Starting phenix.real_space_refine on Sun Mar 17 09:10:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/03_2024/7kog_22975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/03_2024/7kog_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_22975/03_2024/7kog_22975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/03_2024/7kog_22975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/03_2024/7kog_22975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/03_2024/7kog_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-dev-5265/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: 8.92, 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: 6.91 Conformation dependent library (CDL) restraints added in 3.3 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: 7.35 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.440 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 43.440 Find NCS groups from input model: 0.880 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.560 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B1464 HIS 0.014 0.002 HIS B1193 PHE 0.022 0.003 PHE B1341 TYR 0.061 0.007 TYR B1383 ARG 0.007 0.001 ARG B 897 *********************** 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 : 1.940 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: B 928 MET cc_start: 0.7248 (mmp) cc_final: 0.7002 (mmp) REVERT: B 1036 GLU cc_start: 0.8069 (pt0) cc_final: 0.7786 (mt-10) REVERT: B 1040 ASP cc_start: 0.8093 (m-30) cc_final: 0.7888 (m-30) REVERT: B 1176 GLU cc_start: 0.7051 (tp30) cc_final: 0.6578 (tp30) REVERT: B 1246 MET cc_start: 0.6288 (ttp) cc_final: 0.5699 (ttp) REVERT: B 1345 GLU cc_start: 0.7184 (pt0) cc_final: 0.6520 (pt0) REVERT: B 1377 GLN cc_start: 0.4452 (OUTLIER) cc_final: 0.2211 (tt0) REVERT: B 1475 LEU cc_start: 0.6101 (tp) cc_final: 0.5150 (tp) REVERT: B 1489 LEU cc_start: 0.5036 (tt) cc_final: 0.4835 (tt) REVERT: B 1533 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6784 (tm-30) REVERT: B 1560 GLU cc_start: 0.7807 (tt0) cc_final: 0.7566 (tt0) REVERT: B 1577 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7091 (ttp-170) REVERT: B 1590 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 1634 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6669 (tm-30) REVERT: B 1667 GLU cc_start: 0.6488 (tp30) cc_final: 0.5771 (tp30) REVERT: B 1668 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6304 (mt-10) REVERT: B 1677 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 1716 ASP cc_start: 0.7742 (t0) cc_final: 0.7153 (t0) REVERT: B 1789 LYS cc_start: 0.8439 (tppt) cc_final: 0.8189 (ttmm) REVERT: B 1800 GLU cc_start: 0.7969 (mp0) cc_final: 0.7723 (mp0) REVERT: B 1840 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7797 (ttp80) REVERT: B 1863 ASP cc_start: 0.7498 (t0) cc_final: 0.7052 (t70) REVERT: B 1871 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7210 (ptt90) REVERT: B 1872 MET cc_start: 0.7836 (tpp) cc_final: 0.7542 (tpp) REVERT: B 1879 LEU cc_start: 0.7779 (mt) cc_final: 0.7472 (mt) REVERT: B 1884 LYS cc_start: 0.8413 (tptm) cc_final: 0.8206 (tptm) REVERT: B 1894 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6532 (tm-30) REVERT: B 1895 GLU cc_start: 0.7919 (mp0) cc_final: 0.7095 (mp0) REVERT: B 1903 LYS cc_start: 0.8343 (mptt) cc_final: 0.7947 (mmmm) REVERT: B 1906 LYS cc_start: 0.8746 (tppt) cc_final: 0.8309 (tppp) REVERT: B 1911 LEU cc_start: 0.8218 (tt) cc_final: 0.7501 (tp) REVERT: A 1092 ASP cc_start: 0.7035 (t0) cc_final: 0.6793 (t0) REVERT: A 1266 GLU cc_start: 0.5371 (tm-30) cc_final: 0.5144 (tm-30) REVERT: A 1288 LEU cc_start: 0.6650 (tp) cc_final: 0.6411 (tp) REVERT: A 1345 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6051 (mt-10) REVERT: A 1412 ILE cc_start: 0.6233 (tt) cc_final: 0.6008 (mt) REVERT: A 1461 ILE cc_start: 0.6827 (mt) cc_final: 0.6613 (tt) REVERT: A 1567 LEU cc_start: 0.8199 (mt) cc_final: 0.7946 (mt) REVERT: A 1571 LEU cc_start: 0.8497 (tp) cc_final: 0.8052 (tp) REVERT: A 1623 LYS cc_start: 0.7873 (tppt) cc_final: 0.7408 (tppt) REVERT: A 1641 ASN cc_start: 0.7862 (m-40) cc_final: 0.6896 (p0) REVERT: A 1646 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 1692 GLU cc_start: 0.7713 (tp30) cc_final: 0.7455 (tp30) REVERT: A 1741 GLU cc_start: 0.7970 (tp30) cc_final: 0.7587 (tp30) REVERT: A 1761 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 1762 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8837 (ttpp) REVERT: A 1775 ASP cc_start: 0.7783 (t0) cc_final: 0.7413 (t0) REVERT: A 1776 GLU cc_start: 0.7227 (tp30) cc_final: 0.6301 (tp30) REVERT: A 1828 ARG cc_start: 0.8370 (ttp-170) cc_final: 0.7904 (ttp-110) REVERT: A 1839 ARG cc_start: 0.8217 (tmt170) cc_final: 0.7964 (ttp80) REVERT: A 1843 ASP cc_start: 0.7338 (t0) cc_final: 0.7061 (t0) REVERT: A 1846 LYS cc_start: 0.8869 (tttm) cc_final: 0.8533 (ttmm) REVERT: A 1850 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8206 (ttpp) REVERT: A 1860 PHE cc_start: 0.8357 (t80) cc_final: 0.8075 (t80) REVERT: A 1865 ASP cc_start: 0.7871 (t0) cc_final: 0.7613 (t0) REVERT: A 1892 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6935 (mt-10) REVERT: A 1903 LYS cc_start: 0.7766 (mttm) cc_final: 0.7298 (mttp) REVERT: A 1906 LYS cc_start: 0.8507 (tttm) cc_final: 0.8166 (tttm) REVERT: A 1910 GLU cc_start: 0.7895 (tt0) cc_final: 0.7422 (tt0) outliers start: 13 outliers final: 2 residues processed: 661 average time/residue: 0.3802 time to fit residues: 349.6781 Evaluate side-chains 473 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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: 0.5980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 40.0000 chunk 86 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 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: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN A 935 GLN A 947 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 HIS A1204 HIS ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1510 ASN A1512 ASN A1532 HIS ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 GLN A1868 ASN A1900 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17454 Z= 0.189 Angle : 0.674 10.446 23282 Z= 0.372 Chirality : 0.038 0.209 2582 Planarity : 0.005 0.041 3158 Dihedral : 4.818 25.943 2318 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.55 % 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: -1.34 (0.16), residues: 2150 helix: -0.70 (0.10), residues: 2097 sheet: None (None), residues: 0 loop : -0.01 (0.73), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A1379 HIS 0.009 0.001 HIS B1598 PHE 0.015 0.002 PHE A1341 TYR 0.015 0.002 TYR B1383 ARG 0.006 0.001 ARG A1600 *********************** 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 592 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 590 time to evaluate : 1.901 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: B 966 GLU cc_start: 0.7047 (tp30) cc_final: 0.6676 (tm-30) REVERT: B 980 ASP cc_start: 0.7572 (m-30) cc_final: 0.6874 (m-30) REVERT: B 1231 HIS cc_start: 0.5880 (t70) cc_final: 0.5622 (t70) REVERT: B 1243 LEU cc_start: 0.7173 (tt) cc_final: 0.6418 (tt) REVERT: B 1249 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 1303 GLU cc_start: 0.6903 (pt0) cc_final: 0.6702 (pt0) REVERT: B 1345 GLU cc_start: 0.7554 (pt0) cc_final: 0.6951 (pt0) REVERT: B 1357 GLU cc_start: 0.7041 (tp30) cc_final: 0.6744 (tp30) REVERT: B 1470 ASP cc_start: 0.7487 (t0) cc_final: 0.7209 (t0) REVERT: B 1515 ASP cc_start: 0.7160 (p0) cc_final: 0.6954 (p0) REVERT: B 1535 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 1544 GLU cc_start: 0.8281 (pt0) cc_final: 0.8015 (pt0) REVERT: B 1560 GLU cc_start: 0.8383 (tt0) cc_final: 0.8129 (mt-10) REVERT: B 1566 VAL cc_start: 0.7424 (t) cc_final: 0.6992 (t) REVERT: B 1590 GLU cc_start: 0.8623 (mp0) cc_final: 0.8210 (mp0) REVERT: B 1614 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8387 (mtpp) REVERT: B 1638 ASP cc_start: 0.7005 (t0) cc_final: 0.6761 (t0) REVERT: B 1653 LYS cc_start: 0.8495 (tttt) cc_final: 0.8171 (ttpt) REVERT: B 1657 GLN cc_start: 0.6413 (tp40) cc_final: 0.5697 (tp40) REVERT: B 1667 GLU cc_start: 0.7404 (tp30) cc_final: 0.6833 (tp30) REVERT: B 1668 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6190 (mt-10) REVERT: B 1670 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7575 (mtm110) REVERT: B 1741 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7207 (tm-30) REVERT: B 1760 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 1764 LYS cc_start: 0.8542 (mmmt) cc_final: 0.7391 (mmmm) REVERT: B 1765 LYS cc_start: 0.8812 (tttm) cc_final: 0.8435 (ttmm) REVERT: B 1795 GLU cc_start: 0.8069 (pt0) cc_final: 0.7812 (pt0) REVERT: B 1818 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8222 (mmmm) REVERT: B 1824 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 1837 GLU cc_start: 0.8257 (tp30) cc_final: 0.7157 (tp30) REVERT: B 1840 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7932 (ttp-110) REVERT: B 1860 PHE cc_start: 0.8473 (t80) cc_final: 0.8027 (t80) REVERT: B 1872 MET cc_start: 0.8001 (tpp) cc_final: 0.7678 (mpp) REVERT: B 1882 LYS cc_start: 0.8850 (tttp) cc_final: 0.8347 (ttmm) REVERT: B 1888 ARG cc_start: 0.8328 (mtp85) cc_final: 0.7898 (mtp85) REVERT: B 1892 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 1894 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 1903 LYS cc_start: 0.8888 (tptt) cc_final: 0.8600 (mptt) REVERT: B 1908 GLN cc_start: 0.8124 (tt0) cc_final: 0.7806 (tp40) REVERT: B 1911 LEU cc_start: 0.8517 (tt) cc_final: 0.8289 (tp) REVERT: B 1923 GLN cc_start: 0.8422 (pp30) cc_final: 0.8122 (pp30) REVERT: A 924 GLU cc_start: 0.6961 (mp0) cc_final: 0.6574 (mm-30) REVERT: A 1092 ASP cc_start: 0.7550 (t0) cc_final: 0.7252 (t0) REVERT: A 1185 ASP cc_start: 0.7916 (m-30) cc_final: 0.7688 (m-30) REVERT: A 1259 GLN cc_start: 0.6676 (tp40) cc_final: 0.6068 (tp40) REVERT: A 1316 LEU cc_start: 0.6850 (mt) cc_final: 0.6475 (mt) REVERT: A 1356 GLU cc_start: 0.6806 (tp30) cc_final: 0.6237 (tp30) REVERT: A 1413 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 1501 GLU cc_start: 0.8262 (pt0) cc_final: 0.7920 (pt0) REVERT: A 1535 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 1542 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6988 (tm-30) REVERT: A 1553 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 1603 ASP cc_start: 0.7611 (t0) cc_final: 0.7338 (t0) REVERT: A 1622 MET cc_start: 0.6893 (mmm) cc_final: 0.6643 (mmm) REVERT: A 1623 LYS cc_start: 0.7945 (tppt) cc_final: 0.7641 (tppt) REVERT: A 1646 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 1668 GLU cc_start: 0.6640 (tm-30) cc_final: 0.6231 (tm-30) REVERT: A 1741 GLU cc_start: 0.8273 (tp30) cc_final: 0.7981 (tp30) REVERT: A 1761 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 1762 LYS cc_start: 0.9159 (ttmt) cc_final: 0.8925 (ttmt) REVERT: A 1775 ASP cc_start: 0.7797 (t0) cc_final: 0.7452 (t0) REVERT: A 1776 GLU cc_start: 0.7631 (tp30) cc_final: 0.6785 (tp30) REVERT: A 1780 GLU cc_start: 0.7840 (tt0) cc_final: 0.7630 (tt0) REVERT: A 1782 ASP cc_start: 0.8070 (t0) cc_final: 0.7744 (t0) REVERT: A 1792 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8824 (mtpp) REVERT: A 1795 GLU cc_start: 0.7441 (tp30) cc_final: 0.6715 (tp30) REVERT: A 1797 GLN cc_start: 0.8121 (mm110) cc_final: 0.7865 (mm110) REVERT: A 1802 GLN cc_start: 0.8755 (tt0) cc_final: 0.8554 (tt0) REVERT: A 1807 GLU cc_start: 0.8000 (pp20) cc_final: 0.7778 (pp20) REVERT: A 1824 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 1839 ARG cc_start: 0.8254 (tmt170) cc_final: 0.8034 (tmt170) REVERT: A 1846 LYS cc_start: 0.8997 (tttm) cc_final: 0.8732 (ttmm) REVERT: A 1858 LEU cc_start: 0.8534 (mp) cc_final: 0.8245 (mm) REVERT: A 1860 PHE cc_start: 0.8773 (t80) cc_final: 0.8470 (t80) REVERT: A 1876 VAL cc_start: 0.9155 (m) cc_final: 0.8851 (p) REVERT: A 1892 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 1905 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7919 (tpp80) REVERT: A 1909 GLN cc_start: 0.8413 (tp40) cc_final: 0.7919 (tm-30) REVERT: A 1915 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7762 (tm-30) outliers start: 2 outliers final: 0 residues processed: 592 average time/residue: 0.3233 time to fit residues: 273.4343 Evaluate side-chains 475 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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: 0.0070 chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 173 optimal weight: 0.1980 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 HIS B1037 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 GLN B1292 ASN B1510 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1712 GLN B1718 HIS B1797 GLN B1841 HIS B1900 ASN A 942 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN A1219 ASN A1233 GLN A1259 GLN A1261 GLN ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1881 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17454 Z= 0.158 Angle : 0.572 7.626 23282 Z= 0.316 Chirality : 0.036 0.137 2582 Planarity : 0.003 0.031 3158 Dihedral : 4.366 19.472 2318 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.91 % 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: 1.20 (0.18), residues: 2150 helix: 0.90 (0.11), residues: 2092 sheet: None (None), residues: 0 loop : 0.21 (0.74), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1379 HIS 0.013 0.001 HIS B1598 PHE 0.045 0.002 PHE B1281 TYR 0.019 0.002 TYR A1496 ARG 0.006 0.000 ARG A 858 *********************** 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 576 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 1.922 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: B 948 LYS cc_start: 0.8396 (pttp) cc_final: 0.8087 (pttp) REVERT: B 980 ASP cc_start: 0.7607 (m-30) cc_final: 0.7315 (m-30) REVERT: B 1006 MET cc_start: 0.6802 (ptp) cc_final: 0.6542 (ptp) REVERT: B 1092 ASP cc_start: 0.5677 (m-30) cc_final: 0.4944 (t70) REVERT: B 1243 LEU cc_start: 0.7351 (tt) cc_final: 0.6867 (tt) REVERT: B 1249 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7112 (tm-30) REVERT: B 1296 LEU cc_start: 0.7242 (tt) cc_final: 0.7023 (tp) REVERT: B 1300 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 1305 GLN cc_start: 0.7974 (mt0) cc_final: 0.7771 (mt0) REVERT: B 1345 GLU cc_start: 0.7119 (pt0) cc_final: 0.6876 (pt0) REVERT: B 1400 LYS cc_start: 0.8333 (mtmm) cc_final: 0.8111 (ptpp) REVERT: B 1409 GLU cc_start: 0.7399 (pt0) cc_final: 0.6909 (pt0) REVERT: B 1451 GLU cc_start: 0.7162 (pp20) cc_final: 0.6944 (pp20) REVERT: B 1461 ILE cc_start: 0.7377 (pt) cc_final: 0.7078 (mp) REVERT: B 1533 