Starting phenix.real_space_refine on Sat Sep 28 03:39:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/09_2024/7kog_22975.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/09_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_22975/09_2024/7kog_22975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/09_2024/7kog_22975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/09_2024/7kog_22975.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kog_22975/09_2024/7kog_22975.cif" } 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. Time to flip 164 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.04, per 1000 atoms: 0.52 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.9 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: 0.99 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: 4.49 Time building geometry restraints manager: 4.25 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: 0.00 - 2.03: 22074 2.03 - 4.05: 1061 4.05 - 6.08: 98 6.08 - 8.10: 33 8.10 - 10.13: 16 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 Time spend for trying shortcut: 0.00 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: 2.160 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: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.300 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- 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 : 1.910 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: 0.3640 time to fit residues: 333.2822 Evaluate side-chains 473 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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: 0.8980 chunk 162 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 40.0000 chunk 86 optimal weight: 0.3980 chunk 167 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 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 B1811 ASN ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN A 935 GLN A 947 GLN A1001 ASN 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: 0.6742 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17454 Z= 0.191 Angle : 0.686 10.934 23282 Z= 0.377 Chirality : 0.039 0.216 2582 Planarity : 0.005 0.055 3158 Dihedral : 4.824 26.155 2318 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.16), residues: 2150 helix: -0.76 (0.10), residues: 2104 sheet: None (None), residues: 0 loop : 0.16 (0.87), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1464 HIS 0.010 0.001 HIS B1598 PHE 0.016 0.002 PHE A1341 TYR 0.012 0.002 TYR B1496 ARG 0.008 0.001 ARG B1380 *********************** 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 : 1.799 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: B 857 MET cc_start: 0.5280 (mmp) cc_final: 0.5011 (mmt) REVERT: B 966 GLU cc_start: 0.7090 (tp30) cc_final: 0.6742 (tm-30) REVERT: B 980 ASP cc_start: 0.7599 (m-30) cc_final: 0.6916 (m-30) REVERT: B 1231 HIS cc_start: 0.5840 (t70) cc_final: 0.5618 (t70) REVERT: B 1243 LEU cc_start: 0.7183 (tt) cc_final: 0.6629 (tt) REVERT: B 1345 GLU cc_start: 0.7503 (pt0) cc_final: 0.7001 (pt0) REVERT: B 1357 GLU cc_start: 0.7106 (tp30) cc_final: 0.6801 (tp30) REVERT: B 1409 GLU cc_start: 0.7205 (pt0) cc_final: 0.6912 (pt0) REVERT: B 1415 LEU cc_start: 0.7478 (mm) cc_final: 0.7271 (mt) REVERT: B 1466 LEU cc_start: 0.8023 (mt) cc_final: 0.7803 (mt) REVERT: B 1470 ASP cc_start: 0.7492 (t0) cc_final: 0.7196 (t0) REVERT: B 1509 GLU cc_start: 0.7460 (tt0) cc_final: 0.7214 (tt0) REVERT: B 1518 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8393 (mmtm) REVERT: B 1526 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 1566 VAL cc_start: 0.7504 (t) cc_final: 0.7108 (t) REVERT: B 1590 GLU cc_start: 0.8611 (mp0) cc_final: 0.8196 (mp0) REVERT: B 1593 ASN cc_start: 0.7728 (t0) cc_final: 0.7223 (t0) REVERT: B 1597 ASN cc_start: 0.8447 (m-40) cc_final: 0.8195 (m-40) REVERT: B 1612 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 1614 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8383 (mtpp) REVERT: B 1638 ASP cc_start: 0.7021 (t0) cc_final: 0.6712 (t0) REVERT: B 1653 LYS cc_start: 0.8516 (tttt) cc_final: 0.8232 (ttpt) REVERT: B 1657 GLN cc_start: 0.6414 (tp40) cc_final: 0.6143 (tp40) REVERT: B 1668 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6479 (mm-30) REVERT: B 1690 GLN cc_start: 0.8483 (tt0) cc_final: 0.8257 (tt0) REVERT: B 1705 ARG cc_start: 0.8203 (ptm-80) cc_final: 0.7934 (ptm-80) REVERT: B 1708 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8468 (mtm-85) REVERT: B 1719 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: B 1741 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 1760 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 1764 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7439 (mmmm) REVERT: B 1765 LYS cc_start: 0.8814 (tttm) cc_final: 0.8448 (ttmm) REVERT: B 1788 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 1795 GLU cc_start: 0.8076 (pt0) cc_final: 0.7758 (pt0) REVERT: B 1818 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8220 (mmmm) REVERT: B 1824 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 1837 GLU cc_start: 0.8264 (tp30) cc_final: 0.6540 (mm-30) REVERT: B 1852 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 1865 ASP cc_start: 0.8017 (m-30) cc_final: 0.7800 (m-30) REVERT: B 1871 ARG cc_start: 0.7958 (ptt90) cc_final: 0.7570 (ptt90) REVERT: B 1882 LYS cc_start: 0.8948 (tttp) cc_final: 0.8299 (ttmm) REVERT: B 1884 LYS cc_start: 0.8393 (tptm) cc_final: 0.8137 (tptm) REVERT: B 1888 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8006 (mtp85) REVERT: B 1892 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 1894 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6747 (tm-30) REVERT: B 1903 LYS cc_start: 0.8883 (tptt) cc_final: 0.8591 (mptt) REVERT: B 1906 LYS cc_start: 0.9029 (tppt) cc_final: 0.8794 (tppt) REVERT: B 1908 GLN cc_start: 0.8124 (tt0) cc_final: 0.7804 (tp40) REVERT: B 1911 LEU cc_start: 0.8522 (tt) cc_final: 0.7192 (tp) REVERT: B 1923 GLN cc_start: 0.8413 (pp30) cc_final: 0.8133 (pp30) REVERT: A 924 GLU cc_start: 0.6993 (mp0) cc_final: 0.6477 (tp30) REVERT: A 1092 ASP cc_start: 0.7513 (t0) cc_final: 0.7214 (t0) REVERT: A 1185 ASP cc_start: 0.7930 (m-30) cc_final: 0.7710 (m-30) REVERT: A 1259 GLN cc_start: 0.6605 (tp40) cc_final: 0.5813 (tp40) REVERT: A 1316 LEU cc_start: 0.6976 (mt) cc_final: 0.6495 (mt) REVERT: A 1321 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5807 (tm-30) REVERT: A 1345 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6113 (mt-10) REVERT: A 1356 GLU cc_start: 0.6877 (tp30) cc_final: 0.6335 (tp30) REVERT: A 1358 GLU cc_start: 0.7295 (tp30) cc_final: 0.6423 (tp30) REVERT: A 1480 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8218 (mtmm) REVERT: A 1501 GLU cc_start: 0.8266 (pt0) cc_final: 0.7876 (pt0) REVERT: A 1542 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6920 (tm-30) REVERT: A 1553 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8073 (mt-10) REVERT: A 1591 PHE cc_start: 0.7530 (m-10) cc_final: 0.7308 (m-10) REVERT: A 1603 ASP cc_start: 0.7584 (t0) cc_final: 0.7334 (t0) REVERT: A 1622 MET cc_start: 0.6841 (mmm) cc_final: 0.6574 (mmm) REVERT: A 1623 LYS cc_start: 0.7960 (tppt) cc_final: 0.7666 (tppt) REVERT: A 1646 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 1741 GLU cc_start: 0.8273 (tp30) cc_final: 0.7957 (tp30) REVERT: A 1761 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 1762 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8908 (ttmt) REVERT: A 1775 ASP cc_start: 0.7825 (t0) cc_final: 0.7457 (t0) REVERT: A 1776 GLU cc_start: 0.7645 (tp30) cc_final: 0.6768 (tp30) REVERT: A 1782 ASP cc_start: 0.8127 (t0) cc_final: 0.7764 (t0) REVERT: A 1792 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8814 (mtpp) REVERT: A 1795 GLU cc_start: 0.7461 (tp30) cc_final: 0.6767 (tp30) REVERT: A 1797 GLN cc_start: 0.8137 (mm110) cc_final: 0.7906 (mm110) REVERT: A 1802 GLN cc_start: 0.8745 (tt0) cc_final: 0.8540 (tt0) REVERT: A 1824 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 1839 ARG cc_start: 0.8266 (tmt170) cc_final: 0.8045 (tmt170) REVERT: A 1846 LYS cc_start: 0.9007 (tttm) cc_final: 0.8727 (ttmm) REVERT: A 1858 LEU cc_start: 0.8520 (mp) cc_final: 0.8223 (mm) REVERT: A 1860 PHE cc_start: 0.8794 (t80) cc_final: 0.8503 (t80) REVERT: A 1876 VAL cc_start: 0.9157 (m) cc_final: 0.8884 (p) REVERT: A 1882 LYS cc_start: 0.9067 (mtpp) cc_final: 0.8855 (ttmm) REVERT: A 1892 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7063 (mt-10) REVERT: A 1905 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7934 (tpp80) REVERT: A 1909 GLN cc_start: 0.8408 (tp40) cc_final: 0.7926 (tm-30) REVERT: A 1910 GLU cc_start: 0.8101 (tt0) cc_final: 0.7493 (tt0) REVERT: A 1915 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 2 outliers final: 0 residues processed: 592 average time/residue: 0.3400 time to fit residues: 288.8995 Evaluate side-chains 477 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 981 HIS B1037 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 GLN B1606 GLN B1712 GLN B1718 HIS B1900 ASN A 942 ASN A1026 ASN A1199 ASN A1219 ASN A1233 GLN A1259 GLN A1402 GLN A1783 HIS A1881 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.8494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17454 Z= 0.202 Angle : 0.662 7.579 23282 Z= 0.367 Chirality : 0.040 0.157 2582 Planarity : 0.004 0.030 3158 Dihedral : 4.437 18.372 2318 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.16 % Allowed : 6.34 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2150 helix: 0.74 (0.11), residues: 2093 sheet: None (None), residues: 0 loop : 0.62 (0.83), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A1379 HIS 0.012 0.001 HIS B1598 PHE 0.036 0.003 PHE B1281 TYR 0.026 0.003 TYR A1496 ARG 0.009 0.001 ARG B1839 *********************** 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 613 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 610 time to evaluate : 1.811 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 980 ASP cc_start: 0.7618 (m-30) cc_final: 0.7369 (m-30) REVERT: B 1009 GLU cc_start: 0.6060 (tm-30) cc_final: 0.5827 (tm-30) REVERT: B 1092 ASP cc_start: 0.5672 (m-30) cc_final: 0.4833 (t70) REVERT: B 1243 LEU cc_start: 0.7327 (tt) cc_final: 0.6833 (tt) REVERT: B 1261 GLN cc_start: 0.8408 (tt0) cc_final: 0.8201 (tt0) REVERT: B 1300 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 1357 GLU cc_start: 0.7264 (tp30) cc_final: 0.6916 (tp30) REVERT: B 1395 GLU cc_start: 0.7190 (pp20) cc_final: 0.6690 (tm-30) REVERT: B 1400 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8131 (mtmm) REVERT: B 1413 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 1420 ILE cc_start: 0.8800 (pt) cc_final: 0.8488 (pt) REVERT: B 1458 ASP cc_start: 0.7335 (t0) cc_final: 0.7002 (t0) REVERT: B 1461 ILE cc_start: 0.7660 (pt) cc_final: 0.7313 (mm) REVERT: B 1468 VAL cc_start: 0.8253 (m) cc_final: 0.7939 (p) REVERT: B 1479 GLN cc_start: 0.8214 (mt0) cc_final: 0.7963 (mt0) REVERT: B 1481 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7492 (mp0) REVERT: B 1501 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 1503 LEU cc_start: 0.8707 (mt) cc_final: 0.8496 (mt) REVERT: B 1509 GLU cc_start: 0.7955 (tt0) cc_final: 0.7547 (tt0) REVERT: B 1515 ASP cc_start: 0.7462 (p0) cc_final: 0.6816 (p0) REVERT: B 1538 LYS cc_start: 0.8661 (pptt) cc_final: 0.8328 (pptt) REVERT: B 1544 GLU cc_start: 0.8355 (pt0) cc_final: 0.8036 (pt0) REVERT: B 1546 ASP cc_start: 0.8819 (m-30) cc_final: 0.8537 (m-30) REVERT: B 1560 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7799 (mm-30) REVERT: B 1565 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7223 (tmtt) REVERT: B 1567 LEU cc_start: 0.8707 (tt) cc_final: 0.8472 (tt) REVERT: B 1588 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: B 1592 GLU cc_start: 0.8446 (mp0) cc_final: 0.8103 (mp0) REVERT: B 1593 ASN cc_start: 0.7780 (t0) cc_final: 0.7458 (t0) REVERT: B 1614 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8297 (mtpp) REVERT: B 1627 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 1629 ASP cc_start: 0.7922 (t70) cc_final: 0.7580 (t70) REVERT: B 1634 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 1638 ASP cc_start: 0.7624 (t0) cc_final: 0.6988 (t0) REVERT: B 1644 ASN cc_start: 0.8702 (m-40) cc_final: 0.8313 (t0) REVERT: B 1646 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 1653 LYS cc_start: 0.9024 (tttt) cc_final: 0.8552 (ttpt) REVERT: B 1668 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7089 (mm-30) REVERT: B 1677 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 1683 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 1720 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8528 (tp40) REVERT: B 1737 LYS cc_start: 0.9232 (tmtt) cc_final: 0.8890 (tptp) REVERT: B 1741 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 1750 ASP cc_start: 0.7540 (t0) cc_final: 0.7291 (t0) REVERT: B 1759 SER cc_start: 0.8629 (p) cc_final: 0.8285 (p) REVERT: B 1760 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 1764 LYS cc_start: 0.8885 (mmmt) cc_final: 0.7575 (mmmm) REVERT: B 1767 MET cc_start: 0.7916 (ppp) cc_final: 0.7695 (ppp) REVERT: B 1772 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8389 (ttm-80) REVERT: B 1780 GLU cc_start: 0.7285 (tp30) cc_final: 0.6854 (tp30) REVERT: B 1783 HIS cc_start: 0.8307 (t-90) cc_final: 0.8018 (t70) REVERT: B 1788 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 1818 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8600 (mmmm) REVERT: B 1824 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 1828 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8379 (mtp85) REVERT: B 1833 GLU cc_start: 0.8014 (tp30) cc_final: 0.7480 (tp30) REVERT: B 1840 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8170 (ttp80) REVERT: B 1853 ARG cc_start: 0.8354 (mmt90) cc_final: 0.8039 (tpp80) REVERT: B 1860 PHE cc_start: 0.8692 (t80) cc_final: 0.8342 (t80) REVERT: B 1863 ASP cc_start: 0.7925 (m-30) cc_final: 0.7359 (t70) REVERT: B 1867 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8326 (mmmm) REVERT: B 1870 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 1882 LYS cc_start: 0.9102 (tttp) cc_final: 0.8726 (tttm) REVERT: B 1885 THR cc_start: 0.8822 (p) cc_final: 0.8592 (t) REVERT: B 1889 GLN cc_start: 0.8649 (mt0) cc_final: 0.8394 (mt0) REVERT: B 1894 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 1903 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8671 (mmtt) REVERT: B 1906 LYS cc_start: 0.9052 (tppt) cc_final: 0.8518 (tppt) REVERT: B 1922 GLU cc_start: 0.8419 (tp30) cc_final: 0.7934 (tm-30) REVERT: B 1927 LYS cc_start: 0.9219 (tttt) cc_final: 0.9011 (tttt) REVERT: A 1016 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 1072 GLU cc_start: 0.8655 (pt0) cc_final: 0.8263 (mt-10) REVERT: A 1092 ASP cc_start: 0.7796 (t0) cc_final: 0.7479 (t0) REVERT: A 1174 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8534 (mmtp) REVERT: A 1179 MET cc_start: 0.5762 (ppp) cc_final: 0.5476 (ppp) REVERT: A 1183 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7389 (mpp80) REVERT: A 1185 ASP cc_start: 0.7811 (m-30) cc_final: 0.7562 (m-30) REVERT: A 1187 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 1226 GLU cc_start: 0.5656 (tm-30) cc_final: 0.5366 (tm-30) REVERT: A 1250 LYS cc_start: 0.8177 (pttp) cc_final: 0.7889 (ptmm) REVERT: A 1266 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6086 (tm-30) REVERT: A 1276 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7542 (ptp-110) REVERT: A 1345 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7569 (mt-10) REVERT: A 1356 GLU cc_start: 0.7461 (tp30) cc_final: 0.7020 (tp30) REVERT: A 1386 GLU cc_start: 0.4630 (tm-30) cc_final: 0.3601 (tp30) REVERT: A 1392 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 1413 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7361 (mp0) REVERT: A 1453 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7966 (mtpp) REVERT: A 1465 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7430 (mmtm) REVERT: A 1467 LYS cc_start: 0.7286 (mttm) cc_final: 0.6973 (ttmm) REVERT: A 1488 GLU cc_start: 0.6990 (tp30) cc_final: 0.6429 (tp30) REVERT: A 1492 LEU cc_start: 0.8180 (mt) cc_final: 0.7658 (mt) REVERT: A 1553 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 1554 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 1561 GLN cc_start: 0.7095 (pp30) cc_final: 0.6326 (tm-30) REVERT: A 1570 GLN cc_start: 0.7991 (mt0) cc_final: 0.7600 (mm-40) REVERT: A 1579 GLU cc_start: 0.7978 (mp0) cc_final: 0.7772 (mp0) REVERT: A 1614 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8060 (mtmm) REVERT: A 1623 LYS cc_start: 0.8112 (tppt) cc_final: 0.7700 (tppt) REVERT: A 1625 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8152 (mmmm) REVERT: A 1646 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 1656 GLN cc_start: 0.8531 (mm110) cc_final: 0.8271 (mm-40) REVERT: A 1662 GLN cc_start: 0.8661 (tt0) cc_final: 0.8290 (tp40) REVERT: A 1683 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 1690 GLN cc_start: 0.8588 (tt0) cc_final: 0.8187 (tp40) REVERT: A 1729 THR cc_start: 0.8741 (p) cc_final: 0.8490 (t) REVERT: A 1741 GLU cc_start: 0.8347 (tp30) cc_final: 0.7977 (tp30) REVERT: A 1754 ASN cc_start: 0.8328 (t0) cc_final: 0.8062 (t0) REVERT: A 1775 ASP cc_start: 0.7919 (t0) cc_final: 0.7599 (t0) REVERT: A 1776 GLU cc_start: 0.7897 (tp30) cc_final: 0.6813 (tp30) REVERT: A 1777 LEU cc_start: 0.9067 (tt) cc_final: 0.8844 (tt) REVERT: A 1778 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8027 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8175 (t0) cc_final: 0.7874 (t0) REVERT: A 1789 LYS cc_start: 0.9025 (ttpp) cc_final: 0.8791 (ttmm) REVERT: A 1792 LYS cc_start: 0.9310 (ttmt) cc_final: 0.8917 (ttmm) REVERT: A 1794 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (mm) REVERT: A 1802 GLN cc_start: 0.8780 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 1809 GLU cc_start: 0.8495 (pt0) cc_final: 0.8218 (pt0) REVERT: A 1822 LYS cc_start: 0.8593 (tttm) cc_final: 0.8274 (ttpp) REVERT: A 1824 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 1833 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 1839 ARG cc_start: 0.8285 (tmt170) cc_final: 0.8002 (tmt170) REVERT: A 1846 LYS cc_start: 0.9168 (tttm) cc_final: 0.8857 (ttmm) REVERT: A 1849 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.8077 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8794 (ptmt) cc_final: 0.8441 (ptmt) REVERT: A 1853 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.7734 (ttm110) REVERT: A 1858 LEU cc_start: 0.8658 (mp) cc_final: 0.8403 (mm) REVERT: A 1860 PHE cc_start: 0.9009 (t80) cc_final: 0.8778 (t80) REVERT: A 1864 GLU cc_start: 0.7870 (tp30) cc_final: 0.6629 (tp30) REVERT: A 1865 ASP cc_start: 0.8009 (t0) cc_final: 0.7755 (t0) REVERT: A 1868 ASN cc_start: 0.8652 (m110) cc_final: 0.6807 (m-40) REVERT: A 1870 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7819 (mm-30) REVERT: A 1876 VAL cc_start: 0.9148 (m) cc_final: 0.8914 (p) REVERT: A 1881 GLN cc_start: 0.8628 (tp-100) cc_final: 0.8260 (tp40) REVERT: A 1882 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8922 (ttmm) REVERT: A 1884 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8686 (ttpt) REVERT: A 1889 GLN cc_start: 0.7962 (pp30) cc_final: 0.7468 (pp30) REVERT: A 1909 GLN cc_start: 0.8563 (tp40) cc_final: 0.7949 (tm-30) REVERT: A 1915 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7727 (tm-30) outliers start: 3 outliers final: 1 residues processed: 611 average time/residue: 0.3328 time to fit residues: 289.1622 Evaluate side-chains 527 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 525 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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: 0.6980 chunk 146 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 55 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 B1037 GLN B1168 GLN ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1797 GLN B1802 GLN B1869 HIS B1900 ASN B1908 GLN A1500 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 1.0595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17454 Z= 0.197 Angle : 0.635 7.911 23282 Z= 0.355 Chirality : 0.042 0.150 2582 Planarity : 0.003 0.045 3158 Dihedral : 4.354 15.644 2318 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.11 % Allowed : 4.44 % Favored : 95.45 % 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: 1.73 (0.18), residues: 2150 helix: 1.23 (0.11), residues: 2099 sheet: None (None), residues: 0 loop : 0.76 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A1379 HIS 0.006 0.001 HIS A1193 PHE 0.028 0.003 PHE A 945 TYR 0.039 0.003 TYR A1383 ARG 0.007 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 662 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 660 time to evaluate : 2.069 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: B 857 MET cc_start: 0.5230 (mmp) cc_final: 0.4924 (mmp) REVERT: B 966 GLU cc_start: 0.6964 (tp30) cc_final: 0.6348 (tm-30) REVERT: B 980 ASP cc_start: 0.7634 (m-30) cc_final: 0.7410 (m-30) REVERT: B 1182 LEU cc_start: 0.7382 (mp) cc_final: 0.7180 (mp) REVERT: B 1224 LYS cc_start: 0.7992 (tptm) cc_final: 0.7724 (tptm) REVERT: B 1254 GLU cc_start: 0.8021 (tt0) cc_final: 0.7665 (tt0) REVERT: B 1261 GLN cc_start: 0.8844 (tt0) cc_final: 0.7864 (tm-30) REVERT: B 1282 ASP cc_start: 0.7828 (m-30) cc_final: 0.7626 (m-30) REVERT: B 1303 GLU cc_start: 0.8003 (pt0) cc_final: 0.7407 (pp20) REVERT: B 1320 LEU cc_start: 0.8610 (mt) cc_final: 0.8260 (tt) REVERT: B 1358 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6076 (tm-30) REVERT: B 1395 GLU cc_start: 0.7227 (pp20) cc_final: 0.6831 (tm-30) REVERT: B 1400 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8483 (mtpp) REVERT: B 1416 ASN cc_start: 0.8262 (t0) cc_final: 0.8041 (t0) REVERT: B 1423 GLU cc_start: 0.8389 (pt0) cc_final: 0.7998 (pt0) REVERT: B 1460 ILE cc_start: 0.8565 (tt) cc_final: 0.8096 (tt) REVERT: B 1464 TRP cc_start: 0.8304 (m100) cc_final: 0.6709 (m100) REVERT: B 1467 LYS cc_start: 0.8065 (mttt) cc_final: 0.7802 (mmmm) REVERT: B 1493 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8618 (ttmm) REVERT: B 1497 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6765 (tm-30) REVERT: B 1504 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 1515 ASP cc_start: 0.7798 (p0) cc_final: 0.7343 (p0) REVERT: B 1516 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 1535 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 1536 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8411 (tmtt) REVERT: B 1538 LYS cc_start: 0.8895 (pptt) cc_final: 0.8462 (pptt) REVERT: B 1544 GLU cc_start: 0.8461 (pt0) cc_final: 0.8228 (pt0) REVERT: B 1546 ASP cc_start: 0.8887 (m-30) cc_final: 0.8343 (m-30) REVERT: B 1549 GLN cc_start: 0.8475 (pp30) cc_final: 0.7976 (pp30) REVERT: B 1565 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7483 (tmtt) REVERT: B 1573 LEU cc_start: 0.8741 (pp) cc_final: 0.8408 (tt) REVERT: B 1582 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7191 (ppt90) REVERT: B 1586 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 1593 ASN cc_start: 0.7911 (t0) cc_final: 0.7590 (t0) REVERT: B 1614 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8389 (mtpp) REVERT: B 1622 MET cc_start: 0.7730 (ppp) cc_final: 0.7164 (ppp) REVERT: B 1633 LEU cc_start: 0.8889 (mp) cc_final: 0.8661 (mm) REVERT: B 1634 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7337 (tm-30) REVERT: B 1638 ASP cc_start: 0.7789 (t0) cc_final: 0.7309 (t0) REVERT: B 1653 LYS cc_start: 0.8874 (tttt) cc_final: 0.8240 (ttmm) REVERT: B 1655 GLN cc_start: 0.8780 (mt0) cc_final: 0.8467 (mt0) REVERT: B 1657 GLN cc_start: 0.7715 (tp40) cc_final: 0.7320 (tp40) REVERT: B 1667 GLU cc_start: 0.8217 (tp30) cc_final: 0.7879 (tp30) REVERT: B 1677 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 1683 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7121 (tm-30) REVERT: B 1708 ARG cc_start: 0.8517 (mpt90) cc_final: 0.8309 (mtm-85) REVERT: B 1723 GLU cc_start: 0.8430 (pt0) cc_final: 0.8217 (pt0) REVERT: B 1737 LYS cc_start: 0.9343 (tmtt) cc_final: 0.8878 (tptp) REVERT: B 1744 THR cc_start: 0.8591 (p) cc_final: 0.8377 (p) REVERT: B 1748 ASP cc_start: 0.8003 (m-30) cc_final: 0.7608 (m-30) REVERT: B 1750 ASP cc_start: 0.7768 (t0) cc_final: 0.7494 (t0) REVERT: B 1757 LYS cc_start: 0.8923 (tttp) cc_final: 0.8510 (ttpp) REVERT: B 1760 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 1764 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8589 (mmmm) REVERT: B 1772 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8446 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8124 (t0) cc_final: 0.7912 (t0) REVERT: B 1789 LYS cc_start: 0.8927 (tppp) cc_final: 0.8625 (tppp) REVERT: B 1797 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8962 (tp40) REVERT: B 1818 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8538 (mmmt) REVERT: B 1822 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8931 (mtpp) REVERT: B 1824 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 1828 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8122 (mtp85) REVERT: B 1833 GLU cc_start: 0.8140 (tp30) cc_final: 0.7152 (tp30) REVERT: B 1840 ARG cc_start: 0.8883 (ttp-110) cc_final: 0.8146 (mtp-110) REVERT: B 1848 LEU cc_start: 0.9116 (tp) cc_final: 0.8776 (tt) REVERT: B 1853 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8169 (tpp80) REVERT: B 1865 ASP cc_start: 0.8051 (m-30) cc_final: 0.7788 (m-30) REVERT: B 1873 GLN cc_start: 0.8809 (tp40) cc_final: 0.8378 (tm-30) REVERT: B 1878 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7831 (mmmt) REVERT: B 1881 GLN cc_start: 0.8451 (pm20) cc_final: 0.8249 (pm20) REVERT: B 1882 LYS cc_start: 0.9122 (tttp) cc_final: 0.8634 (tmtt) REVERT: B 1885 THR cc_start: 0.8835 (p) cc_final: 0.8621 (t) REVERT: B 1888 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7775 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8564 (mt0) cc_final: 0.8132 (tp40) REVERT: B 1892 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 1903 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8618 (mmtt) REVERT: B 1906 LYS cc_start: 0.9089 (tppt) cc_final: 0.8720 (tppt) REVERT: B 1908 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7897 (tp40) REVERT: B 1915 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 1927 LYS cc_start: 0.9127 (tttt) cc_final: 0.8917 (tttt) REVERT: A 1250 LYS cc_start: 0.8321 (pttp) cc_final: 0.7769 (ptmm) REVERT: A 1258 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8574 (mmtp) REVERT: A 1261 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8627 (mm110) REVERT: A 1273 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 1276 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7639 (ttm-80) REVERT: A 1300 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8170 (mm-30) REVERT: A 1333 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 1345 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 1353 GLU cc_start: 0.8078 (mp0) cc_final: 0.7807 (mp0) REVERT: A 1358 GLU cc_start: 0.8377 (mm-30) cc_final: 0.6752 (mm-30) REVERT: A 1401 LEU cc_start: 0.7666 (tt) cc_final: 0.7458 (tt) REVERT: A 1405 LEU cc_start: 0.8268 (tt) cc_final: 0.7942 (tt) REVERT: A 1413 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7285 (mp0) REVERT: A 1419 VAL cc_start: 0.8917 (m) cc_final: 0.8588 (p) REVERT: A 1424 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7835 (mmmm) REVERT: A 1427 GLN cc_start: 0.7650 (pp30) cc_final: 0.7184 (pp30) REVERT: A 1432 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 1434 GLU cc_start: 0.8186 (mp0) cc_final: 0.7957 (mp0) REVERT: A 1440 VAL cc_start: 0.8791 (m) cc_final: 0.8560 (p) REVERT: A 1442 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7659 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8131 (t0) cc_final: 0.7851 (t0) REVERT: A 1451 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 1457 ILE cc_start: 0.8221 (mm) cc_final: 0.7880 (mm) REVERT: A 1458 ASP cc_start: 0.7483 (p0) cc_final: 0.7179 (p0) REVERT: A 1465 LYS cc_start: 0.7784 (mmtm) cc_final: 0.5429 (mmtt) REVERT: A 1467 LYS cc_start: 0.7774 (mttm) cc_final: 0.7554 (ttmm) REVERT: A 1475 LEU cc_start: 0.8618 (tp) cc_final: 0.8371 (tt) REVERT: A 1480 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8465 (ttmm) REVERT: A 1488 GLU cc_start: 0.6953 (tp30) cc_final: 0.6350 (tp30) REVERT: A 1501 GLU cc_start: 0.8462 (pt0) cc_final: 0.8082 (pt0) REVERT: A 1504 GLU cc_start: 0.7916 (mp0) cc_final: 0.7481 (mp0) REVERT: A 1506 VAL cc_start: 0.8088 (m) cc_final: 0.7805 (p) REVERT: A 1510 ASN cc_start: 0.8034 (m-40) cc_final: 0.7719 (m-40) REVERT: A 1511 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8514 (mmmm) REVERT: A 1516 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 1523 GLN cc_start: 0.7881 (mt0) cc_final: 0.7374 (tt0) REVERT: A 1554 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 1560 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 1561 GLN cc_start: 0.7513 (pp30) cc_final: 0.6566 (pp30) REVERT: A 1563 GLU cc_start: 0.7986 (tp30) cc_final: 0.7738 (tp30) REVERT: A 1565 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8156 (mttp) REVERT: A 1567 LEU cc_start: 0.8985 (mt) cc_final: 0.8757 (mm) REVERT: A 1570 GLN cc_start: 0.8307 (mt0) cc_final: 0.7996 (mm-40) REVERT: A 1582 ARG cc_start: 0.7698 (ppt170) cc_final: 0.7369 (ttp80) REVERT: A 1599 GLN cc_start: 0.8534 (tt0) cc_final: 0.8115 (tp40) REVERT: A 1623 LYS cc_start: 0.8308 (tppt) cc_final: 0.7925 (tppt) REVERT: A 1631 ASN cc_start: 0.8715 (m-40) cc_final: 0.8437 (t0) REVERT: A 1634 GLU cc_start: 0.8062 (pt0) cc_final: 0.7823 (pt0) REVERT: A 1637 LEU cc_start: 0.8768 (mp) cc_final: 0.8290 (tt) REVERT: A 1642 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8202 (mtpp) REVERT: A 1656 GLN cc_start: 0.8663 (mm110) cc_final: 0.8463 (tp40) REVERT: A 1660 ASP cc_start: 0.8114 (p0) cc_final: 0.7853 (p0) REVERT: A 1662 GLN cc_start: 0.8622 (tt0) cc_final: 0.8265 (tp40) REVERT: A 1690 GLN cc_start: 0.8421 (tt0) cc_final: 0.8143 (tp40) REVERT: A 1705 ARG cc_start: 0.8346 (ttt90) cc_final: 0.7917 (ttm-80) REVERT: A 1711 GLU cc_start: 0.7864 (pt0) cc_final: 0.7447 (pt0) REVERT: A 1712 GLN cc_start: 0.8824 (mm110) cc_final: 0.8590 (mm-40) REVERT: A 1735 LYS cc_start: 0.8917 (ptmm) cc_final: 0.8125 (ttpp) REVERT: A 1737 LYS cc_start: 0.8954 (tttt) cc_final: 0.8560 (ttpp) REVERT: A 1739 GLU cc_start: 0.8380 (pt0) cc_final: 0.7578 (pt0) REVERT: A 1754 ASN cc_start: 0.8442 (t0) cc_final: 0.8170 (t0) REVERT: A 1757 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8738 (ttpt) REVERT: A 1778 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8178 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8088 (t0) cc_final: 0.7847 (t0) REVERT: A 1792 LYS cc_start: 0.9318 (ttmt) cc_final: 0.8957 (ttmm) REVERT: A 1794 LEU cc_start: 0.8760 (mt) cc_final: 0.8496 (mm) REVERT: A 1795 GLU cc_start: 0.7802 (tp30) cc_final: 0.7297 (tp30) REVERT: A 1796 THR cc_start: 0.8968 (p) cc_final: 0.8696 (t) REVERT: A 1798 ILE cc_start: 0.9008 (tt) cc_final: 0.8605 (tt) REVERT: A 1809 GLU cc_start: 0.8422 (pt0) cc_final: 0.8095 (pt0) REVERT: A 1822 LYS cc_start: 0.8536 (tttm) cc_final: 0.8190 (ttpp) REVERT: A 1824 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 1828 ARG cc_start: 0.8427 (ptt-90) cc_final: 0.7928 (ptt-90) REVERT: A 1839 ARG cc_start: 0.8347 (tmt170) cc_final: 0.7956 (tmt170) REVERT: A 1846 LYS cc_start: 0.9177 (tttm) cc_final: 0.8692 (ttmm) REVERT: A 1853 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7756 (ttm110) REVERT: A 1860 PHE cc_start: 0.9031 (t80) cc_final: 0.8768 (t80) REVERT: A 1864 GLU cc_start: 0.7912 (tp30) cc_final: 0.7052 (tp30) REVERT: A 1865 ASP cc_start: 0.8056 (t0) cc_final: 0.7713 (t0) REVERT: A 1868 ASN cc_start: 0.8605 (m110) cc_final: 0.7471 (m-40) REVERT: A 1870 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 1871 ARG cc_start: 0.8621 (tpm170) cc_final: 0.8072 (tpm170) REVERT: A 1874 ASP cc_start: 0.8020 (m-30) cc_final: 0.7165 (m-30) REVERT: A 1878 LYS cc_start: 0.8977 (tttp) cc_final: 0.8730 (ttmm) REVERT: A 1889 GLN cc_start: 0.7908 (pp30) cc_final: 0.7623 (pp30) REVERT: A 1892 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 1909 GLN cc_start: 0.8642 (tp40) cc_final: 0.8137 (tm-30) REVERT: A 1910 GLU cc_start: 0.8514 (tt0) cc_final: 0.7824 (tt0) REVERT: A 1915 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 2 outliers final: 0 residues processed: 662 average time/residue: 0.3421 time to fit residues: 321.0440 Evaluate side-chains 560 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 559 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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: 0.6980 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 105 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** B1231 HIS B1606 GLN B1841 HIS ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 1.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17454 Z= 0.174 Angle : 0.609 6.740 23282 Z= 0.337 Chirality : 0.041 0.212 2582 Planarity : 0.003 0.057 3158 Dihedral : 4.283 15.915 2318 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.70 % 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: 2.36 (0.18), residues: 2150 helix: 1.62 (0.11), residues: 2107 sheet: None (None), residues: 0 loop : 0.84 (0.83), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1379 HIS 0.014 0.001 HIS A1598 PHE 0.012 0.002 PHE A1341 TYR 0.021 0.003 TYR A1496 ARG 0.007 0.001 ARG A1840 *********************** 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 658 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 655 time to evaluate : 2.112 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 857 MET cc_start: 0.5211 (mmp) cc_final: 0.4964 (mmp) REVERT: B 966 GLU cc_start: 0.7136 (tp30) cc_final: 0.6822 (tm-30) REVERT: B 1182 LEU cc_start: 0.7575 (mp) cc_final: 0.7355 (mp) REVERT: B 1194 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 1214 GLN cc_start: 0.7751 (mt0) cc_final: 0.7191 (mt0) REVERT: B 1224 LYS cc_start: 0.8164 (tptm) cc_final: 0.7810 (tptm) REVERT: B 1247 CYS cc_start: 0.8325 (m) cc_final: 0.8072 (p) REVERT: B 1261 GLN cc_start: 0.8852 (tt0) cc_final: 0.7322 (tm-30) REVERT: B 1300 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 1303 GLU cc_start: 0.8289 (pt0) cc_final: 0.7575 (pp20) REVERT: B 1317 THR cc_start: 0.8732 (p) cc_final: 0.8516 (t) REVERT: B 1320 LEU cc_start: 0.8810 (mt) cc_final: 0.8544 (tt) REVERT: B 1324 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8654 (mtmt) REVERT: B 1333 GLU cc_start: 0.8327 (tt0) cc_final: 0.7889 (tt0) REVERT: B 1353 GLU cc_start: 0.7650 (pm20) cc_final: 0.7406 (pm20) REVERT: B 1358 GLU cc_start: 0.7632 (tm-30) cc_final: 0.5843 (tm-30) REVERT: B 1367 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7833 (tpp80) REVERT: B 1392 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 1400 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8399 (mtmm) REVERT: B 1409 GLU cc_start: 0.7731 (pt0) cc_final: 0.7462 (pt0) REVERT: B 1415 LEU cc_start: 0.9143 (mt) cc_final: 0.8884 (mm) REVERT: B 1423 GLU cc_start: 0.8400 (pt0) cc_final: 0.8060 (pt0) REVERT: B 1455 LYS cc_start: 0.8370 (mptt) cc_final: 0.8096 (mptt) REVERT: B 1457 ILE cc_start: 0.8990 (pt) cc_final: 0.8570 (mm) REVERT: B 1460 ILE cc_start: 0.8570 (tt) cc_final: 0.8222 (tt) REVERT: B 1464 TRP cc_start: 0.7900 (m100) cc_final: 0.6277 (m100) REVERT: B 1467 LYS cc_start: 0.8037 (mttt) cc_final: 0.7803 (mmmm) REVERT: B 1478 SER cc_start: 0.8818 (m) cc_final: 0.8551 (p) REVERT: B 1493 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8538 (ttmm) REVERT: B 1496 TYR cc_start: 0.8957 (t80) cc_final: 0.8638 (t80) REVERT: B 1504 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 1509 GLU cc_start: 0.8212 (tt0) cc_final: 0.7971 (tt0) REVERT: B 1516 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 1536 LYS cc_start: 0.8724 (tptp) cc_final: 0.8382 (tptp) REVERT: B 1538 LYS cc_start: 0.8980 (pptt) cc_final: 0.8674 (pptt) REVERT: B 1544 GLU cc_start: 0.8335 (pt0) cc_final: 0.7958 (pt0) REVERT: B 1546 ASP cc_start: 0.8762 (m-30) cc_final: 0.8203 (m-30) REVERT: B 1556 GLU cc_start: 0.7920 (mp0) cc_final: 0.7650 (mp0) REVERT: B 1560 GLU cc_start: 0.8733 (tt0) cc_final: 0.8429 (mm-30) REVERT: B 1562 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7921 (tt0) REVERT: B 1565 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7664 (tmtt) REVERT: B 1582 ARG cc_start: 0.8096 (ptt90) cc_final: 0.7790 (ppt170) REVERT: B 1593 ASN cc_start: 0.8051 (t0) cc_final: 0.7719 (t0) REVERT: B 1614 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8486 (mtpp) REVERT: B 1627 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 1634 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 1638 ASP cc_start: 0.8064 (t0) cc_final: 0.7500 (t0) REVERT: B 1651 ILE cc_start: 0.9070 (mt) cc_final: 0.8477 (mt) REVERT: B 1653 LYS cc_start: 0.9082 (tttt) cc_final: 0.8511 (ttmm) REVERT: B 1655 GLN cc_start: 0.8809 (mt0) cc_final: 0.8476 (mm-40) REVERT: B 1667 GLU cc_start: 0.8249 (tp30) cc_final: 0.8017 (tp30) REVERT: B 1677 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 1678 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8189 (mp10) REVERT: B 1683 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 1713 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 1736 ARG cc_start: 0.8891 (mpt-90) cc_final: 0.8643 (mpp80) REVERT: B 1737 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9018 (tptp) REVERT: B 1741 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 1749 LEU cc_start: 0.8374 (tp) cc_final: 0.8147 (tt) REVERT: B 1757 LYS cc_start: 0.8911 (tttp) cc_final: 0.8511 (ttpp) REVERT: B 1760 