" O ALA B1251 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B1263 " --> pdb=" O GLN B1259 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN B1268 " --> pdb=" O VAL B1264 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B1269 " --> pdb=" O ASN B1265 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B1277 " --> pdb=" O GLU B1273 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B1281 " --> pdb=" O THR B1277 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP B1282 " --> pdb=" O LEU B1278 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B1287 " --> pdb=" O SER B1283 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B1297 " --> pdb=" O SER B1293 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN B1298 " --> pdb=" O ASP B1294 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B1303 " --> pdb=" O LEU B1299 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B1308 " --> pdb=" O SER B1304 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS B1311 " --> pdb=" O SER B1307 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B1312 " --> pdb=" O GLN B1308 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B1314 " --> pdb=" O SER B1310 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B1318 " --> pdb=" O VAL B1314 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B1321 " --> pdb=" O THR B1317 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B1335 " --> pdb=" O ALA B1331 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B1336 " --> pdb=" O ARG B1332 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B1343 " --> pdb=" O GLY B1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1343 through 1365 removed outlier: 3.584A pdb=" N ARG B1352 " --> pdb=" O LEU B1348 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B1353 " --> pdb=" O ASP B1349 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B1358 " --> pdb=" O GLN B1354 " (cutoff:3.500A) Processing helix chain 'B' and resid 1367 through 1553 removed outlier: 3.830A pdb=" N ASN B1373 " --> pdb=" O LEU B1369 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B1375 " --> pdb=" O LYS B1371 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA B1376 " --> pdb=" O ALA B1372 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA B1389 " --> pdb=" O SER B1385 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B1395 " --> pdb=" O ALA B1391 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B1400 " --> pdb=" O GLU B1396 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1405 " --> pdb=" O LEU B1401 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B1410 " --> pdb=" O ALA B1406 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B1411 " --> pdb=" O GLU B1407 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B1417 " --> pdb=" O GLU B1413 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B1418 " --> pdb=" O SER B1414 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B1422 " --> pdb=" O LYS B1418 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B1428 " --> pdb=" O LYS B1424 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1429 " --> pdb=" O THR B1425 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1431 " --> pdb=" O GLN B1427 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B1433 " --> pdb=" O LEU B1429 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B1437 " --> pdb=" O VAL B1433 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1438 " --> pdb=" O GLU B1434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B1439 " --> pdb=" O ASP B1435 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B1441 " --> pdb=" O GLN B1437 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B1448 " --> pdb=" O THR B1444 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B1452 " --> pdb=" O ASN B1448 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B1453 " --> pdb=" O ALA B1449 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B1461 " --> pdb=" O ILE B1457 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B1462 " --> pdb=" O ASP B1458 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B1467 " --> pdb=" O GLU B1463 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP B1469 " --> pdb=" O LYS B1465 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1477 " --> pdb=" O ALA B1473 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1481 " --> pdb=" O ALA B1477 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B1486 " --> pdb=" O CYS B1482 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B1488 " --> pdb=" O ASN B1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B1490 " --> pdb=" O SER B1486 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B1495 " --> pdb=" O ARG B1491 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B1501 " --> pdb=" O GLU B1497 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU B1516 " --> pdb=" O ASN B1512 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B1532 " --> pdb=" O GLY B1528 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B1535 " --> pdb=" O ILE B1531 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B1551 " --> pdb=" O GLU B1547 " (cutoff:3.500A) Processing helix chain 'B' and resid 1554 through 1578 removed outlier: 3.614A pdb=" N LYS B1565 " --> pdb=" O GLN B1561 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B1566 " --> pdb=" O GLU B1562 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B1570 " --> pdb=" O VAL B1566 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B1573 " --> pdb=" O SER B1569 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B1575 " --> pdb=" O LEU B1571 " (cutoff:3.500A) Processing helix chain 'B' and resid 1579 through 1803 removed outlier: 3.568A pdb=" N ARG B1583 " --> pdb=" O GLU B1579 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B1584 " --> pdb=" O ILE B1580 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B1585 " --> pdb=" O ASP B1581 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU B1588 " --> pdb=" O ILE B1584 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B1589 " --> pdb=" O GLN B1585 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B1593 " --> pdb=" O GLU B1589 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B1600 " --> pdb=" O LYS B1596 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B1603 " --> pdb=" O GLN B1599 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B1618 " --> pdb=" O LYS B1614 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B1619 " --> pdb=" O GLY B1615 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B1624 " --> pdb=" O LEU B1620 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B1628 " --> pdb=" O LYS B1624 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU B1634 " --> pdb=" O ILE B1630 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B1635 " --> pdb=" O ASN B1631 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B1636 " --> pdb=" O GLU B1632 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B1650 " --> pdb=" O GLU B1646 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1655 " --> pdb=" O ILE B1651 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B1656 " --> pdb=" O LYS B1652 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B1657 " --> pdb=" O LYS B1653 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B1670 " --> pdb=" O GLU B1666 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B1673 " --> pdb=" O GLN B1669 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B1674 " --> pdb=" O ARG B1670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B1675 " --> pdb=" O ALA B1671 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B1684 " --> pdb=" O GLY B1680 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B1690 " --> pdb=" O ALA B1686 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B1692 " --> pdb=" O ALA B1688 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B1698 " --> pdb=" O GLU B1694 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B1705 " --> pdb=" O GLU B1701 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B1706 " --> pdb=" O GLN B1702 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B1713 " --> pdb=" O GLN B1709 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B1719 " --> pdb=" O GLY B1715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B1725 " --> pdb=" O ILE B1721 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B1730 " --> pdb=" O ALA B1726 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B1736 " --> pdb=" O SER B1732 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B1741 " --> pdb=" O LYS B1737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B1744 " --> pdb=" O GLY B1740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B1747 " --> pdb=" O GLN B1743 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B1750 " --> pdb=" O HIS B1746 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B1751 " --> pdb=" O ALA B1747 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B1762 " --> pdb=" O ASN B1758 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B1763 " --> pdb=" O SER B1759 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B1783 " --> pdb=" O ALA B1779 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B1796 " --> pdb=" O LYS B1792 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B1799 " --> pdb=" O GLU B1795 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B1801 " --> pdb=" O GLN B1797 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1808 Processing helix chain 'B' and resid 1812 through 1815 Processing helix chain 'B' and resid 1816 through 1841 removed outlier: 3.520A pdb=" N VAL B1827 " --> pdb=" O LEU B1823 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B1829 " --> pdb=" O GLN B1825 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B1832 " --> pdb=" O ARG B1828 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B1839 " --> pdb=" O ASP B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1841 through 1929 removed outlier: 3.504A pdb=" N LYS B1850 " --> pdb=" O LYS B1846 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B1854 " --> pdb=" O LYS B1850 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B1859 " --> pdb=" O ILE B1855 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B1860 " --> pdb=" O LYS B1856 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B1864 " --> pdb=" O PHE B1860 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B1871 " --> pdb=" O LYS B1867 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B1872 " --> pdb=" O ASN B1868 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B1874 " --> pdb=" O GLU B1870 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B1881 " --> pdb=" O ASP B1877 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B1882 " --> pdb=" O LYS B1878 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B1884 " --> pdb=" O GLN B1880 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU B1895 " --> pdb=" O GLU B1891 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B1904 " --> pdb=" O ASN B1900 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B1909 " --> pdb=" O ARG B1905 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B1910 " --> pdb=" O LYS B1906 