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 1540 ARG cc_start: 0.8664 (ptm160) cc_final: 0.8261 (ptp-110) REVERT: B 1544 GLU cc_start: 0.8170 (pt0) cc_final: 0.7944 (pt0) REVERT: B 1560 GLU cc_start: 0.8477 (tt0) cc_final: 0.8256 (tt0) REVERT: B 1586 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 1593 ASN cc_start: 0.7488 (t0) cc_final: 0.7101 (t0) REVERT: B 1597 ASN cc_start: 0.8231 (m-40) cc_final: 0.7992 (m110) REVERT: B 1614 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8214 (mtpp) REVERT: B 1627 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 1638 ASP cc_start: 0.7574 (t0) cc_final: 0.6984 (t0) REVERT: B 1646 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 1649 LYS cc_start: 0.8300 (tptp) cc_final: 0.7946 (mptp) REVERT: B 1653 LYS cc_start: 0.8790 (tttt) cc_final: 0.8391 (ttpt) REVERT: B 1667 GLU cc_start: 0.7719 (tp30) cc_final: 0.6882 (tp30) REVERT: B 1668 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 1670 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7652 (mtm110) REVERT: B 1708 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.7824 (mtm-85) REVERT: B 1741 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 1750 ASP cc_start: 0.7450 (t0) cc_final: 0.7219 (t0) REVERT: B 1760 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7293 (tm-30) REVERT: B 1764 LYS cc_start: 0.8673 (mmmt) cc_final: 0.7456 (mmmm) REVERT: B 1765 LYS cc_start: 0.8957 (tttm) cc_final: 0.8422 (ttmm) REVERT: B 1818 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8405 (mmmm) REVERT: B 1824 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 1833 GLU cc_start: 0.7947 (tp30) cc_final: 0.7475 (tp30) REVERT: B 1837 GLU cc_start: 0.8397 (tp30) cc_final: 0.7172 (mm-30) REVERT: B 1840 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.7940 (ttp-110) REVERT: B 1853 ARG cc_start: 0.8303 (mmt90) cc_final: 0.8041 (tpp80) REVERT: B 1860 PHE cc_start: 0.8486 (t80) cc_final: 0.8043 (t80) REVERT: B 1871 ARG cc_start: 0.7903 (ptt90) cc_final: 0.7497 (ptt90) REVERT: B 1873 GLN cc_start: 0.8890 (tp40) cc_final: 0.8652 (tp40) REVERT: B 1882 LYS cc_start: 0.8907 (tttp) cc_final: 0.8553 (ttmm) REVERT: B 1889 GLN cc_start: 0.8602 (mt0) cc_final: 0.8272 (mt0) REVERT: B 1892 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 1895 GLU cc_start: 0.7944 (mp0) cc_final: 0.7262 (mp0) REVERT: B 1903 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8708 (mmtt) REVERT: B 1922 GLU cc_start: 0.8337 (tp30) cc_final: 0.8069 (tp30) REVERT: A 924 GLU cc_start: 0.6926 (mp0) cc_final: 0.6693 (mm-30) REVERT: A 1072 GLU cc_start: 0.8536 (pt0) cc_final: 0.8047 (tm-30) REVERT: A 1092 ASP cc_start: 0.7594 (t0) cc_final: 0.7271 (t0) REVERT: A 1179 MET cc_start: 0.5539 (ppp) cc_final: 0.5320 (ppp) REVERT: A 1185 ASP cc_start: 0.7728 (m-30) cc_final: 0.7508 (m-30) REVERT: A 1316 LEU cc_start: 0.7545 (mt) cc_final: 0.7182 (mt) REVERT: A 1356 GLU cc_start: 0.7243 (tp30) cc_final: 0.6428 (tp30) REVERT: A 1418 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7777 (ttmm) REVERT: A 1458 ASP cc_start: 0.6488 (p0) cc_final: 0.5851 (p0) REVERT: A 1480 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8336 (ttmm) REVERT: A 1553 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 1614 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7965 (mtmm) REVERT: A 1622 MET cc_start: 0.7037 (mmm) cc_final: 0.6707 (mmm) REVERT: A 1623 LYS cc_start: 0.8000 (tppt) cc_final: 0.7744 (tppt) REVERT: A 1642 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8064 (mtmt) REVERT: A 1646 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 1690 GLN cc_start: 0.8396 (tt0) cc_final: 0.7934 (tp40) REVERT: A 1741 GLU cc_start: 0.8364 (tp30) cc_final: 0.8015 (tp30) REVERT: A 1754 ASN cc_start: 0.8156 (t0) cc_final: 0.7865 (t0) REVERT: A 1757 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8546 (ttpt) REVERT: A 1775 ASP cc_start: 0.7916 (t0) cc_final: 0.7576 (t0) REVERT: A 1776 GLU cc_start: 0.7716 (tp30) cc_final: 0.6836 (tp30) REVERT: A 1782 ASP cc_start: 0.8093 (t0) cc_final: 0.7806 (t0) REVERT: A 1789 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8688 (ttmm) REVERT: A 1792 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8832 (ttmm) REVERT: A 1794 LEU cc_start: 0.8319 (mt) cc_final: 0.8078 (mt) REVERT: A 1797 GLN cc_start: 0.8262 (mm110) cc_final: 0.8054 (mm110) REVERT: A 1807 GLU cc_start: 0.8019 (pp20) cc_final: 0.7793 (pp20) REVERT: A 1809 GLU cc_start: 0.8531 (pt0) cc_final: 0.8187 (pt0) REVERT: A 1822 LYS cc_start: 0.8555 (tttm) cc_final: 0.8273 (ttpp) REVERT: A 1824 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 1828 ARG cc_start: 0.8370 (ptp-170) cc_final: 0.7858 (ptt-90) REVERT: A 1839 ARG cc_start: 0.8240 (tmt170) cc_final: 0.7969 (tmt170) REVERT: A 1843 ASP cc_start: 0.7583 (t70) cc_final: 0.7355 (t0) REVERT: A 1846 LYS cc_start: 0.9093 (tttm) cc_final: 0.8752 (ttmm) REVERT: A 1858 LEU cc_start: 0.8452 (mp) cc_final: 0.8203 (mm) REVERT: A 1860 PHE cc_start: 0.8878 (t80) cc_final: 0.8541 (t80) REVERT: A 1864 GLU cc_start: 0.7719 (tp30) cc_final: 0.6582 (tp30) REVERT: A 1865 ASP cc_start: 0.7684 (t0) cc_final: 0.7434 (t0) REVERT: A 1868 ASN cc_start: 0.8458 (m110) cc_final: 0.6902 (m-40) REVERT: A 1870 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 1889 GLN cc_start: 0.7820 (pp30) cc_final: 0.7516 (pp30) REVERT: A 1909 GLN cc_start: 0.8455 (tp40) cc_final: 0.7990 (tm-30) REVERT: A 1915 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7760 (tm-30) outliers start: 3 outliers final: 1 residues processed: 574 average time/residue: 0.3564 time to fit residues: 297.0986 Evaluate side-chains 491 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 490 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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: 0.5980 chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 942 ASN B1037 GLN B1168 GLN ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1350 ASN B1570 GLN ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1869 HIS B1900 ASN A 970 GLN A 987 ASN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 GLN A1783 HIS ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.9573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17454 Z= 0.198 Angle : 0.639 7.497 23282 Z= 0.350 Chirality : 0.040 0.153 2582 Planarity : 0.003 0.044 3158 Dihedral : 4.399 22.611 2318 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.12 % 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: 2.03 (0.18), residues: 2150 helix: 1.41 (0.11), residues: 2098 sheet: None (None), residues: 0 loop : 0.83 (0.82), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A1379 HIS 0.009 0.001 HIS B1598 PHE 0.021 0.002 PHE B1281 TYR 0.029 0.003 TYR A1383 ARG 0.006 0.001 ARG A1791 *********************** 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 607 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 606 time to evaluate : 2.048 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: B 928 MET cc_start: 0.8136 (mmp) cc_final: 0.7874 (mmp) REVERT: B 1249 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 1286 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8477 (mtmm) REVERT: B 1300 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 1324 LYS cc_start: 0.8355 (pttp) cc_final: 0.7954 (pttp) REVERT: B 1333 GLU cc_start: 0.8265 (tt0) cc_final: 0.7878 (tt0) REVERT: B 1334 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7311 (mmm-85) REVERT: B 1358 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6379 (tm-30) REVERT: B 1400 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8189 (mtmm) REVERT: B 1409 GLU cc_start: 0.7587 (pt0) cc_final: 0.7277 (pt0) REVERT: B 1416 ASN cc_start: 0.8113 (t0) cc_final: 0.7871 (t0) REVERT: B 1420 ILE cc_start: 0.8912 (pt) cc_final: 0.8496 (pt) REVERT: B 1423 GLU cc_start: 0.8245 (pt0) cc_final: 0.7869 (pt0) REVERT: B 1439 GLU cc_start: 0.8194 (mp0) cc_final: 0.7900 (mp0) REVERT: B 1455 LYS cc_start: 0.8269 (mptt) cc_final: 0.7951 (mptt) REVERT: B 1458 ASP cc_start: 0.7255 (t0) cc_final: 0.6982 (t0) REVERT: B 1461 ILE cc_start: 0.7866 (pt) cc_final: 0.7589 (mm) REVERT: B 1467 LYS cc_start: 0.8074 (mttt) cc_final: 0.7707 (mmmm) REVERT: B 1468 VAL cc_start: 0.8321 (m) cc_final: 0.8117 (p) REVERT: B 1516 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 1523 GLN cc_start: 0.8252 (mt0) cc_final: 0.8021 (mt0) REVERT: B 1540 ARG cc_start: 0.8566 (ptm160) cc_final: 0.8075 (mtp-110) REVERT: B 1562 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 1565 LYS cc_start: 0.7639 (tmtt) cc_final: 0.7309 (tmtt) REVERT: B 1573 LEU cc_start: 0.8765 (pp) cc_final: 0.8311 (tt) REVERT: B 1585 GLN cc_start: 0.7066 (pp30) cc_final: 0.6729 (pp30) REVERT: B 1586 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 1597 ASN cc_start: 0.8160 (m-40) cc_final: 0.6203 (m-40) REVERT: B 1600 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8031 (ptp90) REVERT: B 1634 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 1638 ASP cc_start: 0.7821 (t0) cc_final: 0.7320 (t0) REVERT: B 1641 ASN cc_start: 0.8836 (m-40) cc_final: 0.8523 (t0) REVERT: B 1646 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 1649 LYS cc_start: 0.8407 (tptp) cc_final: 0.7928 (mptp) REVERT: B 1653 LYS cc_start: 0.8855 (tttt) cc_final: 0.8242 (ttmm) REVERT: B 1677 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 1683 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 1708 ARG cc_start: 0.8580 (mpt90) cc_final: 0.8259 (mtm-85) REVERT: B 1709 GLN cc_start: 0.8741 (pp30) cc_final: 0.8500 (pp30) REVERT: B 1737 LYS cc_start: 0.9287 (tmtt) cc_final: 0.8931 (tptp) REVERT: B 1748 ASP cc_start: 0.7835 (m-30) cc_final: 0.7582 (m-30) REVERT: B 1750 ASP cc_start: 0.7505 (t0) cc_final: 0.7243 (t0) REVERT: B 1757 LYS cc_start: 0.8899 (tttp) cc_final: 0.8544 (ttpp) REVERT: B 1759 SER cc_start: 0.8830 (p) cc_final: 0.8327 (p) REVERT: B 1762 LYS cc_start: 0.8507 (mttp) cc_final: 0.8191 (mttp) REVERT: B 1764 LYS cc_start: 0.8701 (mmmt) cc_final: 0.7456 (mmmm) REVERT: B 1767 MET cc_start: 0.7774 (ppp) cc_final: 0.7420 (ppp) REVERT: B 1772 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8359 (ttm-80) REVERT: B 1780 GLU cc_start: 0.7436 (tp30) cc_final: 0.6967 (tp30) REVERT: B 1781 GLN cc_start: 0.8189 (tp40) cc_final: 0.7853 (tp40) REVERT: B 1789 LYS cc_start: 0.8909 (tppp) cc_final: 0.8634 (tppp) REVERT: B 1792 LYS cc_start: 0.8757 (tppt) cc_final: 0.8309 (tppt) REVERT: B 1818 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8375 (mmmm) REVERT: B 1822 LYS cc_start: 0.9270 (ttmt) cc_final: 0.8976 (mtpp) REVERT: B 1824 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 1833 GLU cc_start: 0.8104 (tp30) cc_final: 0.7154 (tp30) REVERT: B 1837 GLU cc_start: 0.8376 (tp30) cc_final: 0.7869 (mm-30) REVERT: B 1840 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8077 (ttp-110) REVERT: B 1852 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7978 (tp30) REVERT: B 1853 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8106 (tpp80) REVERT: B 1860 PHE cc_start: 0.8573 (t80) cc_final: 0.8138 (t80) REVERT: B 1865 ASP cc_start: 0.8032 (m-30) cc_final: 0.7595 (m-30) REVERT: B 1871 ARG cc_start: 0.8072 (ptt90) cc_final: 0.7677 (ptt90) REVERT: B 1873 GLN cc_start: 0.8849 (tp40) cc_final: 0.8286 (tm-30) REVERT: B 1882 LYS cc_start: 0.9043 (tttp) cc_final: 0.8705 (tttm) REVERT: B 1884 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8595 (mmtp) REVERT: B 1888 ARG cc_start: 0.8394 (mtp85) cc_final: 0.7692 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8620 (mt0) cc_final: 0.8146 (tp40) REVERT: B 1892 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 1894 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 1903 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8597 (mmtt) REVERT: B 1906 LYS cc_start: 0.9139 (tppt) cc_final: 0.8612 (tppt) REVERT: B 1915 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 961 ASP cc_start: 0.6988 (t0) cc_final: 0.6648 (t0) REVERT: A 1103 GLU cc_start: 0.8118 (mp0) cc_final: 0.7871 (mt-10) REVERT: A 1188 GLU cc_start: 0.6391 (tp30) cc_final: 0.5931 (tp30) REVERT: A 1250 LYS cc_start: 0.8431 (pptt) cc_final: 0.7968 (ptmm) REVERT: A 1300 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8035 (mm-30) REVERT: A 1330 GLU cc_start: 0.7868 (tt0) cc_final: 0.7355 (mm-30) REVERT: A 1345 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 1353 GLU cc_start: 0.8327 (mp0) cc_final: 0.8018 (mp0) REVERT: A 1356 GLU cc_start: 0.7708 (tp30) cc_final: 0.6982 (tp30) REVERT: A 1358 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 1362 LYS cc_start: 0.7520 (ptmm) cc_final: 0.7299 (ptmm) REVERT: A 1392 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 1424 LYS cc_start: 0.8222 (tttp) cc_final: 0.7582 (mmmm) REVERT: A 1427 GLN cc_start: 0.7252 (pp30) cc_final: 0.7039 (pp30) REVERT: A 1446 ILE cc_start: 0.7894 (tt) cc_final: 0.7681 (tt) REVERT: A 1453 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8470 (mtpp) REVERT: A 1458 ASP cc_start: 0.7363 (p0) cc_final: 0.6773 (p0) REVERT: A 1488 GLU cc_start: 0.6844 (tp30) cc_final: 0.6174 (tp30) REVERT: A 1501 GLU cc_start: 0.8510 (pt0) cc_final: 0.8101 (pt0) REVERT: A 1504 GLU cc_start: 0.7911 (mp0) cc_final: 0.7282 (mp0) REVERT: A 1511 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8499 (mmmm) REVERT: A 1523 GLN cc_start: 0.7801 (mt0) cc_final: 0.7570 (tt0) REVERT: A 1530 ASN cc_start: 0.8085 (m110) cc_final: 0.7781 (m-40) REVERT: A 1554 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 1561 GLN cc_start: 0.6830 (pp30) cc_final: 0.6221 (pp30) REVERT: A 1570 GLN cc_start: 0.8174 (mt0) cc_final: 0.7798 (mm-40) REVERT: A 1622 MET cc_start: 0.7336 (mmm) cc_final: 0.6622 (mmm) REVERT: A 1623 LYS cc_start: 0.8119 (tppt) cc_final: 0.7858 (tppt) REVERT: A 1637 LEU cc_start: 0.8726 (mt) cc_final: 0.8476 (mm) REVERT: A 1642 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8012 (mtpp) REVERT: A 1646 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 1656 GLN cc_start: 0.8602 (mm110) cc_final: 0.8341 (tp40) REVERT: A 1658 LEU cc_start: 0.8627 (mt) cc_final: 0.8293 (mm) REVERT: A 1660 ASP cc_start: 0.8164 (p0) cc_final: 0.7927 (p0) REVERT: A 1662 GLN cc_start: 0.8673 (tt0) cc_final: 0.8422 (tp40) REVERT: A 1690 GLN cc_start: 0.8535 (tt0) cc_final: 0.8237 (tp40) REVERT: A 1692 GLU cc_start: 0.8232 (tp30) cc_final: 0.8001 (tp30) REVERT: A 1705 ARG cc_start: 0.8400 (ttt90) cc_final: 0.8078 (ttm110) REVERT: A 1712 GLN cc_start: 0.8179 (mp10) cc_final: 0.7938 (mp10) REVERT: A 1729 THR cc_start: 0.8740 (p) cc_final: 0.8527 (t) REVERT: A 1737 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8745 (ttpp) REVERT: A 1741 GLU cc_start: 0.8256 (tp30) cc_final: 0.7888 (tp30) REVERT: A 1754 ASN cc_start: 0.8383 (t0) cc_final: 0.8077 (t0) REVERT: A 1757 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8744 (ttpt) REVERT: A 1760 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 1775 ASP cc_start: 0.7802 (t0) cc_final: 0.7543 (t0) REVERT: A 1776 GLU cc_start: 0.8039 (tp30) cc_final: 0.6985 (tp30) REVERT: A 1778 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8218 (t0) cc_final: 0.7955 (t0) REVERT: A 1789 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8810 (ttmm) REVERT: A 1792 LYS cc_start: 0.9304 (ttmt) cc_final: 0.8950 (ttmm) REVERT: A 1794 LEU cc_start: 0.8662 (mt) cc_final: 0.8447 (mm) REVERT: A 1796 THR cc_start: 0.8949 (p) cc_final: 0.8699 (t) REVERT: A 1807 GLU cc_start: 0.7980 (pp20) cc_final: 0.7768 (pp20) REVERT: A 1809 GLU cc_start: 0.8542 (pt0) cc_final: 0.8121 (pt0) REVERT: A 1822 LYS cc_start: 0.8628 (tttm) cc_final: 0.8292 (ttpp) REVERT: A 1824 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 1828 ARG cc_start: 0.8364 (ptp-170) cc_final: 0.7807 (ptt-90) REVERT: A 1833 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 1839 ARG cc_start: 0.8317 (tmt170) cc_final: 0.8040 (tmt170) REVERT: A 1846 LYS cc_start: 0.9171 (tttm) cc_final: 0.8737 (ttmm) REVERT: A 1853 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.7703 (ttm110) REVERT: A 1860 PHE cc_start: 0.9026 (t80) cc_final: 0.8761 (t80) REVERT: A 1864 GLU cc_start: 0.7864 (tp30) cc_final: 0.7564 (tp30) REVERT: A 1865 ASP cc_start: 0.7903 (t0) cc_final: 0.7697 (t0) REVERT: A 1868 ASN cc_start: 0.8584 (m110) cc_final: 0.8219 (m-40) REVERT: A 1870 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 1871 ARG cc_start: 0.8674 (tpt170) cc_final: 0.8463 (tpt170) REVERT: A 1889 GLN cc_start: 0.7871 (pp30) cc_final: 0.7653 (pp30) REVERT: A 1892 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 1894 GLU cc_start: 0.7036 (pp20) cc_final: 0.6822 (pp20) REVERT: A 1909 GLN cc_start: 0.8522 (tp40) cc_final: 0.8024 (tm-30) REVERT: A 1910 GLU cc_start: 0.8478 (tt0) cc_final: 0.7789 (tt0) REVERT: A 1915 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7711 (tm-30) outliers start: 1 outliers final: 0 residues processed: 607 average time/residue: 0.3368 time to fit residues: 289.5706 Evaluate side-chains 535 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 105 optimal weight: 0.0370 chunk 185 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1037 GLN ** 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 B1644 ASN B1900 ASN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS ** 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: 0.7181 moved from start: 1.0382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17454 Z= 0.151 Angle : 0.567 6.554 23282 Z= 0.311 Chirality : 0.038 0.148 2582 Planarity : 0.003 0.056 3158 Dihedral : 4.219 15.887 2318 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.22 % Allowed : 3.14 % Favored : 96.64 % 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: 2.68 (0.18), residues: 2150 helix: 1.82 (0.11), residues: 2099 sheet: None (None), residues: 0 loop : 0.79 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP A1379 HIS 0.008 0.001 HIS A1598 PHE 0.023 0.002 PHE B1281 TYR 0.014 0.002 TYR A1383 ARG 0.007 0.000 ARG B1778 *********************** 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 601 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 597 time to evaluate : 1.927 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: B 928 MET cc_start: 0.8125 (mmp) cc_final: 0.7851 (mmp) REVERT: B 966 GLU cc_start: 0.7106 (tp30) cc_final: 0.6191 (tm-30) REVERT: B 1092 ASP cc_start: 0.6150 (m-30) cc_final: 0.5343 (t70) REVERT: B 1245 GLN cc_start: 0.8032 (mt0) cc_final: 0.7807 (mt0) REVERT: B 1249 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 1254 GLU cc_start: 0.7964 (tt0) cc_final: 0.7661 (tt0) REVERT: B 1261 GLN cc_start: 0.8821 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 1282 ASP cc_start: 0.7955 (m-30) cc_final: 0.7669 (m-30) REVERT: B 1285 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8266 (ptmm) REVERT: B 1286 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8726 (mtmm) REVERT: B 1324 LYS cc_start: 0.8372 (pttp) cc_final: 0.7975 (pttp) REVERT: B 1330 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 1333 GLU cc_start: 0.8347 (tt0) cc_final: 0.7797 (tt0) REVERT: B 1334 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7067 (mmm-85) REVERT: B 1358 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7047 (tm-30) REVERT: B 1420 ILE cc_start: 0.8951 (pt) cc_final: 0.8551 (pt) REVERT: B 1423 GLU cc_start: 0.8196 (pt0) cc_final: 0.7852 (pt0) REVERT: B 1455 LYS cc_start: 0.8361 (mptt) cc_final: 0.7970 (mptt) REVERT: B 1458 ASP cc_start: 0.7291 (t0) cc_final: 0.6951 (t0) REVERT: B 1460 ILE cc_start: 0.8407 (tt) cc_final: 0.7991 (tt) REVERT: B 1461 ILE cc_start: 0.7893 (pt) cc_final: 0.7493 (mm) REVERT: B 1464 TRP cc_start: 0.8580 (m100) cc_final: 0.6096 (m100) REVERT: B 1467 LYS cc_start: 0.7860 (mttt) cc_final: 0.7656 (mmmm) REVERT: B 1492 LEU cc_start: 0.8466 (mt) cc_final: 0.8254 (mm) REVERT: B 1509 GLU cc_start: 0.8176 (tt0) cc_final: 0.7924 (tt0) REVERT: B 1516 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 1523 GLN cc_start: 0.8165 (mt0) cc_final: 0.7931 (mt0) REVERT: B 1535 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 1540 ARG cc_start: 0.8472 (ptm160) cc_final: 0.8148 (ttp80) REVERT: B 1544 GLU cc_start: 0.8430 (pt0) cc_final: 0.7965 (pt0) REVERT: B 1549 GLN cc_start: 0.8342 (pp30) cc_final: 0.7941 (pp30) REVERT: B 1565 LYS cc_start: 0.7746 (tmtt) cc_final: 0.7443 (tmtt) REVERT: B 1573 LEU cc_start: 0.8597 (pp) cc_final: 0.8240 (tt) REVERT: B 1582 ARG cc_start: 0.7957 (ppt170) cc_final: 0.7624 (ppt170) REVERT: B 1588 GLU cc_start: 0.8224 (pm20) cc_final: 0.7705 (pp20) REVERT: B 1614 LYS cc_start: 0.8668 (tttp) cc_final: 0.8216 (tttp) REVERT: B 1627 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 1629 ASP cc_start: 0.8150 (t70) cc_final: 0.7910 (t0) REVERT: B 1634 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7283 (tm-30) REVERT: B 1638 ASP cc_start: 0.7904 (t0) cc_final: 0.7366 (t0) REVERT: B 1641 ASN cc_start: 0.8852 (m-40) cc_final: 0.8505 (t0) REVERT: B 1651 ILE cc_start: 0.9148 (mt) cc_final: 0.8698 (mt) REVERT: B 1653 LYS cc_start: 0.8952 (tttt) cc_final: 0.8299 (ttmm) REVERT: B 1667 GLU cc_start: 0.8138 (tp30) cc_final: 0.7671 (tp30) REVERT: B 1670 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7879 (mtm110) REVERT: B 1677 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 1683 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 1700 LEU cc_start: 0.8736 (tp) cc_final: 0.8286 (tp) REVERT: B 1704 ASP cc_start: 0.7178 (p0) cc_final: 0.6668 (p0) REVERT: B 1708 ARG cc_start: 0.8653 (mpt90) cc_final: 0.8247 (mtm-85) REVERT: B 1723 GLU cc_start: 0.8350 (pt0) cc_final: 0.8150 (pt0) REVERT: B 1737 LYS cc_start: 0.9297 (tmtt) cc_final: 0.8981 (tptp) REVERT: B 1741 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 1748 ASP cc_start: 0.8024 (m-30) cc_final: 0.7735 (m-30) REVERT: B 1750 ASP cc_start: 0.7639 (t0) cc_final: 0.7333 (t0) REVERT: B 1757 LYS cc_start: 0.8892 (tttp) cc_final: 0.8506 (ttpp) REVERT: B 1759 SER cc_start: 0.8833 (p) cc_final: 0.8248 (p) REVERT: B 1760 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 1762 LYS cc_start: 0.8557 (mttp) cc_final: 0.8257 (mttp) REVERT: B 1764 LYS cc_start: 0.8691 (mmmt) cc_final: 0.7335 (mmmm) REVERT: B 1767 MET cc_start: 0.7763 (ppp) cc_final: 0.7275 (ppp) REVERT: B 1772 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8399 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8077 (t0) cc_final: 0.7856 (t0) REVERT: B 1781 GLN cc_start: 0.8216 (tp40) cc_final: 0.7954 (tp40) REVERT: B 1818 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8385 (mmmm) REVERT: B 1822 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8811 (mtpp) REVERT: B 1824 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 1833 GLU cc_start: 0.8076 (tp30) cc_final: 0.7157 (tp30) REVERT: B 1837 GLU cc_start: 0.8437 (tp30) cc_final: 0.8124 (mm-30) REVERT: B 1853 ARG cc_start: 0.8508 (mmt90) cc_final: 0.8152 (tpp80) REVERT: B 1858 LEU cc_start: 0.8815 (mt) cc_final: 0.8599 (mm) REVERT: B 1860 PHE cc_start: 0.8510 (t80) cc_final: 0.8141 (t80) REVERT: B 1865 ASP cc_start: 0.7963 (m-30) cc_final: 0.7630 (m-30) REVERT: B 1870 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 1871 ARG cc_start: 0.8101 (ptt90) cc_final: 0.7735 (ptt90) REVERT: B 1873 GLN cc_start: 0.8847 (tp40) cc_final: 0.8326 (tm-30) REVERT: B 1878 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7735 (mmmt) REVERT: B 1882 LYS cc_start: 0.8979 (tttp) cc_final: 0.8741 (tttm) REVERT: B 1884 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8647 (mmtp) REVERT: B 1887 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8506 (tppt) REVERT: B 1888 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8190 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8580 (mt0) cc_final: 0.8202 (tp40) REVERT: B 1896 ILE cc_start: 0.8931 (mt) cc_final: 0.8709 (mt) REVERT: B 1903 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8595 (mmtt) REVERT: B 1906 LYS cc_start: 0.9129 (tppt) cc_final: 0.8769 (tppt) REVERT: B 1915 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 1917 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8253 (ttm-80) REVERT: A 1041 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6824 (pm20) REVERT: A 1174 LYS cc_start: 0.8980 (mttp) cc_final: 0.8649 (mttp) REVERT: A 1179 MET cc_start: 0.6281 (ppp) cc_final: 0.5857 (ppp) REVERT: A 1188 GLU cc_start: 0.6698 (tp30) cc_final: 0.6456 (tm-30) REVERT: A 1246 MET cc_start: 0.5956 (ptp) cc_final: 0.5737 (ptp) REVERT: A 1270 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8397 (mmtp) REVERT: A 1300 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7884 (mm-30) REVERT: A 1330 GLU cc_start: 0.8137 (tt0) cc_final: 0.7532 (mm-30) REVERT: A 1345 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 1353 GLU cc_start: 0.8390 (mp0) cc_final: 0.7978 (mp0) REVERT: A 1358 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 1369 LEU cc_start: 0.8506 (mp) cc_final: 0.8288 (tt) REVERT: A 1392 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 1412 ILE cc_start: 0.8577 (pt) cc_final: 0.8026 (mt) REVERT: A 1424 LYS cc_start: 0.8434 (tttp) cc_final: 0.8211 (mmmm) REVERT: A 1440 VAL cc_start: 0.8678 (m) cc_final: 0.8467 (p) REVERT: A 1457 ILE cc_start: 0.7907 (mm) cc_final: 0.7622 (mm) REVERT: A 1458 ASP cc_start: 0.7583 (p0) cc_final: 0.6848 (p0) REVERT: A 1463 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6776 (tm-30) REVERT: A 1465 LYS cc_start: 0.8420 (mmtm) cc_final: 0.6952 (tppt) REVERT: A 1481 GLU cc_start: 0.7597 (tp30) cc_final: 0.7285 (tp30) REVERT: A 1488 GLU cc_start: 0.6790 (tp30) cc_final: 0.6107 (tp30) REVERT: A 1511 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8522 (mmmm) REVERT: A 1554 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 1556 GLU cc_start: 0.7808 (pp20) cc_final: 0.7422 (pp20) REVERT: A 1561 GLN cc_start: 0.7149 (pp30) cc_final: 0.6572 (pp30) REVERT: A 1567 LEU cc_start: 0.8963 (mt) cc_final: 0.8657 (mm) REVERT: A 1570 GLN cc_start: 0.8123 (mt0) cc_final: 0.7841 (mm-40) REVERT: A 1589 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 1623 LYS cc_start: 0.8256 (tppt) cc_final: 0.7902 (tppt) REVERT: A 1625 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8363 (mtpp) REVERT: A 1631 ASN cc_start: 0.8849 (m-40) cc_final: 0.8632 (t0) REVERT: A 1637 LEU cc_start: 0.8837 (mt) cc_final: 0.8322 (tt) REVERT: A 1642 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7767 (mtpp) REVERT: A 1646 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 1649 LYS cc_start: 0.9037 (tttp) cc_final: 0.8629 (ttpp) REVERT: A 1656 GLN cc_start: 0.8675 (mm110) cc_final: 0.8409 (tp40) REVERT: A 1660 ASP cc_start: 0.8151 (p0) cc_final: 0.7935 (p0) REVERT: A 1662 GLN cc_start: 0.8655 (tt0) cc_final: 0.8297 (tp40) REVERT: A 1690 GLN cc_start: 0.8546 (tt0) cc_final: 0.8224 (tp40) REVERT: A 1692 GLU cc_start: 0.8216 (tp30) cc_final: 0.7911 (tp30) REVERT: A 1705 ARG cc_start: 0.8354 (ttt90) cc_final: 0.7993 (ttm110) REVERT: A 1737 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8747 (ttpp) REVERT: A 1741 GLU cc_start: 0.8243 (tp30) cc_final: 0.7922 (tp30) REVERT: A 1754 ASN cc_start: 0.8449 (t0) cc_final: 0.8143 (t0) REVERT: A 1757 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8620 (ttpt) REVERT: A 1778 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8080 (mtt-85) REVERT: A 1780 GLU cc_start: 0.8115 (tt0) cc_final: 0.7608 (tt0) REVERT: A 1782 ASP cc_start: 0.8081 (t0) cc_final: 0.7865 (t0) REVERT: A 1792 LYS cc_start: 0.9305 (ttmt) cc_final: 0.8992 (ttmm) REVERT: A 1794 LEU cc_start: 0.8724 (mt) cc_final: 0.8499 (mm) REVERT: A 1796 THR cc_start: 0.8903 (p) cc_final: 0.8667 (t) REVERT: A 1809 GLU cc_start: 0.8436 (pt0) cc_final: 0.8050 (pt0) REVERT: A 1822 LYS cc_start: 0.8677 (tttm) cc_final: 0.8257 (ttpp) REVERT: A 1824 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 1839 ARG cc_start: 0.8386 (tmt170) cc_final: 0.8031 (tmt170) REVERT: A 1846 LYS cc_start: 0.9177 (tttm) cc_final: 0.8738 (ttmm) REVERT: A 1850 LYS cc_start: 0.8567 (pttp) cc_final: 0.8331 (pttp) REVERT: A 1853 ARG cc_start: 0.8298 (mtp-110) cc_final: 0.7751 (ttm110) REVERT: A 1858 LEU cc_start: 0.8485 (mp) cc_final: 0.8245 (mm) REVERT: A 1860 PHE cc_start: 0.9036 (t80) cc_final: 0.8807 (t80) REVERT: A 1864 GLU cc_start: 0.7895 (tp30) cc_final: 0.7544 (tp30) REVERT: A 1865 ASP cc_start: 0.7925 (t0) cc_final: 0.7636 (t0) REVERT: A 1868 ASN cc_start: 0.8562 (m110) cc_final: 0.8187 (m-40) REVERT: A 1870 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 1881 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8221 (tp-100) REVERT: A 1882 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8859 (ttmm) REVERT: A 1884 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8758 (ttpp) REVERT: A 1889 GLN cc_start: 0.7795 (pp30) cc_final: 0.7577 (pp30) REVERT: A 1892 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 1909 GLN cc_start: 0.8597 (tp40) cc_final: 0.8196 (tm-30) REVERT: A 1910 GLU cc_start: 0.8464 (tt0) cc_final: 0.7817 (tt0) REVERT: A 1915 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 1922 GLU cc_start: 0.8368 (mp0) cc_final: 0.7913 (pp20) outliers start: 4 outliers final: 0 residues processed: 601 average time/residue: 0.3353 time to fit residues: 284.8973 Evaluate side-chains 529 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 528 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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: 0.9980 chunk 186 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1037 GLN B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1644 ASN B1655 GLN B1783 HIS ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN A1261 GLN A1417 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 1.