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 1764 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8489 (mmmm) REVERT: B 1772 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8352 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8106 (t0) cc_final: 0.7897 (t0) REVERT: B 1789 LYS cc_start: 0.8904 (tppp) cc_final: 0.8697 (tppp) REVERT: B 1792 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8280 (tppt) REVERT: B 1818 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8498 (tppt) REVERT: B 1820 ILE cc_start: 0.8346 (mt) cc_final: 0.8094 (tp) REVERT: B 1824 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 1833 GLU cc_start: 0.8179 (tp30) cc_final: 0.7221 (tp30) REVERT: B 1840 ARG cc_start: 0.8894 (ttp-110) cc_final: 0.8228 (mtp-110) REVERT: B 1853 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8158 (tpp80) REVERT: B 1865 ASP cc_start: 0.8097 (m-30) cc_final: 0.7868 (m-30) REVERT: B 1867 LYS cc_start: 0.8657 (tptm) cc_final: 0.8428 (mmmm) REVERT: B 1870 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 1873 GLN cc_start: 0.8798 (tp40) cc_final: 0.8380 (tm-30) REVERT: B 1882 LYS cc_start: 0.9109 (tttp) cc_final: 0.8736 (tttm) REVERT: B 1888 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7921 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8634 (mt0) cc_final: 0.8128 (tp40) REVERT: B 1892 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 1903 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8636 (mmtt) REVERT: B 1906 LYS cc_start: 0.9181 (tppt) cc_final: 0.8761 (tppt) REVERT: B 1908 GLN cc_start: 0.8587 (tp-100) cc_final: 0.7905 (tp-100) REVERT: B 1915 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 1917 ARG cc_start: 0.9022 (mtp-110) cc_final: 0.8396 (ttp-110) REVERT: B 1927 LYS cc_start: 0.9081 (tttt) cc_final: 0.8858 (tttt) REVERT: A 959 LYS cc_start: 0.8790 (ptpt) cc_final: 0.8100 (mttm) REVERT: A 1016 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 1041 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: A 1072 GLU cc_start: 0.7880 (pp20) cc_final: 0.7461 (tm-30) REVERT: A 1202 LYS cc_start: 0.8815 (pptt) cc_final: 0.8451 (pptt) REVERT: A 1215 ILE cc_start: 0.7904 (pt) cc_final: 0.7606 (pt) REVERT: A 1221 LEU cc_start: 0.7310 (tp) cc_final: 0.7059 (mt) REVERT: A 1250 LYS cc_start: 0.8549 (pttp) cc_final: 0.8301 (ptmm) REVERT: A 1270 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8582 (mmmm) REVERT: A 1273 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 1276 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7649 (ptp-110) REVERT: A 1283 SER cc_start: 0.8389 (m) cc_final: 0.8176 (p) REVERT: A 1297 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7908 (ptp-110) REVERT: A 1300 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8200 (mm-30) REVERT: A 1344 LEU cc_start: 0.8043 (tp) cc_final: 0.7807 (tp) REVERT: A 1345 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 1350 ASN cc_start: 0.7756 (m110) cc_final: 0.6933 (m110) REVERT: A 1351 ILE cc_start: 0.8797 (pt) cc_final: 0.8594 (pt) REVERT: A 1353 GLU cc_start: 0.8110 (mp0) cc_final: 0.7642 (mp0) REVERT: A 1357 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7983 (mm-30) REVERT: A 1358 GLU cc_start: 0.8366 (mm-30) cc_final: 0.6639 (mm-30) REVERT: A 1362 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7949 (ttmm) REVERT: A 1393 GLU cc_start: 0.7547 (pp20) cc_final: 0.6846 (pp20) REVERT: A 1401 LEU cc_start: 0.8426 (tt) cc_final: 0.8222 (tp) REVERT: A 1405 LEU cc_start: 0.8522 (tt) cc_final: 0.8313 (tt) REVERT: A 1412 ILE cc_start: 0.8553 (tt) cc_final: 0.8323 (tt) REVERT: A 1413 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 1417 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7850 (mm-40) REVERT: A 1427 GLN cc_start: 0.7839 (pp30) cc_final: 0.7392 (pp30) REVERT: A 1432 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 1434 GLU cc_start: 0.8353 (mp0) cc_final: 0.8058 (mm-30) REVERT: A 1439 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6490 (tm-30) REVERT: A 1442 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7683 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8149 (t0) cc_final: 0.7876 (t0) REVERT: A 1458 ASP cc_start: 0.7733 (p0) cc_final: 0.6820 (p0) REVERT: A 1463 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 1465 LYS cc_start: 0.7473 (mmpt) cc_final: 0.6726 (tppt) REVERT: A 1467 LYS cc_start: 0.7764 (mttm) cc_final: 0.7490 (ttmm) REVERT: A 1480 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8389 (ttmm) REVERT: A 1481 GLU cc_start: 0.7505 (tp30) cc_final: 0.7284 (tp30) REVERT: A 1488 GLU cc_start: 0.7098 (tp30) cc_final: 0.6494 (tp30) REVERT: A 1492 LEU cc_start: 0.8493 (mt) cc_final: 0.8126 (mm) REVERT: A 1501 GLU cc_start: 0.8508 (pt0) cc_final: 0.8294 (pt0) REVERT: A 1523 GLN cc_start: 0.7902 (mt0) cc_final: 0.7397 (tt0) REVERT: A 1542 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 1554 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 1559 LEU cc_start: 0.8528 (tp) cc_final: 0.8177 (tp) REVERT: A 1560 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 1561 GLN cc_start: 0.7563 (pp30) cc_final: 0.6743 (pp30) REVERT: A 1563 GLU cc_start: 0.8085 (tp30) cc_final: 0.7728 (tp30) REVERT: A 1565 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8193 (mttt) REVERT: A 1567 LEU cc_start: 0.8992 (mt) cc_final: 0.8699 (mm) REVERT: A 1570 GLN cc_start: 0.8339 (mt0) cc_final: 0.8040 (mm-40) REVERT: A 1614 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8672 (mmmm) REVERT: A 1622 MET cc_start: 0.7814 (mtp) cc_final: 0.7216 (mtp) REVERT: A 1623 LYS cc_start: 0.8394 (tppt) cc_final: 0.8189 (tppt) REVERT: A 1624 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8732 (tppt) REVERT: A 1637 LEU cc_start: 0.8780 (mp) cc_final: 0.8406 (tt) REVERT: A 1642 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8287 (mtpp) REVERT: A 1649 LYS cc_start: 0.9131 (tttp) cc_final: 0.8649 (ttpp) REVERT: A 1656 GLN cc_start: 0.8776 (mm110) cc_final: 0.8509 (tp40) REVERT: A 1662 GLN cc_start: 0.8615 (tt0) cc_final: 0.8083 (tp40) REVERT: A 1672 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7151 (ttp80) REVERT: A 1690 GLN cc_start: 0.8405 (tt0) cc_final: 0.8161 (tp40) REVERT: A 1705 ARG cc_start: 0.8442 (ttt90) cc_final: 0.7966 (ttm-80) REVERT: A 1712 GLN cc_start: 0.8801 (mm110) cc_final: 0.8491 (mm-40) REVERT: A 1735 LYS cc_start: 0.8912 (ptmm) cc_final: 0.8385 (ttpp) REVERT: A 1737 LYS cc_start: 0.8991 (tttt) cc_final: 0.8511 (ttpp) REVERT: A 1739 GLU cc_start: 0.8360 (pt0) cc_final: 0.7827 (pt0) REVERT: A 1741 GLU cc_start: 0.8275 (tp30) cc_final: 0.8024 (tp30) REVERT: A 1749 LEU cc_start: 0.8935 (tp) cc_final: 0.8674 (tp) REVERT: A 1758 ASN cc_start: 0.8449 (t0) cc_final: 0.8091 (t0) REVERT: A 1762 LYS cc_start: 0.9296 (ttmt) cc_final: 0.9088 (ttmt) REVERT: A 1778 ARG cc_start: 0.8379 (mtt-85) cc_final: 0.7996 (mtt-85) REVERT: A 1780 GLU cc_start: 0.8209 (tt0) cc_final: 0.7859 (tt0) REVERT: A 1782 ASP cc_start: 0.8085 (t0) cc_final: 0.7852 (t0) REVERT: A 1792 LYS cc_start: 0.9346 (ttmt) cc_final: 0.8969 (ttmm) REVERT: A 1794 LEU cc_start: 0.8826 (mt) cc_final: 0.8593 (mm) REVERT: A 1822 LYS cc_start: 0.8618 (tttm) cc_final: 0.8362 (ttpp) REVERT: A 1824 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 1840 ARG cc_start: 0.8031 (mpp80) cc_final: 0.7626 (mtm110) REVERT: A 1846 LYS cc_start: 0.9205 (tttm) cc_final: 0.8946 (ttmm) REVERT: A 1849 ARG cc_start: 0.8414 (tpp-160) cc_final: 0.8130 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8247 (ptmt) REVERT: A 1853 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.7800 (ttm110) REVERT: A 1858 LEU cc_start: 0.8495 (mp) cc_final: 0.8275 (mm) REVERT: A 1864 GLU cc_start: 0.7954 (tp30) cc_final: 0.7256 (tp30) REVERT: A 1865 ASP cc_start: 0.8046 (t0) cc_final: 0.7718 (t0) REVERT: A 1868 ASN cc_start: 0.8632 (m110) cc_final: 0.7908 (m-40) REVERT: A 1870 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 1871 ARG cc_start: 0.8560 (tpm170) cc_final: 0.8032 (tpm170) REVERT: A 1878 LYS cc_start: 0.8936 (tttp) cc_final: 0.8733 (ttmm) REVERT: A 1884 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8824 (ttpp) REVERT: A 1889 GLN cc_start: 0.7832 (pp30) cc_final: 0.7514 (pp30) REVERT: A 1892 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 1909 GLN cc_start: 0.8614 (tp40) cc_final: 0.8093 (tm-30) REVERT: A 1910 GLU cc_start: 0.8471 (tt0) cc_final: 0.7826 (tt0) REVERT: A 1915 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 1922 GLU cc_start: 0.8393 (mp0) cc_final: 0.8178 (mp0) outliers start: 3 outliers final: 0 residues processed: 658 average time/residue: 0.3515 time to fit residues: 331.5180 Evaluate side-chains 582 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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: 0.9990 chunk 186 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 207 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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** B1241 HIS ** B1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1570 GLN B1606 GLN B1838 GLN B1900 ASN A1089 GLN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 1.