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B1916 " --> pdb=" O GLU B1912 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B1917 " --> pdb=" O GLU B1913 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1918 " --> pdb=" O ALA B1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 907 removed outlier: 3.916A pdb=" N LYS A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 897 " --> pdb=" O THR A 893 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 907 " --> pdb=" O LYS A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 1127 removed outlier: 3.520A pdb=" N ALA A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 923 " --> pdb=" O GLN A 919 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 949 " --> pdb=" O PHE A 945 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 951 " --> pdb=" O GLN A 947 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 977 " --> pdb=" O ASP A 973 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 985 " --> pdb=" O HIS A 981 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 996 " --> pdb=" O HIS A 992 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A1014 " --> pdb=" O HIS A1010 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A1100 " --> pdb=" O ALA A1096 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A1103 " --> pdb=" O THR A1099 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A1109 " --> pdb=" O GLU A1105 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A1120 " --> pdb=" O ILE A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1192 removed outlier: 3.507A pdb=" N GLU A1131 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A1146 " --> pdb=" O LYS A1142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1159 " --> pdb=" O GLY A1155 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A1184 " --> pdb=" O SER A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1559 removed outlier: 3.794A pdb=" N THR A1196 " --> pdb=" O GLN A1192 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A1235 " --> pdb=" O HIS A1231 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A1241 " --> pdb=" O ASN A1237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A1245 " --> pdb=" O HIS A1241 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A1268 " --> pdb=" O VAL A1264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1290 " --> pdb=" O LYS A1286 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A1307 " --> pdb=" O GLU A1303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A1310 " --> pdb=" O VAL A1306 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1312 " --> pdb=" O GLN A1308 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1318 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A1332 " --> pdb=" O ASP A1328 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1336 " --> pdb=" O ARG A1332 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A1347 " --> pdb=" O ASN A1343 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A1353 " --> pdb=" O ASP A1349 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1356 " --> pdb=" O ARG A1352 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A1365 " --> pdb=" O GLY A1361 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1370 " --> pdb=" O GLN A1366 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1374 " --> pdb=" O SER A1370 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1377 " --> pdb=" O ASN A1373 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A1385 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A1386 " --> pdb=" O LYS A1382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A1388 " --> pdb=" O GLU A1384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A1389 " --> pdb=" O SER A1385 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1395 " --> pdb=" O ALA A1391 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A1404 " --> pdb=" O LYS A1400 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A1408 " --> pdb=" O ARG A1404 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1413 " --> pdb=" O GLU A1409 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A1420 " --> pdb=" O ASN A1416 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A1432 " --> pdb=" O ARG A1428 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A1434 " --> pdb=" O ALA A1430 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A1437 " --> pdb=" O VAL A1433 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A1442 " --> pdb=" O LEU A1438 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1444 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A1447 " --> pdb=" O ALA A1443 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A1452 " --> pdb=" O ASN A1448 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1456 " --> pdb=" O LYS A1452 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A1458 " --> pdb=" O ALA A1454 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS A1459 " --> pdb=" O LYS A1455 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A1460 " --> pdb=" O ALA A1456 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU A1463 " --> pdb=" O LYS A1459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A1464 " --> pdb=" O ILE A1460 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A1473 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A1474 " --> pdb=" O ASP A1470 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1475 " --> pdb=" O LEU A1471 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR A1485 " --> pdb=" O GLU A1481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A1488 " --> pdb=" O ASN A1484 