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17454 Z= 0.197 Angle : 0.631 6.912 23282 Z= 0.351 Chirality : 0.041 0.166 2582 Planarity : 0.003 0.029 3158 Dihedral : 4.297 15.857 2318 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.18), residues: 2150 helix: 1.74 (0.11), residues: 2102 sheet: None (None), residues: 0 loop : 0.77 (0.82), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1379 HIS 0.010 0.001 HIS B1598 PHE 0.018 0.002 PHE B1281 TYR 0.031 0.003 TYR A1383 ARG 0.014 0.001 ARG B1053 *********************** 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 646 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 646 time to evaluate : 1.849 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: B 928 MET cc_start: 0.8155 (mmp) cc_final: 0.7846 (mmp) REVERT: B 1127 GLU cc_start: 0.8041 (mp0) cc_final: 0.7829 (mp0) REVERT: B 1211 MET cc_start: 0.7869 (ptp) cc_final: 0.7638 (ptp) REVERT: B 1214 GLN cc_start: 0.7822 (mt0) cc_final: 0.7213 (mt0) REVERT: B 1243 LEU cc_start: 0.8428 (tt) cc_final: 0.8052 (tt) REVERT: B 1248 ARG cc_start: 0.8164 (mmt180) cc_final: 0.7951 (mmt180) REVERT: B 1249 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7233 (tm-30) REVERT: B 1261 GLN cc_start: 0.8891 (tt0) cc_final: 0.7520 (tm-30) REVERT: B 1268 GLN cc_start: 0.8131 (pt0) cc_final: 0.7779 (tt0) REVERT: B 1280 ASP cc_start: 0.8213 (p0) cc_final: 0.8000 (p0) REVERT: B 1285 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8633 (ptmm) REVERT: B 1291 GLU cc_start: 0.6795 (tp30) cc_final: 0.6543 (tp30) REVERT: B 1299 LEU cc_start: 0.8262 (tt) cc_final: 0.7802 (tt) REVERT: B 1300 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7679 (mm-30) REVERT: B 1303 GLU cc_start: 0.7879 (pm20) cc_final: 0.7519 (pm20) REVERT: B 1320 LEU cc_start: 0.8758 (mt) cc_final: 0.8239 (tt) REVERT: B 1324 LYS cc_start: 0.8496 (pttp) cc_final: 0.8039 (pttp) REVERT: B 1330 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 1333 GLU cc_start: 0.8566 (tt0) cc_final: 0.7958 (tt0) REVERT: B 1350 ASN cc_start: 0.7620 (m110) cc_final: 0.7391 (m-40) REVERT: B 1353 GLU cc_start: 0.7748 (pm20) cc_final: 0.7529 (pm20) REVERT: B 1358 GLU cc_start: 0.7793 (tm-30) cc_final: 0.5862 (tm-30) REVERT: B 1400 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8229 (mtmm) REVERT: B 1402 GLN cc_start: 0.8482 (pt0) cc_final: 0.8045 (pt0) REVERT: B 1423 GLU cc_start: 0.8418 (pt0) cc_final: 0.8048 (pt0) REVERT: B 1431 THR cc_start: 0.8586 (m) cc_final: 0.8270 (t) REVERT: B 1455 LYS cc_start: 0.8423 (mptt) cc_final: 0.8169 (mptt) REVERT: B 1457 ILE cc_start: 0.9033 (pt) cc_final: 0.8466 (mm) REVERT: B 1458 ASP cc_start: 0.7415 (t0) cc_final: 0.7190 (t0) REVERT: B 1460 ILE cc_start: 0.8567 (tt) cc_final: 0.8240 (tt) REVERT: B 1461 ILE cc_start: 0.7958 (pt) cc_final: 0.7673 (mm) REVERT: B 1464 TRP cc_start: 0.8681 (m100) cc_final: 0.5294 (m100) REVERT: B 1471 LEU cc_start: 0.8847 (mt) cc_final: 0.8556 (mm) REVERT: B 1497 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 1504 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 1516 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 1544 GLU cc_start: 0.8404 (pt0) cc_final: 0.7602 (pt0) REVERT: B 1549 GLN cc_start: 0.8358 (pp30) cc_final: 0.7645 (tm-30) REVERT: B 1560 GLU cc_start: 0.8653 (tt0) cc_final: 0.8446 (tt0) REVERT: B 1565 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7671 (tmtt) REVERT: B 1573 LEU cc_start: 0.8741 (pp) cc_final: 0.8446 (tt) REVERT: B 1577 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7951 (ttp-170) REVERT: B 1586 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 1590 GLU cc_start: 0.8597 (mp0) cc_final: 0.8233 (mp0) REVERT: B 1614 LYS cc_start: 0.8809 (tttp) cc_final: 0.8467 (tttp) REVERT: B 1627 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7236 (tm-30) REVERT: B 1629 ASP cc_start: 0.8177 (t70) cc_final: 0.7737 (t0) REVERT: B 1633 LEU cc_start: 0.8907 (mm) cc_final: 0.8263 (mm) REVERT: B 1634 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 1638 ASP cc_start: 0.8103 (t0) cc_final: 0.7612 (t0) REVERT: B 1641 ASN cc_start: 0.8811 (m-40) cc_final: 0.8584 (t0) REVERT: B 1649 LYS cc_start: 0.8403 (tptp) cc_final: 0.7977 (mptp) REVERT: B 1653 LYS cc_start: 0.9060 (tttt) cc_final: 0.8738 (ttpp) REVERT: B 1667 GLU cc_start: 0.8246 (tp30) cc_final: 0.7847 (tp30) REVERT: B 1677 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 1683 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 1723 GLU cc_start: 0.8502 (pt0) cc_final: 0.8294 (pt0) REVERT: B 1737 LYS cc_start: 0.9329 (tmtt) cc_final: 0.9023 (tptp) REVERT: B 1750 ASP cc_start: 0.7852 (t0) cc_final: 0.7570 (t0) REVERT: B 1757 LYS cc_start: 0.8953 (tttp) cc_final: 0.8465 (ttpp) REVERT: B 1759 SER cc_start: 0.8957 (p) cc_final: 0.8694 (p) REVERT: B 1760 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 1762 LYS cc_start: 0.8638 (mttp) cc_final: 0.8365 (mttp) REVERT: B 1764 LYS cc_start: 0.8677 (mmmt) cc_final: 0.7219 (mmmm) REVERT: B 1767 MET cc_start: 0.7685 (ppp) cc_final: 0.7214 (ppp) REVERT: B 1772 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8397 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8150 (t0) cc_final: 0.7942 (t0) REVERT: B 1780 GLU cc_start: 0.7426 (tp30) cc_final: 0.7158 (tp30) REVERT: B 1789 LYS cc_start: 0.8955 (tppp) cc_final: 0.8691 (tppp) REVERT: B 1818 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8521 (tppt) REVERT: B 1820 ILE cc_start: 0.8325 (mt) cc_final: 0.8047 (tp) REVERT: B 1824 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 1833 GLU cc_start: 0.8101 (tp30) cc_final: 0.7386 (tp30) REVERT: B 1838 GLN cc_start: 0.8572 (tp40) cc_final: 0.8221 (tp40) REVERT: B 1848 LEU cc_start: 0.9018 (tp) cc_final: 0.8686 (tt) REVERT: B 1852 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 1853 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8162 (tpp80) REVERT: B 1855 ILE cc_start: 0.8844 (tt) cc_final: 0.8549 (tt) REVERT: B 1858 LEU cc_start: 0.8914 (mt) cc_final: 0.8699 (mm) REVERT: B 1860 PHE cc_start: 0.8570 (t80) cc_final: 0.8249 (t80) REVERT: B 1865 ASP cc_start: 0.7942 (m-30) cc_final: 0.7622 (m-30) REVERT: B 1871 ARG cc_start: 0.8107 (ptt90) cc_final: 0.7668 (ptt90) REVERT: B 1873 GLN cc_start: 0.8827 (tp40) cc_final: 0.8339 (tm-30) REVERT: B 1878 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7767 (mmmt) REVERT: B 1882 LYS cc_start: 0.9112 (tttp) cc_final: 0.8669 (tttm) REVERT: B 1884 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8625 (mmtp) REVERT: B 1888 ARG cc_start: 0.8567 (mtp85) cc_final: 0.7976 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8627 (mt0) cc_final: 0.8144 (tp40) REVERT: B 1892 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 1903 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8706 (mmtt) REVERT: B 1906 LYS cc_start: 0.9177 (tppt) cc_final: 0.8693 (tppt) REVERT: B 1910 GLU cc_start: 0.8240 (pp20) cc_final: 0.7971 (pp20) REVERT: B 1911 LEU cc_start: 0.8690 (tt) cc_final: 0.8017 (tt) REVERT: B 1915 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 1917 ARG cc_start: 0.9020 (mtp-110) cc_final: 0.8552 (ttp-110) REVERT: B 1927 LYS cc_start: 0.9025 (tttm) cc_final: 0.8805 (tttm) REVERT: A 1159 GLU cc_start: 0.8488 (mp0) cc_final: 0.7938 (mt-10) REVERT: A 1174 LYS cc_start: 0.9084 (mttp) cc_final: 0.8824 (mttp) REVERT: A 1179 MET cc_start: 0.6693 (ppp) cc_final: 0.6211 (ppp) REVERT: A 1188 GLU cc_start: 0.6732 (tp30) cc_final: 0.6404 (tm-30) REVERT: A 1202 LYS cc_start: 0.8756 (pptt) cc_final: 0.8542 (pptt) REVERT: A 1215 ILE cc_start: 0.7968 (pt) cc_final: 0.7683 (pt) REVERT: A 1250 LYS cc_start: 0.8625 (pptt) cc_final: 0.8341 (pptt) REVERT: A 1298 GLN cc_start: 0.8065 (mp10) cc_final: 0.7600 (mp10) REVERT: A 1299 LEU cc_start: 0.8464 (mt) cc_final: 0.8239 (mm) REVERT: A 1300 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8106 (mm-30) REVERT: A 1329 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7706 (tm-30) REVERT: A 1330 GLU cc_start: 0.8345 (tt0) cc_final: 0.7777 (mm-30) REVERT: A 1338 LEU cc_start: 0.8593 (mp) cc_final: 0.8379 (mm) REVERT: A 1353 GLU cc_start: 0.8578 (mp0) cc_final: 0.8063 (mp0) REVERT: A 1357 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 1358 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 1392 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 1401 LEU cc_start: 0.8273 (tt) cc_final: 0.8031 (tp) REVERT: A 1405 LEU cc_start: 0.8685 (tt) cc_final: 0.8397 (tt) REVERT: A 1407 GLU cc_start: 0.7881 (pp20) cc_final: 0.7560 (pp20) REVERT: A 1409 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 1420 ILE cc_start: 0.8595 (pt) cc_final: 0.8345 (mm) REVERT: A 1424 LYS cc_start: 0.8653 (tttp) cc_final: 0.8249 (mmmm) REVERT: A 1439 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6496 (tm-30) REVERT: A 1442 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7580 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8147 (t0) cc_final: 0.7804 (t0) REVERT: A 1457 ILE cc_start: 0.8317 (mm) cc_final: 0.7892 (mm) REVERT: A 1458 ASP cc_start: 0.7781 (p0) cc_final: 0.7019 (p0) REVERT: A 1465 LYS cc_start: 0.8323 (mmtm) cc_final: 0.6610 (tppt) REVERT: A 1467 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7832 (ttmm) REVERT: A 1481 GLU cc_start: 0.7533 (tp30) cc_final: 0.7144 (tp30) REVERT: A 1488 GLU cc_start: 0.6906 (tp30) cc_final: 0.6248 (tp30) REVERT: A 1489 LEU cc_start: 0.8809 (tt) cc_final: 0.8474 (tp) REVERT: A 1492 LEU cc_start: 0.8476 (mt) cc_final: 0.7945 (mm) REVERT: A 1511 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8658 (tppt) REVERT: A 1516 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 1523 GLN cc_start: 0.7965 (mt0) cc_final: 0.7473 (tt0) REVERT: A 1556 GLU cc_start: 0.7704 (pp20) cc_final: 0.7463 (pp20) REVERT: A 1561 GLN cc_start: 0.7348 (pp30) cc_final: 0.6891 (pp30) REVERT: A 1567 LEU cc_start: 0.8992 (mt) cc_final: 0.8741 (mm) REVERT: A 1570 GLN cc_start: 0.8258 (mt0) cc_final: 0.7994 (mm-40) REVERT: A 1589 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 1599 GLN cc_start: 0.8417 (tt0) cc_final: 0.8097 (tp40) REVERT: A 1623 LYS cc_start: 0.8369 (tppt) cc_final: 0.7929 (tppt) REVERT: A 1625 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8403 (mtpp) REVERT: A 1631 ASN cc_start: 0.8701 (m-40) cc_final: 0.8441 (t0) REVERT: A 1637 LEU cc_start: 0.8937 (mt) cc_final: 0.8373 (tt) REVERT: A 1642 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8022 (mtpp) REVERT: A 1646 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 1649 LYS cc_start: 0.9158 (tttp) cc_final: 0.8625 (ttpp) REVERT: A 1660 ASP cc_start: 0.8189 (p0) cc_final: 0.7945 (p0) REVERT: A 1662 GLN cc_start: 0.8640 (tt0) cc_final: 0.8036 (tp40) REVERT: A 1672 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7690 (ttp80) REVERT: A 1690 GLN cc_start: 0.8572 (tt0) cc_final: 0.8290 (tp40) REVERT: A 1692 GLU cc_start: 0.8280 (tp30) cc_final: 0.7980 (tp30) REVERT: A 1705 ARG cc_start: 0.8487 (ttt90) cc_final: 0.8113 (ttp-110) REVERT: A 1735 LYS cc_start: 0.8947 (ptmm) cc_final: 0.8653 (ttpp) REVERT: A 1737 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8746 (ttpp) REVERT: A 1749 LEU cc_start: 0.8936 (tp) cc_final: 0.8699 (tp) REVERT: A 1762 LYS cc_start: 0.9302 (ttmt) cc_final: 0.9068 (ttmt) REVERT: A 1765 LYS cc_start: 0.8751 (tppt) cc_final: 0.8459 (tppp) REVERT: A 1776 GLU cc_start: 0.8055 (tp30) cc_final: 0.7691 (tp30) REVERT: A 1782 ASP cc_start: 0.8123 (t0) cc_final: 0.7885 (t0) REVERT: A 1792 LYS cc_start: 0.9320 (ttmt) cc_final: 0.8986 (ttmm) REVERT: A 1794 LEU cc_start: 0.8891 (mt) cc_final: 0.8686 (mm) REVERT: A 1822 LYS cc_start: 0.8593 (tttm) cc_final: 0.8360 (ttpp) REVERT: A 1824 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 1839 ARG cc_start: 0.8454 (tmt170) cc_final: 0.8040 (tmt170) REVERT: A 1846 LYS cc_start: 0.9161 (tttm) cc_final: 0.8897 (ttmm) REVERT: A 1853 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.7759 (ttm110) REVERT: A 1858 LEU cc_start: 0.8517 (mp) cc_final: 0.8265 (mm) REVERT: A 1860 PHE cc_start: 0.9084 (t80) cc_final: 0.8882 (t80) REVERT: A 1864 GLU cc_start: 0.7926 (tp30) cc_final: 0.7471 (tp30) REVERT: A 1865 ASP cc_start: 0.8128 (t0) cc_final: 0.7802 (t0) REVERT: A 1868 ASN cc_start: 0.8599 (m110) cc_final: 0.8163 (m-40) REVERT: A 1870 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 1878 LYS cc_start: 0.8970 (tppt) cc_final: 0.8661 (mmmm) REVERT: A 1882 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8892 (ttmm) REVERT: A 1892 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 1909 GLN cc_start: 0.8623 (tp40) cc_final: 0.8168 (tm-30) REVERT: A 1910 GLU cc_start: 0.8477 (tt0) cc_final: 0.7901 (tt0) REVERT: A 1915 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7727 (tm-30) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.3385 time to fit residues: 307.9164 Evaluate side-chains 575 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 575 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1037 GLN B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1305 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1900 ASN A 947 GLN ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 ASN A1373 ASN A1500 GLN A1502 GLN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS ** 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: 0.7343 moved from start: 1.