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17454 Z= 0.155 Angle : 0.599 10.654 23282 Z= 0.323 Chirality : 0.040 0.149 2582 Planarity : 0.003 0.033 3158 Dihedral : 4.210 17.733 2318 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.18), residues: 2150 helix: 1.89 (0.11), residues: 2101 sheet: None (None), residues: 0 loop : 1.04 (0.81), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B1464 HIS 0.011 0.001 HIS B1598 PHE 0.010 0.001 PHE B 945 TYR 0.021 0.002 TYR A1383 ARG 0.009 0.001 ARG B1577 *********************** 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 656 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 656 time to evaluate : 1.960 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: B 1182 LEU cc_start: 0.7851 (mp) cc_final: 0.7625 (mp) REVERT: B 1224 LYS cc_start: 0.8190 (tptm) cc_final: 0.7800 (tptm) REVERT: B 1243 LEU cc_start: 0.7761 (tt) cc_final: 0.7330 (mt) REVERT: B 1260 LEU cc_start: 0.8216 (tt) cc_final: 0.7862 (tt) REVERT: B 1261 GLN cc_start: 0.8709 (tt0) cc_final: 0.8000 (tp40) REVERT: B 1271 LEU cc_start: 0.9242 (mt) cc_final: 0.8903 (tp) REVERT: B 1291 GLU cc_start: 0.7361 (tp30) cc_final: 0.6667 (tp30) REVERT: B 1297 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7499 (mtp-110) REVERT: B 1300 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 1303 GLU cc_start: 0.8224 (pt0) cc_final: 0.7397 (pp20) REVERT: B 1320 LEU cc_start: 0.8805 (mt) cc_final: 0.8549 (tt) REVERT: B 1324 LYS cc_start: 0.9038 (mtmt) cc_final: 0.8728 (mtmt) REVERT: B 1357 GLU cc_start: 0.8062 (tp30) cc_final: 0.7849 (tp30) REVERT: B 1358 GLU cc_start: 0.7864 (tm-30) cc_final: 0.5945 (tm-30) REVERT: B 1362 LYS cc_start: 0.7824 (mtmm) cc_final: 0.6865 (mtmt) REVERT: B 1367 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7971 (tpp80) REVERT: B 1392 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 1400 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8416 (mtmm) REVERT: B 1409 GLU cc_start: 0.7600 (pt0) cc_final: 0.7341 (pt0) REVERT: B 1418 LYS cc_start: 0.8255 (ptpt) cc_final: 0.7868 (ptpp) REVERT: B 1419 VAL cc_start: 0.8800 (m) cc_final: 0.8562 (p) REVERT: B 1431 THR cc_start: 0.8671 (m) cc_final: 0.8318 (t) REVERT: B 1455 LYS cc_start: 0.8384 (mptt) cc_final: 0.8113 (mptt) REVERT: B 1457 ILE cc_start: 0.9005 (pt) cc_final: 0.8579 (mm) REVERT: B 1467 LYS cc_start: 0.7964 (mttt) cc_final: 0.7692 (mmmm) REVERT: B 1478 SER cc_start: 0.8854 (m) cc_final: 0.8569 (p) REVERT: B 1497 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6961 (tm-30) REVERT: B 1498 GLU cc_start: 0.7939 (pp20) cc_final: 0.7428 (pp20) REVERT: B 1504 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 1516 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 1536 LYS cc_start: 0.8819 (tptp) cc_final: 0.8616 (tptp) REVERT: B 1538 LYS cc_start: 0.8957 (pptt) cc_final: 0.8729 (pptt) REVERT: B 1543 VAL cc_start: 0.9187 (t) cc_final: 0.8941 (p) REVERT: B 1544 GLU cc_start: 0.8373 (pt0) cc_final: 0.7937 (pt0) REVERT: B 1547 GLU cc_start: 0.8287 (pp20) cc_final: 0.7910 (pp20) REVERT: B 1549 GLN cc_start: 0.8618 (tt0) cc_final: 0.7878 (tm-30) REVERT: B 1556 GLU cc_start: 0.7822 (mp0) cc_final: 0.7602 (mp0) REVERT: B 1560 GLU cc_start: 0.8771 (tt0) cc_final: 0.8528 (mm-30) REVERT: B 1562 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7848 (tt0) REVERT: B 1571 LEU cc_start: 0.8674 (mt) cc_final: 0.8216 (mt) REVERT: B 1577 ARG cc_start: 0.8112 (ptp-170) cc_final: 0.7681 (ptp-170) REVERT: B 1582 ARG cc_start: 0.8121 (ptt90) cc_final: 0.7723 (ppt170) REVERT: B 1585 GLN cc_start: 0.7154 (pp30) cc_final: 0.5846 (pp30) REVERT: B 1586 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6816 (mm-30) REVERT: B 1588 GLU cc_start: 0.8181 (pm20) cc_final: 0.7946 (pm20) REVERT: B 1590 GLU cc_start: 0.8588 (mp0) cc_final: 0.8226 (mp0) REVERT: B 1593 ASN cc_start: 0.8011 (t0) cc_final: 0.7735 (t0) REVERT: B 1614 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8503 (mtpp) REVERT: B 1627 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 1634 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7291 (tm-30) REVERT: B 1638 ASP cc_start: 0.8048 (t0) cc_final: 0.7564 (t0) REVERT: B 1653 LYS cc_start: 0.9128 (tttt) cc_final: 0.8758 (ttpp) REVERT: B 1655 GLN cc_start: 0.8834 (mt0) cc_final: 0.8572 (mm-40) REVERT: B 1659 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8133 (ttmm) REVERT: B 1667 GLU cc_start: 0.8265 (tp30) cc_final: 0.7939 (tp30) REVERT: B 1677 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 1678 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8190 (mp10) REVERT: B 1683 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 1708 ARG cc_start: 0.8545 (mpt-90) cc_final: 0.8214 (mtm-85) REVERT: B 1737 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9046 (tptp) REVERT: B 1741 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 1757 LYS cc_start: 0.8898 (tttp) cc_final: 0.8471 (ttpp) REVERT: B 1760 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 1764 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8447 (mmmm) REVERT: B 1772 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8387 (ttm-80) REVERT: B 1786 THR cc_start: 0.8919 (p) cc_final: 0.8507 (t) REVERT: B 1789 LYS cc_start: 0.8926 (tppp) cc_final: 0.8613 (tppp) REVERT: B 1792 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8279 (tppt) REVERT: B 1818 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8489 (tppt) REVERT: B 1820 ILE cc_start: 0.8327 (mt) cc_final: 0.8074 (tp) REVERT: B 1824 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 1826 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8424 (tpt-90) REVERT: B 1833 GLU cc_start: 0.8123 (tp30) cc_final: 0.7180 (tp30) REVERT: B 1840 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8382 (mtm-85) REVERT: B 1848 LEU cc_start: 0.9152 (tp) cc_final: 0.8801 (tt) REVERT: B 1853 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8138 (tpp80) REVERT: B 1857 GLU cc_start: 0.8027 (pp20) cc_final: 0.7812 (pp20) REVERT: B 1860 PHE cc_start: 0.8591 (t80) cc_final: 0.8167 (t80) REVERT: B 1865 ASP cc_start: 0.7910 (m-30) cc_final: 0.7612 (m-30) REVERT: B 1867 LYS cc_start: 0.8639 (tptm) cc_final: 0.8343 (mmmm) REVERT: B 1870 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 1873 GLN cc_start: 0.8784 (tp40) cc_final: 0.8388 (tm-30) REVERT: B 1878 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7838 (mmmt) REVERT: B 1882 LYS cc_start: 0.9173 (tttp) cc_final: 0.8593 (tmtt) REVERT: B 1889 GLN cc_start: 0.8646 (mt0) cc_final: 0.8168 (tp40) REVERT: B 1900 ASN cc_start: 0.7814 (t160) cc_final: 0.7568 (t0) REVERT: B 1903 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8633 (mmtt) REVERT: B 1906 LYS cc_start: 0.9161 (tppt) cc_final: 0.8822 (tppt) REVERT: B 1908 GLN cc_start: 0.8679 (tp-100) cc_final: 0.7869 (tp-100) REVERT: B 1910 GLU cc_start: 0.8202 (pp20) cc_final: 0.7920 (pp20) REVERT: B 1911 LEU cc_start: 0.8703 (tt) cc_final: 0.7946 (tt) REVERT: B 1915 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 961 ASP cc_start: 0.6875 (t0) cc_final: 0.6467 (m-30) REVERT: A 1016 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 1072 GLU cc_start: 0.7912 (pp20) cc_final: 0.7479 (tm-30) REVERT: A 1179 MET cc_start: 0.6885 (ppp) cc_final: 0.6274 (ppp) REVERT: A 1188 GLU cc_start: 0.6524 (tm-30) cc_final: 0.5847 (tp30) REVERT: A 1202 LYS cc_start: 0.8826 (pptt) cc_final: 0.8573 (pptt) REVERT: A 1215 ILE cc_start: 0.7871 (pt) cc_final: 0.7554 (pt) REVERT: A 1250 LYS cc_start: 0.8591 (pttp) cc_final: 0.8283 (ptmm) REVERT: A 1270 LYS cc_start: 0.8822 (mmpt) cc_final: 0.8471 (mmmm) REVERT: A 1276 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7439 (ttm-80) REVERT: A 1297 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8124 (ptp-110) REVERT: A 1299 LEU cc_start: 0.8482 (mt) cc_final: 0.7966 (tp) REVERT: A 1300 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8099 (mm-30) REVERT: A 1330 GLU cc_start: 0.8516 (tt0) cc_final: 0.8137 (mt-10) REVERT: A 1344 LEU cc_start: 0.8135 (tp) cc_final: 0.7894 (tp) REVERT: A 1350 ASN cc_start: 0.7769 (m110) cc_final: 0.7054 (t0) REVERT: A 1353 GLU cc_start: 0.8093 (mp0) cc_final: 0.7656 (mp0) REVERT: A 1356 GLU cc_start: 0.8533 (tp30) cc_final: 0.8105 (tp30) REVERT: A 1357 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 1358 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 1413 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 1417 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7891 (mm-40) REVERT: A 1427 GLN cc_start: 0.7856 (pp30) cc_final: 0.7363 (pp30) REVERT: A 1432 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 1434 GLU cc_start: 0.8266 (mp0) cc_final: 0.7782 (mm-30) REVERT: A 1439 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 1442 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7691 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8212 (t0) cc_final: 0.7819 (t0) REVERT: A 1451 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 1457 ILE cc_start: 0.8326 (mm) cc_final: 0.7770 (mm) REVERT: A 1458 ASP cc_start: 0.7769 (p0) cc_final: 0.6866 (p0) REVERT: A 1463 GLU cc_start: 0.7247 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 1467 LYS cc_start: 0.7811 (mttm) cc_final: 0.7537 (ttmm) REVERT: A 1488 GLU cc_start: 0.7114 (tp30) cc_final: 0.6134 (tp30) REVERT: A 1489 LEU cc_start: 0.8762 (tt) cc_final: 0.8324 (tp) REVERT: A 1492 LEU cc_start: 0.8471 (mt) cc_final: 0.7652 (mm) REVERT: A 1501 GLU cc_start: 0.8632 (pt0) cc_final: 0.8407 (pt0) REVERT: A 1511 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8501 (mmmm) REVERT: A 1523 GLN cc_start: 0.7894 (mt0) cc_final: 0.7443 (tt0) REVERT: A 1542 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7137 (tm-30) REVERT: A 1548 LEU cc_start: 