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1493 " --> pdb=" O LEU A1489 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A1498 " --> pdb=" O GLY A1494 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A1518 " --> pdb=" O ALA A1514 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A1519 " --> pdb=" O ASP A1515 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1520 " --> pdb=" O GLU A1516 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A1532 " --> pdb=" O GLY A1528 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1534 " --> pdb=" O ASN A1530 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A1538 " --> pdb=" O ILE A1534 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A1540 " --> pdb=" O LYS A1536 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1574 removed outlier: 4.188A pdb=" N GLU A1563 " --> pdb=" O LEU A1559 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1567 " --> pdb=" O GLU A1563 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A1569 " --> pdb=" O LYS A1565 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A1570 " --> pdb=" O VAL A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1923 removed outlier: 3.705A pdb=" N GLU A1579 " --> pdb=" O GLN A1575 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A1581 " --> pdb=" O ARG A1577 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A1584 " --> pdb=" O ILE A1580 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A1585 " --> pdb=" O ASP A1581 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A1593 " --> pdb=" O GLU A1589 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A1594 " --> pdb=" O GLU A1590 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A1600 " --> pdb=" O LYS A1596 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A1608 " --> pdb=" O SER A1604 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A1614 " --> pdb=" O GLU A1610 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A1621 " --> pdb=" O ALA A1617 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A1622 " --> pdb=" O GLU A1618 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A1638 " --> pdb=" O GLU A1634 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A1639 " --> pdb=" O ILE A1635 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A1643 " --> pdb=" O HIS A1639 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A1652 " --> pdb=" O GLN A1648 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1654 " --> pdb=" O THR A1650 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A1659 " --> pdb=" O GLN A1655 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1661 " --> pdb=" O GLN A1657 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A1670 " --> pdb=" O GLU A1666 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1685 " --> pdb=" O ILE A1681 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A1690 " --> pdb=" O ALA A1686 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A1691 " --> pdb=" O ASN A1687 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A1698 " --> pdb=" O GLU A1694 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A1703 " --> pdb=" O LEU A1699 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A1704 " --> pdb=" O LEU A1700 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A1708 " --> pdb=" O ASP A1704 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A1709 " --> pdb=" O ARG A1705 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A1712 " --> pdb=" O ARG A1708 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1717 " --> pdb=" O GLU A1713 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A1722 " --> pdb=" O HIS A1718 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A1725 " --> pdb=" O ILE A1721 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A1746 " --> pdb=" O LEU A1742 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A1769 " --> pdb=" O LYS A1765 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A1770 " --> pdb=" O ALA A1766 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A1776 " --> pdb=" O ARG A1772 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A1782 " --> pdb=" O ARG A1778 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A1791 " --> pdb=" O GLN A1787 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A1792 " --> pdb=" O GLU A1788 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1796 " --> pdb=" O LYS A1792 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A1798 " --> pdb=" O LEU A1794 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A1802 " --> pdb=" O ILE A1798 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A1835 " --> pdb=" O GLU A1831 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A1836 " --> pdb=" O ASN A1832 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A1843 " --> pdb=" O ARG A1839 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1844 " --> pdb=" O ARG A1840 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A1853 " --> pdb=" O ARG A1849 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A1856 " --> pdb=" O GLU A1852 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A1861 " --> pdb=" O GLU A1857 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A1870 " --> pdb=" O ARG A1866 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A1874 " --> pdb=" O GLU A1870 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A1875 " --> pdb=" O ARG A1871 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A1879 " --> pdb=" O LEU A1875 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A1882 " --> pdb=" O LYS A1878 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A1884 " --> pdb=" O GLN A1880 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A1889 " --> pdb=" O THR A1885 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A1891 " --> pdb=" O LYS A1887 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A1892 " --> pdb=" O ARG A1888 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A1900 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A1903 " --> pdb=" O LEU A1899 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A1904 " --> pdb=" O ASN A1900 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A1912 " --> pdb=" O GLN A1908 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1913 " --> pdb=" O GLN A1909 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1920 " --> pdb=" O GLU A1916 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1921 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A1923 " --> pdb=" O ASP A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1928 removed outlier: 3.775A pdb=" N PHE A1928 " --> pdb=" O ALA A1924 " (cutoff:3.500A) 1625 hydrogen bonds defined for protein. 4872 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: 4.69 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5633 1.33 - 1.46: 1913 1.46 - 1.58: 9860 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 17454 Sorted by residual: bond pdb=" N ALA A1075 " pdb=" CA ALA A1075 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" CA GLY B1387 " pdb=" C GLY B1387 " ideal model delta sigma weight residual 1.517 1.483 0.033 1.14e-02 7.69e+03 8.45e+00 bond pdb=" CA TYR B1383 " pdb=" C TYR B1383 " ideal model delta sigma weight residual 1.524 1.491 0.032 1.27e-02 6.20e+03 6.45e+00 bond pdb=" CA VAL A1074 " pdb=" C VAL A1074 " ideal model delta sigma weight residual 1.524 1.555 -0.032 1.30e-02 5.92e+03 5.95e+00 bond pdb=" CA ASN B1373 " pdb=" C ASN B1373 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.32e-02 5.74e+03 4.89e+00 ... (remaining 17449 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.01: 25 106.01 - 113.20: 9655 113.20 - 120.39: 7730 120.39 - 127.58: 5822 127.58 - 134.77: 50 Bond angle restraints: 23282 Sorted by residual: angle pdb=" N VAL A1074 " pdb=" CA VAL A1074 " pdb=" C VAL A1074 " ideal model delta sigma weight residual 110.72 118.70 -7.98 1.01e+00 9.80e-01 6.24e+01 angle pdb=" N GLU A1375 " pdb=" CA GLU A1375 " pdb=" C GLU A1375 " ideal model delta sigma weight residual 111.07 117.93 -6.86 1.07e+00 8.73e-01 4.11e+01 angle pdb=" C ALA A1075 " pdb=" N ASP A1076 " pdb=" CA ASP A1076 " ideal model delta sigma weight residual 120.38 128.64 -8.26 1.46e+00 4.69e-01 3.20e+01 angle pdb=" CA TYR B1383 " pdb=" CB TYR B1383 " pdb=" CG TYR B1383 " ideal model delta sigma weight residual 113.90 123.76 -9.86 1.80e+00 3.09e-01 3.00e+01 angle pdb=" C SER B1385 " pdb=" N GLU B1386 " pdb=" CA GLU B1386 " ideal model delta sigma weight residual 122.36 114.03 8.33 1.72e+00 3.38e-01 2.35e+01 ... (remaining 23277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9613 17.97 - 35.93: 1295 35.93 - 53.90: 316 53.90 - 71.86: 74 71.86 - 89.83: 48 Dihedral angle restraints: 11346 sinusoidal: 4992 harmonic: 6354 Sorted by residual: dihedral pdb=" C VAL A1074 " pdb=" N VAL A1074 " pdb=" CA VAL A1074 " pdb=" CB VAL A1074 " ideal model delta harmonic sigma weight residual -122.00 -136.16 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" N VAL A1074 " pdb=" C VAL A1074 " pdb=" CA VAL A1074 " pdb=" CB VAL A1074 " ideal model delta harmonic sigma weight residual 123.40 136.97 -13.57 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" CA LYS B1465 " pdb=" C LYS B1465 " pdb=" N LEU B1466 " pdb=" CA LEU B1466 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 11343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2517 0.098 - 0.196: 58 0.196 - 0.294: 6 0.294 - 0.392: 0 0.392 - 0.490: 1 Chirality restraints: 2582 Sorted by residual: chirality pdb=" CA VAL A1074 " pdb=" N VAL A1074 " pdb=" C VAL A1074 " pdb=" CB VAL A1074 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA GLU A1375 " pdb=" N GLU A1375 " pdb=" C GLU A1375 " pdb=" CB GLU A1375 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA SER B1385 " pdb=" N SER B1385 " pdb=" C SER B1385 " pdb=" CB SER B1385 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2579 not shown) Planarity restraints: 3158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1384 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C GLU B1384 " 0.076 2.00e-02 2.50e+03 pdb=" O GLU B1384 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B1385 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1383 " 0.054 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR B1383 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B1383 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B1383 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B1383 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1383 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B1383 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B1383 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1372 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ALA B1372 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B1372 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN B1373 " 0.021 2.00e-02 2.50e+03 ... (remaining 3155 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 28 2.24 - 2.91: 6360 2.91 - 3.57: 28789 3.57 - 4.24: 38888 4.24 - 4.90: 59369 Nonbonded interactions: 133434 Sorted by model distance: nonbonded pdb=" CG ARG B1380 " pdb=" CD2 TRP A1379 " model vdw 1.580 3.660 nonbonded pdb=" OH TYR B1383 " pdb=" CA GLU