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17454 Z= 0.170 Angle : 0.615 7.447 23282 Z= 0.333 Chirality : 0.039 0.155 2582 Planarity : 0.003 0.039 3158 Dihedral : 4.225 15.518 2318 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.05 % 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: 2.83 (0.18), residues: 2150 helix: 1.92 (0.11), residues: 2109 sheet: None (None), residues: 0 loop : 0.54 (0.93), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A1379 HIS 0.011 0.001 HIS B1598 PHE 0.016 0.002 PHE A 945 TYR 0.028 0.003 TYR A1383 ARG 0.007 0.001 ARG A1390 *********************** 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 658 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 656 time to evaluate : 2.003 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: B 928 MET cc_start: 0.8127 (mmp) cc_final: 0.7872 (mmp) REVERT: B 948 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8238 (ptpt) REVERT: B 1047 GLU cc_start: 0.8171 (mp0) cc_final: 0.7873 (pm20) REVERT: B 1057 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7133 (pp20) REVERT: B 1127 GLU cc_start: 0.8227 (mp0) cc_final: 0.7844 (mp0) REVERT: B 1182 LEU cc_start: 0.7875 (mp) cc_final: 0.7551 (mp) REVERT: B 1243 LEU cc_start: 0.8631 (tt) cc_final: 0.8206 (tt) REVERT: B 1246 MET cc_start: 0.7800 (ppp) cc_final: 0.7527 (ppp) REVERT: B 1248 ARG cc_start: 0.8289 (mmt180) cc_final: 0.7982 (mmt180) REVERT: B 1249 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 1250 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8382 (ptmm) REVERT: B 1261 GLN cc_start: 0.8836 (tt0) cc_final: 0.8137 (tp40) REVERT: B 1265 ASN cc_start: 0.8281 (m110) cc_final: 0.7981 (m-40) REVERT: B 1268 GLN cc_start: 0.8376 (pt0) cc_final: 0.7989 (tt0) REVERT: B 1271 LEU cc_start: 0.9189 (mt) cc_final: 0.8869 (tp) REVERT: B 1291 GLU cc_start: 0.7092 (tp30) cc_final: 0.6762 (tp30) REVERT: B 1320 LEU cc_start: 0.8795 (mt) cc_final: 0.8434 (tt) REVERT: B 1324 LYS cc_start: 0.8482 (pttp) cc_final: 0.8025 (pttp) REVERT: B 1330 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 1333 GLU cc_start: 0.8495 (tt0) cc_final: 0.7781 (tt0) REVERT: B 1357 GLU cc_start: 0.7990 (tp30) cc_final: 0.7329 (tp30) REVERT: B 1358 GLU cc_start: 0.8029 (tm-30) cc_final: 0.5950 (tm-30) REVERT: B 1362 LYS cc_start: 0.7802 (mtmm) cc_final: 0.6586 (mtmt) REVERT: B 1367 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.8026 (tpp80) REVERT: B 1379 TRP cc_start: 0.6307 (t60) cc_final: 0.6043 (t60) REVERT: B 1400 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8592 (mtpp) REVERT: B 1402 GLN cc_start: 0.8517 (pt0) cc_final: 0.8151 (pt0) REVERT: B 1419 VAL cc_start: 0.8806 (m) cc_final: 0.8507 (p) REVERT: B 1423 GLU cc_start: 0.8329 (pt0) cc_final: 0.8059 (pt0) REVERT: B 1431 THR cc_start: 0.8643 (m) cc_final: 0.8370 (t) REVERT: B 1455 LYS cc_start: 0.8424 (mptt) cc_final: 0.8175 (mptt) REVERT: B 1457 ILE cc_start: 0.9023 (pt) cc_final: 0.8507 (mm) REVERT: B 1458 ASP cc_start: 0.7398 (t0) cc_final: 0.7181 (t0) REVERT: B 1464 TRP cc_start: 0.8239 (m100) cc_final: 0.6089 (m100) REVERT: B 1471 LEU cc_start: 0.8841 (mt) cc_final: 0.8618 (mm) REVERT: B 1497 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6927 (tm-30) REVERT: B 1504 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 1516 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 1540 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7838 (ttp80) REVERT: B 1542 GLU cc_start: 0.8053 (tp30) cc_final: 0.7563 (tp30) REVERT: B 1544 GLU cc_start: 0.8291 (pt0) cc_final: 0.7842 (pt0) REVERT: B 1549 GLN cc_start: 0.8256 (pp30) cc_final: 0.7694 (tm-30) REVERT: B 1560 GLU cc_start: 0.8725 (tt0) cc_final: 0.8003 (mm-30) REVERT: B 1573 LEU cc_start: 0.8752 (pp) cc_final: 0.8443 (tt) REVERT: B 1577 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7976 (ttp-170) REVERT: B 1586 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 1600 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7971 (ttm110) REVERT: B 1634 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 1638 ASP cc_start: 0.8151 (t0) cc_final: 0.7676 (t0) REVERT: B 1644 ASN cc_start: 0.8506 (m-40) cc_final: 0.8213 (t0) REVERT: B 1646 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 1653 LYS cc_start: 0.9101 (tttt) cc_final: 0.8657 (ttmm) REVERT: B 1667 GLU cc_start: 0.8267 (tp30) cc_final: 0.7873 (tp30) REVERT: B 1668 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 1677 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 1683 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7058 (tm-30) REVERT: B 1700 LEU cc_start: 0.8872 (tp) cc_final: 0.8354 (tp) REVERT: B 1704 ASP cc_start: 0.7024 (p0) cc_final: 0.6647 (p0) REVERT: B 1708 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8194 (mtm-85) REVERT: B 1723 GLU cc_start: 0.8458 (pt0) cc_final: 0.8181 (pt0) REVERT: B 1737 LYS cc_start: 0.9346 (tmtt) cc_final: 0.9103 (tptp) REVERT: B 1741 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 1757 LYS cc_start: 0.8939 (tttp) cc_final: 0.8419 (ttpp) REVERT: B 1760 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 1762 LYS cc_start: 0.8663 (mttp) cc_final: 0.8416 (mttp) REVERT: B 1764 LYS cc_start: 0.8726 (mmmt) cc_final: 0.7335 (mmmm) REVERT: B 1767 MET cc_start: 0.7744 (ppp) cc_final: 0.7279 (ppp) REVERT: B 1772 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8402 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8079 (t0) cc_final: 0.7867 (t0) REVERT: B 1780 GLU cc_start: 0.7472 (tp30) cc_final: 0.7216 (tp30) REVERT: B 1781 GLN cc_start: 0.8286 (tp40) cc_final: 0.7850 (tp40) REVERT: B 1788 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 1789 LYS cc_start: 0.8962 (tppp) cc_final: 0.8658 (tppp) REVERT: B 1818 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8517 (tppt) REVERT: B 1820 ILE cc_start: 0.8319 (mt) cc_final: 0.8038 (tp) REVERT: B 1824 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 1826 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8482 (tpt-90) REVERT: B 1833 GLU cc_start: 0.8131 (tp30) cc_final: 0.7360 (tp30) REVERT: B 1837 GLU cc_start: 0.8406 (tp30) cc_final: 0.8142 (mm-30) REVERT: B 1838 GLN cc_start: 0.8642 (tp40) cc_final: 0.8266 (tp40) REVERT: B 1848 LEU cc_start: 0.9053 (tp) cc_final: 0.8683 (tt) REVERT: B 1853 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8180 (tpp80) REVERT: B 1860 PHE cc_start: 0.8598 (t80) cc_final: 0.8189 (t80) REVERT: B 1865 ASP cc_start: 0.7937 (m-30) cc_final: 0.7621 (m-30) REVERT: B 1871 ARG cc_start: 0.8166 (ptt90) cc_final: 0.7722 (ptt90) REVERT: B 1873 GLN cc_start: 0.8827 (tp40) cc_final: 0.8349 (tm-30) REVERT: B 1878 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7848 (mmmt) REVERT: B 1882 LYS cc_start: 0.9146 (tttp) cc_final: 0.8659 (tttm) REVERT: B 1884 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8622 (mmtp) REVERT: B 1888 ARG cc_start: 0.8532 (mtp85) cc_final: 0.8318 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8625 (mt0) cc_final: 0.8207 (tp40) REVERT: B 1903 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8638 (mmtt) REVERT: B 1906 LYS cc_start: 0.9170 (tppt) cc_final: 0.8757 (tppt) REVERT: B 1910 GLU cc_start: 0.8225 (pp20) cc_final: 0.7980 (pp20) REVERT: B 1911 LEU cc_start: 0.8694 (tt) cc_final: 0.8047 (tt) REVERT: B 1915 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 1917 ARG cc_start: 0.8999 (mtp-110) cc_final: 0.8545 (ttp-110) REVERT: A 1103 GLU cc_start: 0.8348 (mp0) cc_final: 0.6979 (tp30) REVERT: A 1159 GLU cc_start: 0.8616 (mp0) cc_final: 0.8194 (mt-10) REVERT: A 1174 LYS cc_start: 0.9000 (mttp) cc_final: 0.8771 (mttp) REVERT: A 1202 LYS cc_start: 0.8903 (pptt) cc_final: 0.8629 (pptt) REVERT: A 1250 LYS cc_start: 0.8751 (pptt) cc_final: 0.8249 (pptt) REVERT: A 1270 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8282 (mmtp) REVERT: A 1298 GLN cc_start: 0.7894 (mp10) cc_final: 0.7551 (mp10) REVERT: A 1299 LEU cc_start: 0.8496 (mt) cc_final: 0.7854 (tp) REVERT: A 1300 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8081 (mm-30) REVERT: A 1319 GLN cc_start: 0.8229 (mt0) cc_final: 0.7923 (mt0) REVERT: A 1322 ASP cc_start: 0.8012 (m-30) cc_final: 0.7800 (m-30) REVERT: A 1329 GLU cc_start: 0.8240 (tp30) cc_final: 0.7915 (tp30) REVERT: A 1338 LEU cc_start: 0.8750 (mp) cc_final: 0.8482 (mm) REVERT: A 1344 LEU cc_start: 0.8228 (tp) cc_final: 0.7949 (tp) REVERT: A 1350 ASN cc_start: 0.7638 (m-40) cc_final: 0.7219 (t0) REVERT: A 1351 ILE cc_start: 0.8878 (pt) cc_final: 0.8672 (pt) REVERT: A 1353 GLU cc_start: 0.8413 (mp0) cc_final: 0.7844 (mp0) REVERT: A 1357 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 1358 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 1360 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 1392 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 1405 LEU cc_start: 0.8713 (tt) cc_final: 0.8460 (tt) REVERT: A 1407 GLU cc_start: 0.7914 (pp20) cc_final: 0.7565 (pp20) REVERT: A 1409 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6924 (tm-30) REVERT: A 1413 GLU cc_start: 0.7758 (mp0) cc_final: 0.7379 (mp0) REVERT: A 1419 VAL cc_start: 0.9010 (m) cc_final: 0.8795 (p) REVERT: A 1424 LYS cc_start: 0.8653 (tttp) cc_final: 0.8312 (tppp) REVERT: A 1432 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 1439 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6487 (tm-30) REVERT: A 1442 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7549 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8091 (t0) cc_final: 0.7782 (t0) REVERT: A 1457 ILE cc_start: 0.8356 (mm) cc_final: 0.7827 (mm) REVERT: A 1458 ASP cc_start: 0.7853 (p0) cc_final: 0.7097 (p0) REVERT: A 1463 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 1465 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7039 (tppt) REVERT: A 1467 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7851 (ttmm) REVERT: A 1481 GLU cc_start: 0.7554 (tp30) cc_final: 0.7222 (tp30) REVERT: A 1488 GLU cc_start: 0.7019 (tp30) cc_final: 0.6125 (tp30) REVERT: A 1492 LEU cc_start: 0.8449 (mt) cc_final: 0.7712 (mm) REVERT: A 1511 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8563 (tppt) REVERT: A 1531 ILE cc_start: 0.8684 (pt) cc_final: 0.8374 (pt) REVERT: A 1535 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 1539 LYS cc_start: 0.8202 (pttm) cc_final: 0.7827 (pttm) REVERT: A 1542 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 1570 GLN cc_start: 0.8326 (mt0) cc_final: 0.7974 (mm-40) REVERT: A 1574 SER cc_start: 0.9018 (t) cc_final: 0.8802 (p) REVERT: A 1589 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 1597 ASN cc_start: 0.8878 (m-40) cc_final: 0.8485 (t0) REVERT: A 1599 GLN cc_start: 0.8419 (tt0) cc_final: 0.8104 (tp40) REVERT: A 1618 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 1623 LYS cc_start: 0.8436 (tppt) cc_final: 0.8148 (tppt) REVERT: A 1624 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8646 (tppt) REVERT: A 1625 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8433 (mtpp) REVERT: A 1637 LEU cc_start: 0.8833 (mt) cc_final: 0.8539 (tt) REVERT: A 1642 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7919 (mtpp) REVERT: A 1646 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 1649 LYS cc_start: 0.9189 (tttp) cc_final: 0.8784 (ttmm) REVERT: A 1660 ASP cc_start: 0.8207 (p0) cc_final: 0.7922 (p0) REVERT: A 1662 GLN cc_start: 0.8628 (tt0) cc_final: 0.8067 (tp40) REVERT: A 1676 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8574 (mmm-85) REVERT: A 1690 GLN cc_start: 0.8558 (tt0) cc_final: 0.8226 (tp40) REVERT: A 1692 GLU cc_start: 0.8255 (tp30) cc_final: 0.7942 (tp30) REVERT: A 1705 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8050 (ttp-110) REVERT: A 1737 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8718 (ttpp) REVERT: A 1741 GLU cc_start: 0.8230 (tp30) cc_final: 0.7930 (tp30) REVERT: A 1754 ASN cc_start: 0.8510 (t0) cc_final: 0.8196 (t0) REVERT: A 1757 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8616 (ttpt) REVERT: A 1758 ASN cc_start: 0.8520 (t0) cc_final: 0.8160 (t0) REVERT: A 1762 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9086 (ttmt) REVERT: A 1765 LYS cc_start: 0.8833 (tppt) cc_final: 0.8605 (tppp) REVERT: A 1776 GLU cc_start: 0.8103 (tp30) cc_final: 0.7832 (tp30) REVERT: A 1778 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.8060 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8104 (t0) cc_final: 0.7836 (t0) REVERT: A 1792 LYS cc_start: 0.9362 (ttmt) cc_final: 0.9035 (ttmm) REVERT: A 1795 GLU cc_start: 0.7893 (tp30) cc_final: 0.7662 (tp30) REVERT: A 1822 LYS cc_start: 0.8622 (tttm) cc_final: 0.8403 (ttpp) REVERT: A 1839 ARG cc_start: 0.8472 (tmt170) cc_final: 0.8049 (tmt170) REVERT: A 1840 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8047 (mtm110) REVERT: A 1846 LYS cc_start: 0.9175 (tttm) cc_final: 0.8933 (ttmm) REVERT: A 1853 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.7748 (ttm110) REVERT: A 1858 LEU cc_start: 0.8507 (mp) cc_final: 0.8286 (mm) REVERT: A 1864 GLU cc_start: 0.7935 (tp30) cc_final: 0.7468 (tp30) REVERT: A 1865 ASP cc_start: 0.8060 (t0) cc_final: 0.7756 (t0) REVERT: A 1868 ASN cc_start: 0.8576 (m110) cc_final: 0.8162 (m-40) REVERT: A 1870 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 1878 LYS cc_start: 0.8998 (tppt) cc_final: 0.8780 (mmmm) REVERT: A 1881 GLN cc_start: 0.8677 (tp40) cc_final: 0.8306 (tp40) REVERT: A 1882 LYS cc_start: 0.9193 (ttmm) cc_final: 0.8892 (ttmm) REVERT: A 1884 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8821 (ttpp) REVERT: A 1889 GLN cc_start: 0.7704 (pp30) cc_final: 0.7467 (pp30) REVERT: A 1892 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 1894 GLU cc_start: 0.7076 (pp20) cc_final: 0.6864 (pp20) REVERT: A 1909 GLN cc_start: 0.8676 (tp40) cc_final: 0.8236 (tm-30) REVERT: A 1910 GLU cc_start: 0.8480 (tt0) cc_final: 0.7932 (tt0) REVERT: A 1915 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7741 (tm-30) outliers start: 2 outliers final: 1 residues processed: 658 average time/residue: 0.3423 time to fit residues: 319.5764 Evaluate side-chains 593 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 591 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** B1204 HIS ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1089 GLN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1417 GLN A1523 GLN ** 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: 0.7374 moved from start: 1.