0.8710 (tp) cc_final: 0.8416 (tt) REVERT: A 1554 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 1559 LEU cc_start: 0.8470 (tp) cc_final: 0.8233 (tp) REVERT: A 1561 GLN cc_start: 0.7657 (pp30) cc_final: 0.7135 (pp30) REVERT: A 1563 GLU cc_start: 0.8197 (tp30) cc_final: 0.7860 (tp30) REVERT: A 1565 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8289 (mttm) REVERT: A 1567 LEU cc_start: 0.8986 (mt) cc_final: 0.8758 (mm) REVERT: A 1570 GLN cc_start: 0.8269 (mt0) cc_final: 0.8009 (mm-40) REVERT: A 1572 GLU cc_start: 0.7809 (tp30) cc_final: 0.7081 (tp30) REVERT: A 1622 MET cc_start: 0.7808 (mtp) cc_final: 0.7278 (mtp) REVERT: A 1623 LYS cc_start: 0.8498 (tppt) cc_final: 0.8169 (tppt) REVERT: A 1625 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8566 (mtpp) REVERT: A 1634 GLU cc_start: 0.8127 (pt0) cc_final: 0.7897 (pt0) REVERT: A 1642 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8374 (mtpp) REVERT: A 1649 LYS cc_start: 0.9167 (tttp) cc_final: 0.8753 (ttmm) REVERT: A 1662 GLN cc_start: 0.8708 (tt0) cc_final: 0.8173 (tp40) REVERT: A 1672 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7447 (ttp80) REVERT: A 1687 ASN cc_start: 0.8130 (p0) cc_final: 0.7600 (t0) REVERT: A 1695 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 1712 GLN cc_start: 0.8799 (mm110) cc_final: 0.8508 (mm-40) REVERT: A 1737 LYS cc_start: 0.8973 (tttt) cc_final: 0.8551 (ttpp) REVERT: A 1741 GLU cc_start: 0.8325 (tp30) cc_final: 0.8096 (tp30) REVERT: A 1749 LEU cc_start: 0.8927 (tp) cc_final: 0.8708 (tp) REVERT: A 1754 ASN cc_start: 0.8448 (t0) cc_final: 0.8224 (t0) REVERT: A 1757 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8588 (ttmt) REVERT: A 1758 ASN cc_start: 0.8491 (t0) cc_final: 0.8110 (t0) REVERT: A 1762 LYS cc_start: 0.9283 (ttmt) cc_final: 0.9064 (ttmt) REVERT: A 1778 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7984 (mtt-85) REVERT: A 1782 ASP cc_start: 0.7996 (t0) cc_final: 0.7766 (t0) REVERT: A 1783 HIS cc_start: 0.9136 (t-90) cc_final: 0.8883 (t-170) REVERT: A 1792 LYS cc_start: 0.9358 (ttmt) cc_final: 0.9051 (ttmm) REVERT: A 1802 GLN cc_start: 0.9011 (tp40) cc_final: 0.8365 (tm-30) REVERT: A 1822 LYS cc_start: 0.8512 (tttm) cc_final: 0.8149 (ttpp) REVERT: A 1824 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 1825 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 1828 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.8049 (ptt-90) REVERT: A 1840 ARG cc_start: 0.8021 (mpp80) cc_final: 0.7820 (mtm110) REVERT: A 1846 LYS cc_start: 0.9195 (tttm) cc_final: 0.8947 (ttmm) REVERT: A 1850 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8234 (ptmt) REVERT: A 1853 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.7713 (ttm110) REVERT: A 1858 LEU cc_start: 0.8512 (mp) cc_final: 0.8268 (mm) REVERT: A 1864 GLU cc_start: 0.7937 (tp30) cc_final: 0.6876 (tp30) REVERT: A 1865 ASP cc_start: 0.8058 (t0) cc_final: 0.7675 (t0) REVERT: A 1868 ASN cc_start: 0.8612 (m110) cc_final: 0.7391 (m-40) REVERT: A 1870 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 1871 ARG cc_start: 0.8594 (tpm170) cc_final: 0.8082 (tpm170) REVERT: A 1884 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8801 (ttpp) REVERT: A 1892 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 1894 GLU cc_start: 0.7018 (pp20) cc_final: 0.6687 (pp20) REVERT: A 1909 GLN cc_start: 0.8612 (tp40) cc_final: 0.8287 (tm-30) REVERT: A 1910 GLU cc_start: 0.8490 (tt0) cc_final: 0.8057 (tt0) REVERT: A 1915 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.3397 time to fit residues: 320.0232 Evaluate side-chains 602 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 940 ASN B 942 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 ASN ** B1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1797 GLN A1881 GLN A1900 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 1.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17454 Z= 0.181 Angle : 0.643 9.407 23282 Z= 0.351 Chirality : 0.041 0.149 2582 Planarity : 0.003 0.047 3158 Dihedral : 4.224 15.573 2318 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.18), residues: 2150 helix: 1.80 (0.11), residues: 2104 sheet: None (None), residues: 0 loop : 1.19 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP B1379 HIS 0.011 0.001 HIS A1193 PHE 0.010 0.002 PHE A 945 TYR 0.024 0.003 TYR A1383 ARG 0.009 0.001 ARG B1577 *********************** 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 688 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 688 time to evaluate : 1.864 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: B 966 GLU cc_start: 0.7490 (tp30) cc_final: 0.6522 (tm-30) REVERT: B 1076 ASP cc_start: 0.8412 (m-30) cc_final: 0.8204 (m-30) REVERT: B 1181 LYS cc_start: 0.8799 (tppt) cc_final: 0.8291 (tppt) REVERT: B 1182 LEU cc_start: 0.8117 (mp) cc_final: 0.7875 (mp) REVERT: B 1249 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 1254 GLU cc_start: 0.8508 (tt0) cc_final: 0.8007 (tt0) REVERT: B 1258 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8554 (mtmm) REVERT: B 1261 GLN cc_start: 0.8781 (tt0) cc_final: 0.8278 (tp40) REVERT: B 1282 ASP cc_start: 0.8156 (m-30) cc_final: 0.7920 (m-30) REVERT: B 1285 LYS cc_start: 0.9131 (ptmt) cc_final: 0.8856 (tttm) REVERT: B 1291 GLU cc_start: 0.7609 (tp30) cc_final: 0.6816 (tp30) REVERT: B 1295 LEU cc_start: 0.7904 (pp) cc_final: 0.7241 (pp) REVERT: B 1297 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7769 (mtp-110) REVERT: B 1300 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 1303 GLU cc_start: 0.8306 (pt0) cc_final: 0.7374 (pp20) REVERT: B 1310 SER cc_start: 0.8370 (p) cc_final: 0.8155 (t) REVERT: B 1324 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8735 (mtmt) REVERT: B 1330 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 1333 GLU cc_start: 0.8181 (tt0) cc_final: 0.7551 (pp20) REVERT: B 1358 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 1362 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7685 (mtmt) REVERT: B 1367 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8041 (tpp80) REVERT: B 1392 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 1400 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8370 (mtmm) REVERT: B 1418 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8133 (ptpp) REVERT: B 1431 THR cc_start: 0.8737 (m) cc_final: 0.8532 (t) REVERT: B 1457 ILE cc_start: 0.8994 (pt) cc_final: 0.8661 (mm) REVERT: B 1467 LYS cc_start: 0.8053 (mttt) cc_final: 0.7841 (mmmm) REVERT: B 1478 SER cc_start: 0.8756 (m) cc_final: 0.8442 (p) REVERT: B 1480 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8541 (mtpp) REVERT: B 1496 TYR cc_start: 0.8877 (t80) cc_final: 0.8386 (t80) REVERT: B 1497 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7107 (tm-30) REVERT: B 1504 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 1516 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7798 (mm-30) REVERT: B 1538 LYS cc_start: 0.8811 (pptt) cc_final: 0.8254 (ptmm) REVERT: B 1542 GLU cc_start: 0.7999 (tp30) cc_final: 0.7680 (tp30) REVERT: B 1543 VAL cc_start: 0.9190 (t) cc_final: 0.8946 (p) REVERT: B 1544 GLU cc_start: 0.8480 (pt0) cc_final: 0.7532 (pt0) REVERT: B 1549 GLN cc_start: 0.8667 (tt0) cc_final: 0.8115 (tm-30) REVERT: B 1556 GLU cc_start: 0.7820 (mp0) cc_final: 0.7516 (mp0) REVERT: B 1577 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7565 (ptp-170) REVERT: B 1585 GLN cc_start: 0.7020 (pp30) cc_final: 0.6434 (pp30) REVERT: B 1587 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8290 (ttpp) REVERT: B 1588 GLU cc_start: 0.8245 (pm20) cc_final: 0.7886 (pm20) REVERT: B 1590 GLU cc_start: 0.8438 (mp0) cc_final: 0.8101 (mp0) REVERT: B 1593 ASN cc_start: 0.8159 (t0) cc_final: 0.7926 (t0) REVERT: B 1627 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 1634 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 1638 ASP cc_start: 0.8116 (t0) cc_final: 0.7606 (t0) REVERT: B 1651 ILE cc_start: 0.9073 (mt) cc_final: 0.8841 (mt) REVERT: B 1653 LYS cc_start: 0.9091 (tttt) cc_final: 0.8647 (ttmm) REVERT: B 1654 TYR cc_start: 0.8720 (m-80) cc_final: 0.8406 (m-10) REVERT: B 1655 GLN cc_start: 0.8892 (mt0) cc_final: 0.8601 (mm-40) REVERT: B 1667 GLU cc_start: 0.8229 (tp30) cc_final: 0.7616 (tp30) REVERT: B 1677 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 1678 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8205 (mp10) REVERT: B 1683 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 1704 ASP cc_start: 0.7060 (p0) cc_final: 0.5833 (p0) REVERT: B 1708 ARG cc_start: 0.8513 (mpt-90) cc_final: 0.8091 (mtm-85) REVERT: B 1719 GLU cc_start: 0.7539 (pm20) cc_final: 0.7332 (pm20) REVERT: B 1737 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9079 (tptp) REVERT: B 1741 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 1757 LYS cc_start: 0.8874 (tttp) cc_final: 0.8431 (ttpp) REVERT: B 1759 SER cc_start: 0.9118 (p) cc_final: 0.8720 (p) REVERT: B 1760 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7285 (tm-30) REVERT: B 1762 LYS cc_start: 0.8893 (mttp) cc_final: 0.8185 (mttp) REVERT: B 1764 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8119 (mmmm) REVERT: B 1767 MET cc_start: 0.7610 (ppp) cc_final: 0.7293 (ppp) REVERT: B 1772 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8365 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8149 (t0) cc_final: 0.7870 (t0) REVERT: B 1780 GLU cc_start: 0.7487 (tp30) cc_final: 0.7129 (tp30) REVERT: B 1786 