A1384 " model vdw 1.651 3.470 nonbonded pdb=" OH TYR B1383 " pdb=" CB GLU A1384 " model vdw 1.680 3.440 nonbonded pdb=" CH2 TRP B1379 " pdb=" OE1 GLU A1384 " model vdw 1.711 3.340 nonbonded pdb=" CZ TYR B1383 " pdb=" CB GLU A1384 " model vdw 1.744 3.660 ... (remaining 133429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.110 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 44.130 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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 : 0.005 0.041 17454 Z= 0.341 Angle : 1.027 10.130 23282 Z= 0.614 Chirality : 0.044 0.490 2582 Planarity : 0.004 0.044 3158 Dihedral : 18.286 89.827 7154 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.70 % Allowed : 8.99 % Favored : 90.30 % Cbeta Deviations : 0.05 % 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: -6.22 (0.11), residues: 2150 helix: -3.83 (0.07), residues: 2064 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 650 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 661 average time/residue: 0.3778 time to fit residues: 345.7422 Evaluate side-chains 468 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1703 time to fit residues: 3.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 109 optimal weight: 40.0000 chunk 86 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 998 ASN B1007 GLN B1019 GLN B1113 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1402 GLN B1479 GLN B1512 ASN B1597 ASN ** B1712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1802 GLN B1811 ASN B1900 ASN A 931 GLN A 935 GLN A 947 GLN A1001 ASN A1027 HIS A1204 HIS A1308 GLN A1510 ASN A1512 ASN A1530 ASN A1532 HIS ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 GLN A1868 ASN A1900 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17454 Z= 0.200 Angle : 0.693 10.465 23282 Z= 0.381 Chirality : 0.038 0.251 2582 Planarity : 0.005 0.048 3158 Dihedral : 4.816 25.458 2318 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2150 helix: -0.72 (0.10), residues: 2097 sheet: None (None), residues: 0 loop : -0.07 (0.74), residues: 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 599 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 601 average time/residue: 0.3435 time to fit residues: 297.7362 Evaluate side-chains 467 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1824 time to fit residues: 3.3123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 HIS B1037 GLN B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 GLN B1292 ASN ** B1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1510 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1712 GLN B1718 HIS B1900 ASN A 942 ASN A 987 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN A1219 ASN A1233 GLN A1259 GLN ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1783 HIS A1797 GLN A1889 GLN A1900 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17454 Z= 0.184 Angle : 0.611 8.083 23282 Z= 0.336 Chirality : 0.038 0.142 2582 Planarity : 0.003 0.031 3158 Dihedral : 4.435 19.412 2318 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.27 % Allowed : 4.98 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2150 helix: 0.89 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 0.25 (0.77), residues: 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 586 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 589 average time/residue: 0.3396 time to fit residues: 286.2623 Evaluate side-chains 494 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 492 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1812 time to fit residues: 3.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 195 optimal weight: 0.8980 chunk 206 optimal weight: 0.0570 chunk 102 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 942 ASN B1037 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 GLN ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1900 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN A1237 ASN ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.9291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17454 Z= 0.158 Angle : 0.590 8.270 23282 Z= 0.320 Chirality : 0.038 0.157 2582 Planarity : 0.003 0.033 3158 Dihedral : 4.278 17.577 2318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.22 % Allowed : 3.68 % Favored : 96.10 % 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: 2.29 (0.18), residues: 2150 helix: 1.58 (0.11), residues: 2099 sheet: None (None), residues: 0 loop : 0.81 (0.81), residues: 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 592 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 595 average time/residue: 0.3420 time to fit residues: 290.0361 Evaluate side-chains 499 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 2.006 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1856 time to fit residues: 3.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 3 optimal weight: 0.0030 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 105 optimal weight: 0.0570 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1841 HIS ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 GLN A1219 ASN A1308 GLN A1479 GLN A1720 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 1.