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17454 Z= 0.177 Angle : 0.636 9.776 23282 Z= 0.342 Chirality : 0.040 0.162 2582 Planarity : 0.003 0.038 3158 Dihedral : 4.211 15.360 2318 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 2.91 (0.18), residues: 2150 helix: 1.96 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : 1.07 (0.91), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A1379 HIS 0.013 0.001 HIS B1598 PHE 0.031 0.002 PHE A 945 TYR 0.017 0.003 TYR A1383 ARG 0.009 0.001 ARG A1672 *********************** 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 658 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 1.976 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: B 928 MET cc_start: 0.8177 (mmp) cc_final: 0.7934 (mmp) REVERT: B 948 LYS cc_start: 0.8495 (ptpp) cc_final: 0.8262 (ptpt) REVERT: B 1047 GLU cc_start: 0.8132 (mp0) cc_final: 0.7830 (pm20) REVERT: B 1181 LYS cc_start: 0.8705 (tppt) cc_final: 0.8096 (tppt) REVERT: B 1182 LEU cc_start: 0.8099 (mp) cc_final: 0.7781 (mp) REVERT: B 1248 ARG cc_start: 0.8268 (mmt180) cc_final: 0.8024 (mmt180) REVERT: B 1249 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 1250 LYS cc_start: 0.8735 (ptmt) cc_final: 0.8120 (ptmm) REVERT: B 1261 GLN cc_start: 0.8885 (tt0) cc_final: 0.8210 (tp40) REVERT: B 1268 GLN cc_start: 0.8425 (pt0) cc_final: 0.8144 (tt0) REVERT: B 1271 LEU cc_start: 0.9106 (mt) cc_final: 0.8663 (tt) REVERT: B 1285 LYS cc_start: 0.9075 (ptmt) cc_final: 0.8687 (ttmm) REVERT: B 1291 GLU cc_start: 0.7214 (tp30) cc_final: 0.6906 (tp30) REVERT: B 1297 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7784 (mtp180) REVERT: B 1300 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 1320 LEU cc_start: 0.8767 (mt) cc_final: 0.8407 (tt) REVERT: B 1324 LYS cc_start: 0.8412 (pttp) cc_final: 0.8018 (pttp) REVERT: B 1330 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7169 (mm-30) REVERT: B 1333 GLU cc_start: 0.8426 (tt0) cc_final: 0.7822 (tt0) REVERT: B 1358 GLU cc_start: 0.8140 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 1362 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7028 (mtmt) REVERT: B 1367 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8105 (tpp80) REVERT: B 1400 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8605 (ttmm) REVERT: B 1402 GLN cc_start: 0.8530 (pt0) cc_final: 0.8084 (pt0) REVERT: B 1431 THR cc_start: 0.8655 (m) cc_final: 0.8366 (t) REVERT: B 1455 LYS cc_start: 0.8425 (mptt) cc_final: 0.8223 (mptt) REVERT: B 1457 ILE cc_start: 0.8991 (pt) cc_final: 0.8574 (mm) REVERT: B 1464 TRP cc_start: 0.8283 (m100) cc_final: 0.6240 (m100) REVERT: B 1471 LEU cc_start: 0.8847 (mt) cc_final: 0.8605 (mm) REVERT: B 1497 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B 1504 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 1509 GLU cc_start: 0.8181 (tt0) cc_final: 0.7966 (tt0) REVERT: B 1516 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 1535 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 1540 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7825 (ttp80) REVERT: B 1542 GLU cc_start: 0.8132 (tp30) cc_final: 0.7862 (tp30) REVERT: B 1543 VAL cc_start: 0.9171 (t) cc_final: 0.8930 (p) REVERT: B 1544 GLU cc_start: 0.8310 (pt0) cc_final: 0.7884 (pt0) REVERT: B 1546 ASP cc_start: 0.8745 (m-30) cc_final: 0.8398 (m-30) REVERT: B 1549 GLN cc_start: 0.8302 (pp30) cc_final: 0.7946 (tm-30) REVERT: B 1560 GLU cc_start: 0.8779 (tt0) cc_final: 0.8540 (mm-30) REVERT: B 1572 GLU cc_start: 0.8670 (tt0) cc_final: 0.8360 (tt0) REVERT: B 1573 LEU cc_start: 0.8747 (pp) cc_final: 0.8412 (tt) REVERT: B 1577 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7992 (ttp-170) REVERT: B 1614 LYS cc_start: 0.8820 (tttp) cc_final: 0.8611 (tttp) REVERT: B 1627 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 1629 ASP cc_start: 0.8379 (t70) cc_final: 0.8013 (t70) REVERT: B 1634 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 1638 ASP cc_start: 0.8177 (t0) cc_final: 0.7682 (t0) REVERT: B 1644 ASN cc_start: 0.8441 (m-40) cc_final: 0.8113 (t0) REVERT: B 1646 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 1653 LYS cc_start: 0.9134 (tttt) cc_final: 0.8521 (ttmm) REVERT: B 1657 GLN cc_start: 0.7724 (tp40) cc_final: 0.7259 (tp40) REVERT: B 1667 GLU cc_start: 0.8273 (tp30) cc_final: 0.7861 (tp30) REVERT: B 1677 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 1683 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 1692 GLU cc_start: 0.7819 (pp20) cc_final: 0.7477 (pp20) REVERT: B 1708 ARG cc_start: 0.8559 (mpt-90) cc_final: 0.8140 (mtm-85) REVERT: B 1723 GLU cc_start: 0.8420 (pt0) cc_final: 0.8163 (pt0) REVERT: B 1737 LYS cc_start: 0.9321 (tmtt) cc_final: 0.9097 (tptp) REVERT: B 1741 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 1757 LYS cc_start: 0.8925 (tttp) cc_final: 0.8676 (tttp) REVERT: B 1760 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 1762 LYS cc_start: 0.8620 (mttp) cc_final: 0.8402 (mttp) REVERT: B 1764 LYS cc_start: 0.8768 (mmmt) cc_final: 0.7618 (mmmm) REVERT: B 1767 MET cc_start: 0.7768 (ppp) cc_final: 0.7259 (ppp) REVERT: B 1772 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8408 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8097 (t0) cc_final: 0.7880 (t0) REVERT: B 1781 GLN cc_start: 0.8290 (tp40) cc_final: 0.7843 (tp40) REVERT: B 1818 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8536 (tppt) REVERT: B 1820 ILE cc_start: 0.8365 (mt) cc_final: 0.8079 (tp) REVERT: B 1824 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 1833 GLU cc_start: 0.8198 (tp30) cc_final: 0.7393 (tp30) REVERT: B 1837 GLU cc_start: 0.8406 (tp30) cc_final: 0.8147 (mm-30) REVERT: B 1838 GLN cc_start: 0.8627 (tp40) cc_final: 0.8250 (tp40) REVERT: B 1848 LEU cc_start: 0.9022 (tp) cc_final: 0.8675 (tt) REVERT: B 1853 ARG cc_start: 0.8563 (mmt90) cc_final: 0.8103 (tpp80) REVERT: B 1860 PHE cc_start: 0.8553 (t80) cc_final: 0.8101 (t80) REVERT: B 1865 ASP cc_start: 0.7956 (m-30) cc_final: 0.7598 (m-30) REVERT: B 1866 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8075 (tmm-80) REVERT: B 1871 ARG cc_start: 0.8145 (ptt90) cc_final: 0.7757 (ptt90) REVERT: B 1873 GLN cc_start: 0.8790 (tp40) cc_final: 0.8413 (tm-30) REVERT: B 1878 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7784 (mmmt) REVERT: B 1882 LYS cc_start: 0.9154 (tttp) cc_final: 0.8621 (tttp) REVERT: B 1884 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8543 (mmtp) REVERT: B 1888 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8319 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8660 (mt0) cc_final: 0.8127 (tp40) REVERT: B 1896 ILE cc_start: 0.8905 (mt) cc_final: 0.8689 (mt) REVERT: B 1903 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8627 (mmtt) REVERT: B 1906 LYS cc_start: 0.9185 (tppt) cc_final: 0.8775 (tppt) REVERT: B 1910 GLU cc_start: 0.8217 (pp20) cc_final: 0.8006 (pp20) REVERT: B 1911 LEU cc_start: 0.8651 (tt) cc_final: 0.8001 (tt) REVERT: B 1915 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 1917 ARG cc_start: 0.9013 (mtp-110) cc_final: 0.8398 (ttm-80) REVERT: A 1040 ASP cc_start: 0.7097 (m-30) cc_final: 0.6876 (m-30) REVERT: A 1103 GLU cc_start: 0.8269 (mp0) cc_final: 0.6891 (tp30) REVERT: A 1159 GLU cc_start: 0.8613 (mp0) cc_final: 0.8256 (mt-10) REVERT: A 1202 LYS cc_start: 0.8965 (pptt) cc_final: 0.8667 (pptt) REVERT: A 1270 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8323 (mmtp) REVERT: A 1291 GLU cc_start: 0.7231 (pt0) cc_final: 0.6826 (pt0) REVERT: A 1299 LEU cc_start: 0.8377 (mt) cc_final: 0.7850 (tp) REVERT: A 1300 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8134 (tp30) REVERT: A 1329 GLU cc_start: 0.8276 (tp30) cc_final: 0.7884 (tp30) REVERT: A 1350 ASN cc_start: 0.7706 (m-40) cc_final: 0.7316 (t0) REVERT: A 1351 ILE cc_start: 0.8931 (pt) cc_final: 0.8678 (pt) REVERT: A 1353 GLU cc_start: 0.8340 (mp0) cc_final: 0.7550 (mp0) REVERT: A 1357 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 1358 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 1360 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6833 (tm-30) REVERT: A 1392 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 1407 GLU cc_start: 0.7827 (pp20) cc_final: 0.7616 (pp20) REVERT: A 1409 GLU cc_start: 0.7530 (tm-30) cc_final: 0.6068 (tm-30) REVERT: A 1413 GLU cc_start: 0.7901 (mp0) cc_final: 0.7052 (mp0) REVERT: A 1424 LYS cc_start: 0.8617 (tttp) cc_final: 0.8260 (tppp) REVERT: A 1439 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 1442 ARG cc_start: 0.7982 (ptm160) cc_final: 0.7615 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8083 (t0) cc_final: 0.7804 (t0) REVERT: A 1457 ILE cc_start: 0.8393 (mm) cc_final: 0.7907 (mm) REVERT: A 1458 ASP cc_start: 0.7901 (p0) cc_final: 0.7179 (p0) REVERT: A 1463 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 1465 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7132 (tppt) REVERT: A 1467 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7890 (ttmm) REVERT: A 1481 GLU cc_start: 0.7528 (tp30) cc_final: 0.7240 (tp30) REVERT: A 1488 GLU cc_start: 0.7030 (tp30) cc_final: 0.6158 (tp30) REVERT: A 1489 LEU cc_start: 0.8816 (tt) cc_final: 0.8497 (tp) REVERT: A 1492 LEU cc_start: 0.8459 (mt) cc_final: 0.7669 (mm) REVERT: A 1511 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8594 (tppt) REVERT: A 1516 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7378 (mm-30) REVERT: A 1531 ILE cc_start: 0.8690 (pt) cc_final: 0.8364 (pt) REVERT: A 1535 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 1547 GLU cc_start: 0.8282 (tp30) cc_final: 0.8046 (tm-30) REVERT: A 1561 GLN cc_start: 0.7530 (pp30) cc_final: 0.7232 (pp30) REVERT: A 1563 GLU cc_start: 0.8266 (tp30) cc_final: 0.7786 (tp30) REVERT: A 1570 GLN cc_start: 0.8296 (mt0) cc_final: 0.7970 (mm-40) REVERT: A 1572 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 1589 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 1599 GLN cc_start: 0.8404 (tt0) cc_final: 0.8068 (tp40) REVERT: A 1614 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8604 (mmmm) REVERT: A 1623 LYS cc_start: 0.8450 (tppt) cc_final: 0.8090 (tppt) REVERT: A 1625 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8443 (mtpp) REVERT: A 1637 LEU cc_start: 0.8894 (mt) cc_final: 0.8618 (tt) REVERT: A 1642 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8107 (mtpp) REVERT: A 1649 LYS cc_start: 0.9204 (tttp) cc_final: 0.8783 (ttmm) REVERT: A 1660 ASP cc_start: 0.8226 (p0) cc_final: 0.7933 (p0) REVERT: A 1662 GLN cc_start: 0.8636 (tt0) cc_final: 0.8099 (tp40) REVERT: A 1690 GLN cc_start: 0.8541 (tt0) cc_final: 0.8246 (tp40) REVERT: A 1692 GLU cc_start: 0.8211 (tp30) cc_final: 0.7953 (tp30) REVERT: A 1737 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8775 (ttpp) REVERT: A 1741 GLU cc_start: 0.8311 (tp30) cc_final: 0.7883 (tp30) REVERT: A 1752 LEU cc_start: 0.9138 (tp) cc_final: 0.8895 (tt) REVERT: A 1758 ASN cc_start: 0.8521 (t0) cc_final: 0.8158 (t0) REVERT: A 1762 LYS cc_start: 0.9287 (ttmt) cc_final: 0.9052 (ttmt) REVERT: A 1765 LYS cc_start: 0.8884 (tppt) cc_final: 0.8651 (tppp) REVERT: A 1776 GLU cc_start: 0.8094 (tp30) cc_final: 0.7802 (tp30) REVERT: A 1778 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8073 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8083 (t0) cc_final: 0.7831 (t0) REVERT: A 1783 HIS cc_start: 0.9085 (t-90) cc_final: 0.8859 (t-170) REVERT: A 1792 LYS cc_start: 0.9287 (ttmt) cc_final: 0.9007 (tppp) REVERT: A 1822 LYS cc_start: 0.8612 (tttm) cc_final: 0.8400 (ttpp) REVERT: A 1839 ARG cc_start: 0.8466 (tmt170) cc_final: 0.8027 (tmt170) REVERT: A 1840 ARG cc_start: 0.8347 (mtm110) cc_final: 0.8046 (mtm110) REVERT: A 1846 LYS cc_start: 0.9195 (tttm) cc_final: 0.8935 (ttmm) REVERT: A 1850 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8372 (ptmm) REVERT: A 1853 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.7755 (ttm110) REVERT: A 1858 LEU cc_start: 0.8512 (mp) cc_final: 0.8264 (mm) REVERT: A 1860 PHE cc_start: 0.9074 (t80) cc_final: 0.8864 (t80) REVERT: A 1864 GLU cc_start: 0.7952 (tp30) cc_final: 0.7533 (tp30) REVERT: A 1865 ASP cc_start: 0.8025 (t0) cc_final: 0.7721 (t0) REVERT: A 1868 ASN cc_start: 0.8587 (m110) cc_final: 0.8215 (m-40) REVERT: A 1870 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 1871 ARG cc_start: 0.8553 (tpm170) cc_final: 0.7996 (tpm170) REVERT: A 1878 LYS cc_start: 0.9019 (tppt) cc_final: 0.8782 (mmmm) REVERT: A 1881 GLN cc_start: 0.8698 (tp40) cc_final: 0.8492 (tp40) REVERT: A 1882 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8918 (ttmm) REVERT: A 1888 ARG cc_start: 0.8103 (tmm160) cc_final: 0.7395 (ttp80) REVERT: A 1889 GLN cc_start: 0.7703 (pp30) cc_final: 0.7157 (pp30) REVERT: A 1892 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 1894 GLU cc_start: 0.7071 (pp20) cc_final: 0.6722 (pp20) REVERT: A 1909 GLN cc_start: 0.8681 (tp40) cc_final: 0.8216 (tm-30) REVERT: A 1910 GLU cc_start: 0.8490 (tt0) cc_final: 0.7934 (tt0) REVERT: A 1915 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 1922 GLU cc_start: 0.8301 (mp0) cc_final: 0.7750 (pp20) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.3339 time to fit residues: 316.2695 Evaluate side-chains 602 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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: 0.9990 chunk 180 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B1080 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1900 ASN ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7412 moved from start: 1.