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17454 Z= 0.188 Angle : 0.630 9.310 23282 Z= 0.345 Chirality : 0.040 0.183 2582 Planarity : 0.003 0.038 3158 Dihedral : 4.254 17.868 2318 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.22 % Allowed : 3.79 % Favored : 95.99 % 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: 2.53 (0.18), residues: 2150 helix: 1.73 (0.11), residues: 2103 sheet: None (None), residues: 0 loop : 0.75 (0.86), residues: 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 596 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 599 average time/residue: 0.3352 time to fit residues: 289.3510 Evaluate side-chains 513 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1908 time to fit residues: 3.3598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.3980 chunk 186 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1377 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1838 GLN B1900 ASN A1190 ASN A1298 GLN A1530 ASN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS A1881 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 1.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17454 Z= 0.192 Angle : 0.642 8.345 23282 Z= 0.351 Chirality : 0.041 0.160 2582 Planarity : 0.003 0.044 3158 Dihedral : 4.273 16.822 2318 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.18), residues: 2150 helix: 1.76 (0.11), residues: 2104 sheet: None (None), residues: 0 loop : 0.91 (0.76), residues: 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 620 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 622 average time/residue: 0.3330 time to fit residues: 296.4390 Evaluate side-chains 547 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 545 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1884 time to fit residues: 3.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 206 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1900 ASN A1417 GLN ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 1.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17454 Z= 0.187 Angle : 0.659 8.681 23282 Z= 0.356 Chirality : 0.041 0.185 2582 Planarity : 0.004 0.090 3158 Dihedral : 4.257 15.271 2318 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.18), residues: 2150 helix: 1.87 (0.11), residues: 2110 sheet: None (None), residues: 0 loop : 0.35 (0.78), residues: 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 618 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 619 average time/residue: 0.3323 time to fit residues: 296.2460 Evaluate side-chains 550 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1838 GLN B1900 ASN A1190 ASN A1368 GLN ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 1.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17454 Z= 0.210 Angle : 0.706 10.330 23282 Z= 0.382 Chirality : 0.042 0.189 2582 Planarity : 0.004 0.062 3158 Dihedral : 4.334 19.205 2318 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.18), residues: 2150 helix: 1.80 (0.11), residues: 2103 sheet: None (None), residues: 0 loop : 0.41 (0.78), residues: 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 642 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 643 average time/residue: 0.3353 time to fit residues: 311.3466 Evaluate side-chains 577 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN ** A1373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 GLN A1889 GLN A1900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 1.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17454 Z= 0.192 Angle : 0.696 9.376 23282 Z= 0.374 Chirality : 0.041 0.205 2582 Planarity : 0.004 0.070 3158 Dihedral : 4.319 16.758 2318 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.18), residues: 2150 helix: 1.87 (0.11), residues: 2104 sheet: None (None), residues: 0 loop : 0.76 (0.80), residues: 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.3436 time to fit residues: 320.8406 Evaluate side-chains 573 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 213 optimal weight: 0.0970 chunk 196 optimal weight: 0.8980 chunk 169 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1373 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN A1298 GLN A1373 ASN ** A1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 GLN A1720 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 1.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17454 Z= 0.178 Angle : 0.709 9.812 23282 Z= 0.376 Chirality : 0.040 0.162 2582 Planarity : 0.004 0.078 3158 Dihedral : 4.387 17.351 2318 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.18), residues: 2150 helix: 1.92 (0.11), residues: 2104 sheet: None (None), residues: 0 loop : 1.30 (0.81), residues: 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 625 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 625 average time/residue: 0.3356 time to fit residues: 303.4703 Evaluate side-chains 571 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 156 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 149 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1838 GLN ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.124993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.104343 restraints weight = 46902.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.107427 restraints weight = 28525.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.109227 restraints weight = 15345.246| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 1.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17454 Z= 0.183 Angle : 0.707 9.370 23282 Z= 0.376 Chirality : 0.041 0.171 2582 Planarity : 0.004 0.068 3158 Dihedral : 4.321 20.652 2318 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.18), residues: 2150 helix: 1.93 (0.11), residues: 2107 sheet: None (None), residues: 0 loop : 1.50 (0.91), residues: 43 =============================================================================== Job complete usr+sys time: 5592.48 seconds wall clock time: 100 minutes 50.62 seconds (6050.62 seconds total)