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17454 Z= 0.183 Angle : 0.645 9.025 23282 Z= 0.348 Chirality : 0.040 0.141 2582 Planarity : 0.003 0.049 3158 Dihedral : 4.227 17.027 2318 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 2.94 (0.18), residues: 2150 helix: 1.98 (0.11), residues: 2103 sheet: None (None), residues: 0 loop : 1.05 (0.92), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A1379 HIS 0.013 0.001 HIS B1598 PHE 0.014 0.002 PHE B1281 TYR 0.022 0.003 TYR A1383 ARG 0.009 0.001 ARG B 941 *********************** 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 670 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 1.949 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: B 928 MET cc_start: 0.8162 (mmp) cc_final: 0.7937 (mmp) REVERT: B 944 MET cc_start: 0.6103 (tpp) cc_final: 0.4820 (tpp) REVERT: B 948 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8038 (pttp) REVERT: B 1181 LYS cc_start: 0.8848 (tppt) cc_final: 0.8232 (tppt) REVERT: B 1182 LEU cc_start: 0.8208 (mp) cc_final: 0.7878 (mp) REVERT: B 1224 LYS cc_start: 0.8371 (mptt) cc_final: 0.7964 (mptt) REVERT: B 1248 ARG cc_start: 0.8391 (mmt180) cc_final: 0.8080 (mmt180) REVERT: B 1249 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 1250 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8305 (ptmm) REVERT: B 1254 GLU cc_start: 0.8456 (tt0) cc_final: 0.8189 (tt0) REVERT: B 1261 GLN cc_start: 0.8982 (tt0) cc_final: 0.8502 (tp40) REVERT: B 1265 ASN cc_start: 0.8385 (m-40) cc_final: 0.8124 (m-40) REVERT: B 1268 GLN cc_start: 0.8551 (pt0) cc_final: 0.8272 (tt0) REVERT: B 1271 LEU cc_start: 0.9037 (mt) cc_final: 0.8804 (tt) REVERT: B 1282 ASP cc_start: 0.8167 (m-30) cc_final: 0.7514 (t70) REVERT: B 1285 LYS cc_start: 0.9145 (ptmt) cc_final: 0.8742 (ttmm) REVERT: B 1286 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8846 (mtmt) REVERT: B 1291 GLU cc_start: 0.7379 (tp30) cc_final: 0.7155 (tp30) REVERT: B 1295 LEU cc_start: 0.7316 (pp) cc_final: 0.6864 (pp) REVERT: B 1297 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7840 (mtp180) REVERT: B 1300 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 1324 LYS cc_start: 0.8393 (pttp) cc_final: 0.8066 (pttp) REVERT: B 1325 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.7967 (mtm110) REVERT: B 1330 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 1333 GLU cc_start: 0.8386 (tt0) cc_final: 0.7792 (tt0) REVERT: B 1367 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7982 (tpp80) REVERT: B 1400 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8651 (ttmm) REVERT: B 1402 GLN cc_start: 0.8559 (pt0) cc_final: 0.8121 (pt0) REVERT: B 1409 GLU cc_start: 0.7810 (pt0) cc_final: 0.7543 (pt0) REVERT: B 1431 THR cc_start: 0.8635 (m) cc_final: 0.8343 (t) REVERT: B 1435 ASP cc_start: 0.7926 (t70) cc_final: 0.7521 (t70) REVERT: B 1439 GLU cc_start: 0.8294 (mp0) cc_final: 0.7914 (mp0) REVERT: B 1455 LYS cc_start: 0.8426 (mptt) cc_final: 0.8220 (mptt) REVERT: B 1457 ILE cc_start: 0.9005 (pt) cc_final: 0.8616 (mm) REVERT: B 1458 ASP cc_start: 0.7411 (t0) cc_final: 0.7106 (t0) REVERT: B 1464 TRP cc_start: 0.8157 (m100) cc_final: 0.6048 (m100) REVERT: B 1496 TYR cc_start: 0.8867 (t80) cc_final: 0.8254 (t80) REVERT: B 1497 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 1504 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 1516 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 1530 ASN cc_start: 0.8286 (m110) cc_final: 0.8080 (m110) REVERT: B 1535 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 1536 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8619 (ttpp) REVERT: B 1538 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8889 (ttpp) REVERT: B 1540 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7956 (ttp80) REVERT: B 1542 GLU cc_start: 0.8155 (tp30) cc_final: 0.7695 (tp30) REVERT: B 1544 GLU cc_start: 0.8354 (pt0) cc_final: 0.7780 (pt0) REVERT: B 1549 GLN cc_start: 0.8303 (pp30) cc_final: 0.7849 (tm-30) REVERT: B 1560 GLU cc_start: 0.8804 (tt0) cc_final: 0.8563 (mm-30) REVERT: B 1565 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8240 (tmtt) REVERT: B 1568 ARG cc_start: 0.8455 (tpt90) cc_final: 0.8232 (tpt90) REVERT: B 1572 GLU cc_start: 0.8710 (tt0) cc_final: 0.8359 (tt0) REVERT: B 1573 LEU cc_start: 0.8798 (pp) cc_final: 0.8501 (tt) REVERT: B 1585 GLN cc_start: 0.7527 (pp30) cc_final: 0.7091 (pp30) REVERT: B 1586 GLU cc_start: 0.7376 (tp30) cc_final: 0.6951 (tp30) REVERT: B 1614 LYS cc_start: 0.8703 (tttp) cc_final: 0.8420 (tttp) REVERT: B 1627 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 1633 LEU cc_start: 0.8817 (mm) cc_final: 0.8354 (mm) REVERT: B 1634 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 1638 ASP cc_start: 0.8194 (t0) cc_final: 0.7764 (t0) REVERT: B 1644 ASN cc_start: 0.8410 (m-40) cc_final: 0.8140 (t0) REVERT: B 1653 LYS cc_start: 0.9132 (tttt) cc_final: 0.8559 (ttmm) REVERT: B 1657 GLN cc_start: 0.7733 (tp40) cc_final: 0.7282 (tp40) REVERT: B 1667 GLU cc_start: 0.8363 (tp30) cc_final: 0.7778 (tp30) REVERT: B 1677 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 1678 GLN cc_start: 0.8387 (mp10) cc_final: 0.8157 (mp10) REVERT: B 1683 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7056 (tm-30) REVERT: B 1692 GLU cc_start: 0.7764 (pp20) cc_final: 0.7469 (pp20) REVERT: B 1694 GLU cc_start: 0.8210 (tt0) cc_final: 0.7741 (tt0) REVERT: B 1700 LEU cc_start: 0.8888 (tp) cc_final: 0.8525 (tp) REVERT: B 1704 ASP cc_start: 0.6927 (p0) cc_final: 0.6496 (p0) REVERT: B 1708 ARG cc_start: 0.8551 (mpt-90) cc_final: 0.8267 (mtm-85) REVERT: B 1723 GLU cc_start: 0.8425 (pt0) cc_final: 0.8117 (pt0) REVERT: B 1737 LYS cc_start: 0.9330 (tmtt) cc_final: 0.9115 (tptp) REVERT: B 1741 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 1750 ASP cc_start: 0.7889 (t0) cc_final: 0.7645 (t0) REVERT: B 1760 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 1764 LYS cc_start: 0.8687 (mmmt) cc_final: 0.7400 (mmmm) REVERT: B 1765 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8826 (tptm) REVERT: B 1767 MET cc_start: 0.7722 (ppp) cc_final: 0.7181 (ppp) REVERT: B 1772 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8360 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8158 (t0) cc_final: 0.7917 (t0) REVERT: B 1818 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8517 (tppt) REVERT: B 1820 ILE cc_start: 0.8416 (mt) cc_final: 0.8152 (tp) REVERT: B 1824 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 1833 GLU cc_start: 0.8238 (tp30) cc_final: 0.7409 (tp30) REVERT: B 1837 GLU cc_start: 0.8394 (tp30) cc_final: 0.8003 (mm-30) REVERT: B 1838 GLN cc_start: 0.8649 (tp40) cc_final: 0.8268 (tp40) REVERT: B 1840 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8281 (ttm-80) REVERT: B 1848 LEU cc_start: 0.9015 (tp) cc_final: 0.8660 (tt) REVERT: B 1853 ARG cc_start: 0.8591 (mmt90) cc_final: 0.8098 (tpp80) REVERT: B 1860 PHE cc_start: 0.8566 (t80) cc_final: 0.8113 (t80) REVERT: B 1865 ASP cc_start: 0.7935 (m-30) cc_final: 0.7586 (m-30) REVERT: B 1866 ARG cc_start: 0.8634 (ttp-170) cc_final: 0.7917 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8458 (mmmm) REVERT: B 1870 GLU cc_start: 0.7943 (mt-10) cc_final: 0.6600 (mt-10) REVERT: B 1871 ARG cc_start: 0.8229 (ptt90) cc_final: 0.7990 (ptt90) REVERT: B 1873 GLN cc_start: 0.8783 (tp40) cc_final: 0.8407 (tm-30) REVERT: B 1878 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7891 (mmmt) REVERT: B 1882 LYS cc_start: 0.9092 (tttp) cc_final: 0.8645 (tttm) REVERT: B 1884 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8684 (mmtp) REVERT: B 1888 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8228 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8663 (mt0) cc_final: 0.8147 (tp40) REVERT: B 1890 ILE cc_start: 0.8855 (tp) cc_final: 0.8631 (tp) REVERT: B 1903 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8648 (mmtt) REVERT: B 1906 LYS cc_start: 0.9138 (tppt) cc_final: 0.8543 (tppt) REVERT: B 1908 GLN cc_start: 0.8736 (tp40) cc_final: 0.8190 (tp-100) REVERT: B 1910 GLU cc_start: 0.8218 (pp20) cc_final: 0.7951 (pp20) REVERT: B 1911 LEU cc_start: 0.8687 (tt) cc_final: 0.7957 (tt) REVERT: B 1915 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7885 (mt-10) REVERT: A 1040 ASP cc_start: 0.7241 (m-30) cc_final: 0.7003 (m-30) REVERT: A 1103 GLU cc_start: 0.8308 (mp0) cc_final: 0.7685 (pt0) REVERT: A 1179 MET cc_start: 0.6755 (ppp) cc_final: 0.6104 (ppp) REVERT: A 1202 LYS cc_start: 0.9056 (pptt) cc_final: 0.8723 (pptt) REVERT: A 1243 LEU cc_start: 0.7520 (mt) cc_final: 0.7205 (tt) REVERT: A 1279 ASN cc_start: 0.8614 (m110) cc_final: 0.8170 (t0) REVERT: A 1288 LEU cc_start: 0.8693 (mt) cc_final: 0.8343 (mm) REVERT: A 1299 LEU cc_start: 0.8298 (mt) cc_final: 0.8004 (tp) REVERT: A 1338 LEU cc_start: 0.8895 (mm) cc_final: 0.8619 (mt) REVERT: A 1353 GLU cc_start: 0.8355 (mp0) cc_final: 0.7675 (mp0) REVERT: A 1356 GLU cc_start: 0.8596 (tp30) cc_final: 0.8200 (tp30) REVERT: A 1357 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 1358 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 1360 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 1371 LYS cc_start: 0.8612 (pptt) cc_final: 0.8404 (pptt) REVERT: A 1409 GLU cc_start: 0.7473 (tm-30) cc_final: 0.5898 (tm-30) REVERT: A 1413 GLU cc_start: 0.7837 (mp0) cc_final: 0.6718 (pm20) REVERT: A 1424 LYS cc_start: 0.8689 (tttp) cc_final: 0.8309 (tppt) REVERT: A 1439 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 1442 ARG cc_start: 0.8161 (ptm160) cc_final: 0.7827 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8207 (t0) cc_final: 0.7822 (t0) REVERT: A 1451 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 1457 ILE cc_start: 0.8444 (mm) cc_final: 0.8022 (mm) REVERT: A 1458 ASP cc_start: 0.7929 (p0) cc_final: 0.7273 (p0) REVERT: A 1463 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7174 (tm-30) REVERT: A 1465 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7083 (tppt) REVERT: A 1467 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8033 (ttmm) REVERT: A 1488 GLU cc_start: 0.7117 (tp30) cc_final: 0.6270 (tp30) REVERT: A 1489 LEU cc_start: 0.8714 (tt) cc_final: 0.8415 (tp) REVERT: A 1492 LEU cc_start: 0.8534 (mt) cc_final: 0.7857 (mm) REVERT: A 1501 GLU cc_start: 0.8616 (pt0) cc_final: 0.8336 (pt0) REVERT: A 1504 GLU cc_start: 0.7792 (mp0) cc_final: 0.7533 (mp0) REVERT: A 1511 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8631 (tppt) REVERT: A 1516 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 1540 ARG cc_start: 0.8359 (tmt-80) cc_final: 0.7945 (tmt-80) REVERT: A 1542 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 1563 GLU cc_start: 0.8295 (tp30) cc_final: 0.7854 (tp30) REVERT: A 1570 GLN cc_start: 0.8242 (mt0) cc_final: 0.7954 (mm-40) REVERT: A 1572 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 1575 GLN cc_start: 0.8232 (mt0) cc_final: 0.7925 (mt0) REVERT: A 1579 GLU cc_start: 0.7952 (mp0) cc_final: 0.7395 (mp0) REVERT: A 1589 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 1599 GLN cc_start: 0.8386 (tt0) cc_final: 0.8064 (tp40) REVERT: A 1623 LYS cc_start: 0.8481 (tppt) cc_final: 0.8141 (tppt) REVERT: A 1625 LYS cc_start: 0.8826 (mmmm) cc_final: 0.8432 (mtpp) REVERT: A 1634 GLU cc_start: 0.7967 (pt0) cc_final: 0.7663 (pt0) REVERT: A 1637 LEU cc_start: 0.8923 (mt) cc_final: 0.8658 (tt) REVERT: A 1649 LYS cc_start: 0.9211 (tttp) cc_final: 0.8777 (ttmm) REVERT: A 1662 GLN cc_start: 0.8644 (tt0) cc_final: 0.8136 (tp40) REVERT: A 1690 GLN cc_start: 0.8521 (tt0) cc_final: 0.8270 (tp40) REVERT: A 1692 GLU cc_start: 0.8205 (tp30) cc_final: 0.7940 (tp30) REVERT: A 1741 GLU cc_start: 0.8288 (tp30) cc_final: 0.7960 (tp30) REVERT: A 1752 LEU cc_start: 0.9181 (tp) cc_final: 0.8958 (tt) REVERT: A 1754 ASN cc_start: 0.8463 (t0) cc_final: 0.8185 (t0) REVERT: A 1755 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 1757 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8485 (tppt) REVERT: A 1758 ASN cc_start: 0.8520 (t0) cc_final: 0.8108 (t0) REVERT: A 1762 LYS cc_start: 0.9323 (ttmt) cc_final: 0.9088 (ttmt) REVERT: A 1765 LYS cc_start: 0.8980 (tppt) cc_final: 0.8731 (tppp) REVERT: A 1767 MET cc_start: 0.8150 (mmp) cc_final: 0.7950 (mmp) REVERT: A 1775 ASP cc_start: 0.7997 (t0) cc_final: 0.7713 (t0) REVERT: A 1776 GLU cc_start: 0.8122 (tp30) cc_final: 0.7832 (tp30) REVERT: A 1778 ARG cc_start: 0.8457 (mtt-85) cc_final: 0.8045 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8063 (t0) cc_final: 0.7845 (t0) REVERT: A 1783 HIS cc_start: 0.9149 (t-90) cc_final: 0.8927 (t-170) REVERT: A 1792 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9091 (tppp) REVERT: A 1818 LYS cc_start: 0.8771 (mmpt) cc_final: 0.8140 (mmmm) REVERT: A 1822 LYS cc_start: 0.8673 (tttm) cc_final: 0.8441 (ttpp) REVERT: A 1824 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 1839 ARG cc_start: 0.8485 (tmt170) cc_final: 0.8056 (tmt170) REVERT: A 1840 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8106 (mtm110) REVERT: A 1846 LYS cc_start: 0.9199 (tttm) cc_final: 0.8930 (ttmm) REVERT: A 1850 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8208 (ptmm) REVERT: A 1853 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.7777 (ttm110) REVERT: A 1858 LEU cc_start: 0.8517 (mp) cc_final: 0.8308 (mm) REVERT: A 1864 GLU cc_start: 0.7953 (tp30) cc_final: 0.7511 (tp30) REVERT: A 1865 ASP cc_start: 0.8102 (t0) cc_final: 0.7752 (t0) REVERT: A 1868 ASN cc_start: 0.8604 (m110) cc_final: 0.8205 (m-40) REVERT: A 1870 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 1871 ARG cc_start: 0.8575 (tpm170) cc_final: 0.7925 (tpm170) REVERT: A 1874 ASP cc_start: 0.8054 (m-30) cc_final: 0.7067 (m-30) REVERT: A 1878 LYS cc_start: 0.9037 (tppt) cc_final: 0.8784 (mmmm) REVERT: A 1881 GLN cc_start: 0.8758 (tp40) cc_final: 0.8442 (tp40) REVERT: A 1882 LYS cc_start: 0.9213 (ttmm) cc_final: 0.8984 (ttmm) REVERT: A 1884 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8754 (ttpp) REVERT: A 1888 ARG cc_start: 0.8111 (tmm160) cc_final: 0.7369 (ttp80) REVERT: A 1889 GLN cc_start: 0.7573 (pp30) cc_final: 0.7244 (pp30) REVERT: A 1892 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 1909 GLN cc_start: 0.8681 (tp40) cc_final: 0.8188 (tm-30) REVERT: A 1910 GLU cc_start: 0.8517 (tt0) cc_final: 0.7976 (tt0) REVERT: A 1915 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.3359 time to fit residues: 319.0843 Evaluate side-chains 604 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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: 2.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN A1113 GLN ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 ASN A1500 GLN ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 GLN A1797 GLN A1900 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 1.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17454 Z= 0.253 Angle : 0.738 9.686 23282 Z= 0.406 Chirality : 0.045 0.200 2582 Planarity : 0.004 0.048 3158 Dihedral : 4.369 20.086 2318 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 1.71 (0.11), residues: 2105 sheet: None (None), residues: 0 loop : 1.57 (0.96), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.006 TRP B1379 HIS 0.016 0.002 HIS A1193 PHE 0.017 0.003 PHE A1860 TYR 0.039 0.004 TYR A1886 ARG 0.012 0.001 ARG B1157 ********************** 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 681 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 1.995 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: B 928 MET cc_start: 0.8195 (mmp) cc_final: 0.7974 (mmp) REVERT: B 944 MET cc_start: 0.6070 (tpp) cc_final: 0.5088 (tpp) REVERT: B 948 LYS cc_start: 0.8541 (ptpp) cc_final: 0.7991 (pttp) REVERT: B 1047 GLU cc_start: 0.8222 (mp0) cc_final: 0.7935 (pm20) REVERT: B 1124 GLU cc_start: 0.8140 (pt0) cc_final: 0.7940 (pt0) REVERT: B 1150 GLU cc_start: 0.8354 (mp0) cc_final: 0.7865 (mp0) REVERT: B 1176 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8626 (mm-30) REVERT: B 1181 LYS cc_start: 0.8891 (tppt) cc_final: 0.8329 (tppt) REVERT: B 1182 LEU cc_start: 0.8526 (mp) cc_final: 0.8268 (mp) REVERT: B 1194 GLU cc_start: 0.7969 (mp0) cc_final: 0.7540 (mm-30) REVERT: B 1224 LYS cc_start: 0.8462 (mptt) cc_final: 0.7992 (mptt) REVERT: B 1245 GLN cc_start: 0.8319 (pp30) cc_final: 0.8056 (pp30) REVERT: B 1246 MET cc_start: 0.8210 (ppp) cc_final: 0.7623 (ppp) REVERT: B 1248 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8093 (mmt180) REVERT: B 1249 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 1250 LYS cc_start: 0.9004 (ptmt) cc_final: 0.8336 (ptmm) REVERT: B 1261 GLN cc_start: 0.8991 (tt0) cc_final: 0.8489 (tp40) REVERT: B 1266 GLU cc_start: 0.7832 (pp20) cc_final: 0.7540 (pp20) REVERT: B 1267 ILE cc_start: 0.8522 (pt) cc_final: 0.8244 (mm) REVERT: B 1268 GLN cc_start: 0.8593 (pt0) cc_final: 0.8271 (tt0) REVERT: B 1282 ASP cc_start: 0.8234 (m-30) cc_final: 0.7815 (t70) REVERT: B 1286 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8899 (mtmt) REVERT: B 1291 GLU cc_start: 0.7563 (tp30) cc_final: 0.7236 (tp30) REVERT: B 1295 LEU cc_start: 0.7161 (pp) cc_final: 0.6658 (pp) REVERT: B 1297 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7932 (mtp180) REVERT: B 1325 ARG cc_start: 0.8386 (ptm-80) cc_final: 0.8063 (mtm110) REVERT: B 1345 GLU cc_start: 0.7829 (pt0) cc_final: 0.7619 (pt0) REVERT: B 1353 GLU cc_start: 0.7702 (pm20) cc_final: 0.7457 (pm20) REVERT: B 1367 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8049 (tpp80) REVERT: B 1400 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8671 (ttmm) REVERT: B 1402 GLN cc_start: 0.8584 (pt0) cc_final: 0.8207 (pt0) REVERT: B 1409 GLU cc_start: 0.7919 (pt0) cc_final: 0.7626 (pt0) REVERT: B 1457 ILE cc_start: 0.9077 (pt) cc_final: 0.8704 (mm) REVERT: B 1464 TRP cc_start: 0.8067 (m100) cc_final: 0.5935 (m100) REVERT: B 1480 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8649 (mtpp) REVERT: B 1497 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7127 (tm-30) REVERT: B 1498 GLU cc_start: 0.8134 (pp20) cc_final: 0.7587 (pp20) REVERT: B 1504 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 1516 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7957 (mm-30) REVERT: B 1529 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.8111 (ttt-90) REVERT: B 1536 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8581 (ttpp) REVERT: B 1540 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7859 (ttp80) REVERT: B 1542 GLU cc_start: 0.8218 (tp30) cc_final: 0.7339 (tp30) REVERT: B 1543 VAL cc_start: 0.9130 (t) cc_final: 0.8894 (p) REVERT: B 1544 GLU cc_start: 0.8493 (pt0) cc_final: 0.7919 (pt0) REVERT: B 1546 ASP cc_start: 0.8721 (m-30) cc_final: 0.7866 (m-30) REVERT: B 1549 GLN cc_start: 0.8405 (pp30) cc_final: 0.7920 (tm-30) REVERT: B 1560 GLU cc_start: 0.8866 (tt0) cc_final: 0.8281 (mm-30) REVERT: B 1565 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8237 (tmtt) REVERT: B 1572 GLU cc_start: 0.8673 (tt0) cc_final: 0.8285 (tt0) REVERT: B 1573 LEU cc_start: 0.8750 (pp) cc_final: 0.8522 (tt) REVERT: B 1577 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7887 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7734 (pp30) cc_final: 0.7020 (pp30) REVERT: B 1590 GLU cc_start: 0.8392 (mp0) cc_final: 0.8010 (mp0) REVERT: B 1614 LYS cc_start: 0.8740 (tttp) cc_final: 0.8277 (tttp) REVERT: B 1618 GLU cc_start: 0.8041 (pm20) cc_final: 0.7624 (pm20) REVERT: B 1627 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 1633 LEU cc_start: 0.8862 (mm) cc_final: 0.8428 (mm) REVERT: B 1634 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7540 (tm-30) REVERT: B 1638 ASP cc_start: 0.8244 (t0) cc_final: 0.7802 (t0) REVERT: B 1653 LYS cc_start: 0.9218 (tttt) cc_final: 0.8724 (ttmm) REVERT: B 1657 GLN cc_start: 0.7792 (tp40) cc_final: 0.7341 (tp40) REVERT: B 1667 GLU cc_start: 0.8320 (tp30) cc_final: 0.7532 (tp30) REVERT: B 1677 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 1683 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 1692 GLU cc_start: 0.7857 (pp20) cc_final: 0.7583 (pp20) REVERT: B 1694 GLU cc_start: 0.8266 (tt0) cc_final: 0.7829 (tt0) REVERT: B 1700 LEU cc_start: 0.8896 (tp) cc_final: 0.8366 (tp) REVERT: B 1704 ASP cc_start: 0.6918 (p0) cc_final: 0.6636 (p0) REVERT: B 1708 ARG cc_start: 0.8519 (mpt-90) cc_final: 0.8247 (mtm-85) REVERT: B 1737 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9125 (tptp) REVERT: B 1741 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 1750 ASP cc_start: 0.8010 (t0) cc_final: 0.7761 (t0) REVERT: B 1758 ASN cc_start: 0.8215 (t0) cc_final: 0.7844 (t0) REVERT: B 1759 SER cc_start: 0.8930 (p) cc_final: 0.8715 (p) REVERT: B 1760 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 1762 LYS cc_start: 0.8603 (mttp) cc_final: 0.7988 (mttp) REVERT: B 1772 ARG cc_start: 0.8673 (mtp85) cc_final: 0.8419 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8179 (t0) cc_final: 0.7957 (t0) REVERT: B 1780 GLU cc_start: 0.7472 (tp30) cc_final: 0.7246 (tp30) REVERT: B 1818 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8612 (tppt) REVERT: B 1820 ILE cc_start: 0.8485 (mt) cc_final: 0.8205 (tp) REVERT: B 1824 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 1833 GLU cc_start: 0.8278 (tp30) cc_final: 0.7466 (tp30) REVERT: B 1840 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8365 (ttm-80) REVERT: B 1852 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 1853 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8237 (tpp80) REVERT: B 1855 ILE cc_start: 0.8829 (tt) cc_final: 0.8515 (tt) REVERT: B 1860 PHE cc_start: 0.8641 (t80) cc_final: 0.8161 (t80) REVERT: B 1865 ASP cc_start: 0.8038 (m-30) cc_final: 0.7654 (m-30) REVERT: B 1866 ARG cc_start: 0.8639 (ttp-170) cc_final: 0.7879 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8475 (mmmm) REVERT: B 1870 GLU cc_start: 0.8021 (mt-10) cc_final: 0.6614 (mt-10) REVERT: B 1873 GLN cc_start: 0.8792 (tp40) cc_final: 0.8356 (tm-30) REVERT: B 1878 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7859 (mmmt) REVERT: B 1882 LYS cc_start: 0.9168 (tttp) cc_final: 0.8589 (tttm) REVERT: B 1884 LYS cc_start: 0.8972 (mmtp) cc_final: 0.8631 (mmtp) REVERT: B 1888 ARG cc_start: 0.8621 (mtp85) cc_final: 0.8218 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8748 (mt0) cc_final: 0.8209 (tp40) REVERT: B 1892 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 1903 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8734 (mmtt) REVERT: B 1906 LYS cc_start: 0.9160 (tppt) cc_final: 0.8770 (tppt) REVERT: B 1908 GLN cc_start: 0.8771 (tp40) cc_final: 0.8163 (tp-100) REVERT: B 1910 GLU cc_start: 0.8219 (pp20) cc_final: 0.7973 (pp20) REVERT: B 1911 LEU cc_start: 0.8692 (tt) cc_final: 0.8048 (tt) REVERT: B 1915 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 1927 LYS cc_start: 0.8948 (tttp) cc_final: 0.8736 (tttp) REVERT: A 1103 GLU cc_start: 0.8290 (mp0) cc_final: 0.7667 (pt0) REVERT: A 1170 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8370 (mm-30) REVERT: A 1178 GLU cc_start: 0.7665 (mp0) cc_final: 0.7390 (mp0) REVERT: A 1202 LYS cc_start: 0.9218 (pptt) cc_final: 0.8850 (pptt) REVERT: A 1215 ILE cc_start: 0.8103 (pt) cc_final: 0.7474 (pt) REVERT: A 1243 LEU cc_start: 0.7536 (mt) cc_final: 0.7289 (tt) REVERT: A 1267 ILE cc_start: 0.8754 (pt) cc_final: 0.8173 (mm) REVERT: A 1279 ASN cc_start: 0.8725 (m110) cc_final: 0.8220 (t0) REVERT: A 1288 LEU cc_start: 0.8844 (mt) cc_final: 0.8565 (mm) REVERT: A 1291 GLU cc_start: 0.7836 (pt0) cc_final: 0.7524 (pt0) REVERT: A 1299 LEU cc_start: 0.8148 (mt) cc_final: 0.7773 (tp) REVERT: A 1300 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7964 (tp30) REVERT: A 1306 VAL cc_start: 0.8959 (m) cc_final: 0.8726 (p) REVERT: A 1346 HIS cc_start: 0.8679 (t70) cc_final: 0.8448 (t70) REVERT: A 1350 ASN cc_start: 0.7938 (t0) cc_final: 0.7605 (t0) REVERT: A 1351 ILE cc_start: 0.8994 (pt) cc_final: 0.8772 (pt) REVERT: A 1353 GLU cc_start: 0.8237 (mp0) cc_final: 0.7327 (mp0) REVERT: A 1357 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 1358 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8065 (mm-30) REVERT: A 1392 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 1401 LEU cc_start: 0.8799 (tt) cc_final: 0.8548 (tp) REVERT: A 1409 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6275 (tm-30) REVERT: A 1410 GLU cc_start: 0.7326 (tp30) cc_final: 0.6325 (tp30) REVERT: A 1413 GLU cc_start: 0.7891 (mp0) cc_final: 0.6933 (pm20) REVERT: A 1417 GLN cc_start: 0.8159 (tp40) cc_final: 0.7926 (mm-40) REVERT: A 1424 LYS cc_start: 0.8761 (tttp) cc_final: 0.8331 (tppt) REVERT: A 1448 ASN cc_start: 0.8254 (t0) cc_final: 0.7904 (t0) REVERT: A 1451 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 1458 ASP cc_start: 0.7857 (p0) cc_final: 0.7261 (p0) REVERT: A 1465 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7184 (tppt) REVERT: A 1467 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8185 (ttmm) REVERT: A 1482 CYS cc_start: 0.8451 (m) cc_final: 0.8244 (m) REVERT: A 1488 GLU cc_start: 0.7267 (tp30) cc_final: 0.6554 (tp30) REVERT: A 1489 LEU cc_start: 0.8787 (tt) cc_final: 0.8552 (tp) REVERT: A 1492 LEU cc_start: 0.8609 (mt) cc_final: 0.8120 (mm) REVERT: A 1501 GLU cc_start: 0.8668 (pt0) cc_final: 0.8359 (pt0) REVERT: A 1504 GLU cc_start: 0.7976 (mp0) cc_final: 0.7598 (mp0) REVERT: A 1511 LYS cc_start: 0.8894 (mmtm) cc_final: 0.8609 (tppt) REVERT: A 1516 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 1540 ARG cc_start: 0.8479 (tmt-80) cc_final: 0.7998 (tmt-80) REVERT: A 1542 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 1559 LEU cc_start: 0.8623 (tp) cc_final: 0.8381 (tp) REVERT: A 1561 GLN cc_start: 0.7842 (pp30) cc_final: 0.7622 (pp30) REVERT: A 1563 GLU cc_start: 0.8359 (tp30) cc_final: 0.7893 (tp30) REVERT: A 1570 GLN cc_start: 0.8202 (mt0) cc_final: 0.7974 (mm-40) REVERT: A 1585 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 1589 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 1597 ASN cc_start: 0.8854 (m-40) cc_final: 0.8597 (t0) REVERT: A 1599 GLN cc_start: 0.8467 (tt0) cc_final: 0.8196 (tp40) REVERT: A 1614 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8869 (mmmm) REVERT: A 1623 LYS cc_start: 0.8500 (tppt) cc_final: 0.7866 (tppt) REVERT: A 1625 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8597 (mtpp) REVERT: A 1626 LEU cc_start: 0.8813 (mm) cc_final: 0.8411 (mm) REVERT: A 1627 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 1634 GLU cc_start: 0.7898 (pt0) cc_final: 0.7602 (pt0) REVERT: A 1637 LEU cc_start: 0.8918 (mt) cc_final: 0.8617 (tt) REVERT: A 1642 LYS cc_start: 0.8270 (tttm) cc_final: 0.7698 (ttmm) REVERT: A 1646 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 1649 LYS cc_start: 0.9231 (tttp) cc_final: 0.8798 (ttmm) REVERT: A 1662 GLN cc_start: 0.8733 (tt0) cc_final: 0.8143 (tp40) REVERT: A 1672 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7305 (ttp80) REVERT: A 1679 LEU cc_start: 0.8919 (tp) cc_final: 0.8523 (tp) REVERT: A 1681 ILE cc_start: 0.8296 (tt) cc_final: 0.8091 (tt) REVERT: A 1683 GLU cc_start: 0.7573 (pp20) cc_final: 0.7183 (pp20) REVERT: A 1690 GLN cc_start: 0.8662 (tt0) cc_final: 0.8271 (tp40) REVERT: A 1692 GLU cc_start: 0.8250 (tp30) cc_final: 0.7948 (tp30) REVERT: A 1722 ASN cc_start: 0.8587 (t0) cc_final: 0.8385 (t0) REVERT: A 1741 GLU cc_start: 0.8258 (tp30) cc_final: 0.8034 (tp30) REVERT: A 1746 HIS cc_start: 0.8815 (t70) cc_final: 0.8579 (t70) REVERT: A 1752 LEU cc_start: 0.9211 (tp) cc_final: 0.8988 (tt) REVERT: A 1754 ASN cc_start: 0.8553 (t0) cc_final: 0.8268 (t0) REVERT: A 1755 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 1757 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8584 (tppt) REVERT: A 1762 LYS cc_start: 0.9310 (ttmt) cc_final: 0.9096 (ttmt) REVERT: A 1765 LYS cc_start: 0.9091 (tppt) cc_final: 0.8879 (tppp) REVERT: A 1767 MET cc_start: 0.8289 (mmp) cc_final: 0.8082 (mmp) REVERT: A 1775 ASP cc_start: 0.7986 (t0) cc_final: 0.7740 (t0) REVERT: A 1782 ASP cc_start: 0.8129 (t0) cc_final: 0.7894 (t0) REVERT: A 1788 GLU cc_start: 0.7867 (tp30) cc_final: 0.7321 (tp30) REVERT: A 1789 LYS cc_start: 0.9059 (tppp) cc_final: 0.8808 (tppp) REVERT: A 1792 LYS cc_start: 0.9297 (ttmt) cc_final: 0.8927 (ttmm) REVERT: A 1797 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8177 (tp-100) REVERT: A 1818 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8196 (mmmm) REVERT: A 1822 LYS cc_start: 0.8693 (tttm) cc_final: 0.8481 (ttpp) REVERT: A 1839 ARG cc_start: 0.8524 (tmt170) cc_final: 0.8175 (tmt170) REVERT: A 1840 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8112 (mtm110) REVERT: A 1846 LYS cc_start: 0.9219 (tttm) cc_final: 0.8965 (ttmm) REVERT: A 1853 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.7830 (ttm110) REVERT: A 1858 LEU cc_start: 0.8546 (mp) cc_final: 0.8219 (mm) REVERT: A 1864 GLU cc_start: 0.7990 (tp30) cc_final: 0.7505 (tp30) REVERT: A 1865 ASP cc_start: 0.8180 (t0) cc_final: 0.7888 (t0) REVERT: A 1868 ASN cc_start: 0.8655 (m110) cc_final: 0.8228 (m-40) REVERT: A 1870 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 1871 ARG cc_start: 0.8610 (tpm170) cc_final: 0.7990 (tpm170) REVERT: A 1874 ASP cc_start: 0.8106 (m-30) cc_final: 0.7247 (m-30) REVERT: A 1878 LYS cc_start: 0.9051 (tppt) cc_final: 0.8766 (mmmm) REVERT: A 1881 GLN cc_start: 0.8777 (tp40) cc_final: 0.8528 (tp40) REVERT: A 1882 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8962 (ttmm) REVERT: A 1884 LYS cc_start: 0.9242 (ttpp) cc_final: 0.9031 (ttpp) REVERT: A 1888 ARG cc_start: 0.8282 (tmm160) cc_final: 0.7584 (ttp80) REVERT: A 1892 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 1894 GLU cc_start: 0.7216 (pp20) cc_final: 0.6870 (pp20) REVERT: A 1895 GLU cc_start: 0.7757 (tt0) cc_final: 0.7539 (tt0) REVERT: A 1909 GLN cc_start: 0.8752 (tp40) cc_final: 0.8239 (tm-30) REVERT: A 1910 GLU cc_start: 0.8524 (tt0) cc_final: 0.8024 (tt0) REVERT: A 1915 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7646 (tm-30) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.3276 time to fit residues: 318.0712 Evaluate side-chains 611 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1720 GLN B1797 GLN ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS A1900 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.118358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.095888 restraints weight = 46584.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.098499 restraints weight = 27905.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.100251 restraints weight = 18506.095| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 1.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17454 Z= 0.195 Angle : 0.674 9.885 23282 Z= 0.365 Chirality : 0.042 0.180 2582 Planarity : 0.003 0.036 3158 Dihedral : 4.296 21.404 2318 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.16 % Allowed : 0.27 % Favored : 99.57 % 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: 2.79 (0.18), residues: 2150 helix: 1.88 (0.11), residues: 2104 sheet: None (None), residues: 0 loop : 1.30 (1.01), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B1379 HIS 0.017 0.002 HIS B1204 PHE 0.018 0.002 PHE A1860 TYR 0.023 0.003 TYR B1496 ARG 0.009 0.001 ARG A1390 =============================================================================== Job complete usr+sys time: 5735.81 seconds wall clock time: 102 minutes 40.56 seconds (6160.56 seconds total)