THR cc_start: 0.8911 (p) cc_final: 0.8488 (t) REVERT: B 1789 LYS cc_start: 0.8950 (tppp) cc_final: 0.8623 (tppp) REVERT: B 1792 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8308 (tppt) REVERT: B 1818 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8585 (tppt) REVERT: B 1820 ILE cc_start: 0.8452 (mt) cc_final: 0.8171 (tp) REVERT: B 1824 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 1833 GLU cc_start: 0.8169 (tp30) cc_final: 0.7229 (tp30) REVERT: B 1840 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8334 (mtm-85) REVERT: B 1848 LEU cc_start: 0.9127 (tp) cc_final: 0.8759 (tt) REVERT: B 1853 ARG cc_start: 0.8543 (mmt90) cc_final: 0.8142 (tpp80) REVERT: B 1857 GLU cc_start: 0.8067 (pp20) cc_final: 0.7859 (pp20) REVERT: B 1858 LEU cc_start: 0.8778 (mt) cc_final: 0.8563 (mt) REVERT: B 1865 ASP cc_start: 0.8006 (m-30) cc_final: 0.7773 (m-30) REVERT: B 1871 ARG cc_start: 0.8304 (ptt90) cc_final: 0.7777 (ptt90) REVERT: B 1873 GLN cc_start: 0.8789 (tp40) cc_final: 0.8422 (tm-30) REVERT: B 1878 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7926 (mmmt) REVERT: B 1882 LYS cc_start: 0.9200 (tttp) cc_final: 0.8618 (tmtt) REVERT: B 1887 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8490 (ttmm) REVERT: B 1889 GLN cc_start: 0.8689 (mt0) cc_final: 0.8200 (tp40) REVERT: B 1892 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 1903 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8667 (mmtt) REVERT: B 1906 LYS cc_start: 0.9142 (tppt) cc_final: 0.8811 (tppt) REVERT: B 1908 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8057 (tp-100) REVERT: B 1910 GLU cc_start: 0.8200 (pp20) cc_final: 0.7987 (pp20) REVERT: B 1915 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 1917 ARG cc_start: 0.8983 (mtp-110) cc_final: 0.8498 (ttp-110) REVERT: A 924 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6615 (tp30) REVERT: A 952 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 1009 GLU cc_start: 0.7435 (pm20) cc_final: 0.6872 (pm20) REVERT: A 1022 GLU cc_start: 0.7573 (pt0) cc_final: 0.7337 (mt-10) REVERT: A 1072 GLU cc_start: 0.8137 (pp20) cc_final: 0.7647 (tm-30) REVERT: A 1094 GLU cc_start: 0.7931 (pt0) cc_final: 0.7717 (mt-10) REVERT: A 1127 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7722 (tp30) REVERT: A 1174 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8217 (mtmm) REVERT: A 1179 MET cc_start: 0.7331 (ppp) cc_final: 0.6842 (ppp) REVERT: A 1200 LEU cc_start: 0.7315 (mt) cc_final: 0.7061 (mt) REVERT: A 1202 LYS cc_start: 0.9013 (pptt) cc_final: 0.8678 (pptt) REVERT: A 1215 ILE cc_start: 0.7965 (pt) cc_final: 0.7675 (pt) REVERT: A 1246 MET cc_start: 0.7591 (ppp) cc_final: 0.6847 (ppp) REVERT: A 1250 LYS cc_start: 0.8585 (pttp) cc_final: 0.8317 (ptmm) REVERT: A 1254 GLU cc_start: 0.8640 (pt0) cc_final: 0.8367 (pp20) REVERT: A 1258 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8563 (mmtp) REVERT: A 1270 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8521 (ttmm) REVERT: A 1276 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7664 (ttm-80) REVERT: A 1283 SER cc_start: 0.8473 (m) cc_final: 0.8251 (p) REVERT: A 1288 LEU cc_start: 0.8848 (mt) cc_final: 0.8635 (mm) REVERT: A 1297 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8382 (ttm-80) REVERT: A 1298 GLN cc_start: 0.8988 (mt0) cc_final: 0.8656 (mm-40) REVERT: A 1299 LEU cc_start: 0.8341 (mt) cc_final: 0.7883 (tp) REVERT: A 1321 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 1329 GLU cc_start: 0.8395 (tp30) cc_final: 0.7927 (tp30) REVERT: A 1330 GLU cc_start: 0.8224 (tt0) cc_final: 0.7969 (mm-30) REVERT: A 1333 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 1344 LEU cc_start: 0.8303 (tp) cc_final: 0.8033 (tp) REVERT: A 1351 ILE cc_start: 0.8929 (pt) cc_final: 0.8694 (pt) REVERT: A 1352 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8220 (ttp-110) REVERT: A 1353 GLU cc_start: 0.7949 (mp0) cc_final: 0.7646 (mp0) REVERT: A 1356 GLU cc_start: 0.8627 (tp30) cc_final: 0.8110 (tp30) REVERT: A 1357 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 1358 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 1360 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 1371 LYS cc_start: 0.8467 (ptmm) cc_final: 0.8256 (ptmm) REVERT: A 1379 TRP cc_start: 0.7297 (m100) cc_final: 0.6824 (m100) REVERT: A 1386 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6384 (mp0) REVERT: A 1392 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1413 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7335 (mp0) REVERT: A 1417 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8065 (mm-40) REVERT: A 1423 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 1426 LYS cc_start: 0.9207 (tttm) cc_final: 0.8978 (ttpp) REVERT: A 1427 GLN cc_start: 0.8090 (pp30) cc_final: 0.7619 (pp30) REVERT: A 1434 GLU cc_start: 0.8227 (mp0) cc_final: 0.7869 (mp0) REVERT: A 1442 ARG cc_start: 0.8271 (ptm160) cc_final: 0.7982 (tmm-80) REVERT: A 1448 ASN cc_start: 0.8241 (t0) cc_final: 0.7809 (t0) REVERT: A 1451 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 1452 LYS cc_start: 0.9241 (mmmm) cc_final: 0.9009 (tppt) REVERT: A 1457 ILE cc_start: 0.8353 (mm) cc_final: 0.7887 (mm) REVERT: A 1458 ASP cc_start: 0.7947 (p0) cc_final: 0.7233 (p0) REVERT: A 1463 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 1467 LYS cc_start: 0.8052 (mttm) cc_final: 0.7696 (ttmm) REVERT: A 1480 LYS cc_start: 0.8826 (tttp) cc_final: 0.8519 (tttp) REVERT: A 1488 GLU cc_start: 0.7138 (tp30) cc_final: 0.6291 (tp30) REVERT: A 1489 LEU cc_start: 0.8758 (tt) cc_final: 0.8444 (tp) REVERT: A 1492 LEU cc_start: 0.8517 (mt) cc_final: 0.7917 (mm) REVERT: A 1501 GLU cc_start: 0.8637 (pt0) cc_final: 0.8369 (pt0) REVERT: A 1511 LYS cc_start: 0.8929 (mmpt) cc_final: 0.8516 (mmmm) REVERT: A 1542 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 1548 LEU cc_start: 0.8820 (tp) cc_final: 0.8427 (tt) REVERT: A 1554 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 1559 LEU cc_start: 0.8537 (tp) cc_final: 0.8141 (tp) REVERT: A 1560 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 1561 GLN cc_start: 0.7751 (pp30) cc_final: 0.7357 (pp30) REVERT: A 1563 GLU cc_start: 0.8283 (tp30) cc_final: 0.7896 (tp30) REVERT: A 1565 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8488 (mttp) REVERT: A 1567 LEU cc_start: 0.9054 (mt) cc_final: 0.8810 (mm) REVERT: A 1570 GLN cc_start: 0.8319 (mt0) cc_final: 0.8065 (mm-40) REVERT: A 1572 GLU cc_start: 0.7772 (tp30) cc_final: 0.7117 (tp30) REVERT: A 1605 MET cc_start: 0.8665 (mmp) cc_final: 0.8443 (mmp) REVERT: A 1618 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 1623 LYS cc_start: 0.8609 (tppt) cc_final: 0.8177 (tppt) REVERT: A 1625 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8639 (mtpp) REVERT: A 1637 LEU cc_start: 0.8706 (mp) cc_final: 0.8403 (tt) REVERT: A 1642 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8032 (mtpp) REVERT: A 1649 LYS cc_start: 0.9134 (tttp) cc_final: 0.8642 (ttmm) REVERT: A 1660 ASP cc_start: 0.8344 (p0) cc_final: 0.8031 (p0) REVERT: A 1662 GLN cc_start: 0.8722 (tt0) cc_final: 0.8073 (tp40) REVERT: A 1687 ASN cc_start: 0.8209 (p0) cc_final: 0.7651 (t0) REVERT: A 1692 GLU cc_start: 0.8126 (tp30) cc_final: 0.7917 (tp30) REVERT: A 1712 GLN cc_start: 0.8819 (mm110) cc_final: 0.8510 (mm-40) REVERT: A 1741 GLU cc_start: 0.8256 (tp30) cc_final: 0.8020 (tp30) REVERT: A 1754 ASN cc_start: 0.8446 (t0) cc_final: 0.8239 (t0) REVERT: A 1757 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8587 (ttmt) REVERT: A 1758 ASN cc_start: 0.8497 (t0) cc_final: 0.8132 (t0) REVERT: A 1762 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9124 (ttmt) REVERT: A 1778 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.7930 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8090 (t0) cc_final: 0.7858 (t0) REVERT: A 1783 HIS cc_start: 0.9125 (t-90) cc_final: 0.8924 (t-170) REVERT: A 1792 LYS cc_start: 0.9397 (ttmt) cc_final: 0.9020 (ttmm) REVERT: A 1794 LEU cc_start: 0.8779 (mt) cc_final: 0.8569 (mm) REVERT: A 1818 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8228 (mmmm) REVERT: A 1822 LYS cc_start: 0.8619 (tttm) cc_final: 0.8292 (ttpp) REVERT: A 1824 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 1825 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 1828 ARG cc_start: 0.8425 (ptt-90) cc_final: 0.8077 (ptt-90) REVERT: A 1839 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8469 (ttt180) REVERT: A 1840 ARG cc_start: 0.8116 (mpp80) cc_final: 0.7781 (mtm110) REVERT: A 1846 LYS cc_start: 0.9193 (tttm) cc_final: 0.8915 (ttmm) REVERT: A 1849 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8103 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8354 (ptmt) REVERT: A 1853 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7780 (ttm110) REVERT: A 1858 LEU cc_start: 0.8556 (mp) cc_final: 0.8319 (mm) REVERT: A 1864 GLU cc_start: 0.7947 (tp30) cc_final: 0.6952 (tp30) REVERT: A 1865 ASP cc_start: 0.8055 (t0) cc_final: 0.7675 (t0) REVERT: A 1868 ASN cc_start: 0.8653 (m110) cc_final: 0.7540 (m-40) REVERT: A 1878 LYS cc_start: 0.9045 (tppt) cc_final: 0.8782 (tppp) REVERT: A 1889 GLN cc_start: 0.7582 (pp30) cc_final: 0.7364 (pp30) REVERT: A 1892 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 1894 GLU cc_start: 0.7118 (pp20) cc_final: 0.6785 (pp20) REVERT: A 1909 GLN cc_start: 0.8668 (tp40) cc_final: 0.8282 (tm-30) REVERT: A 1910 GLU cc_start: 0.8524 (tt0) cc_final: 0.7974 (tt0) REVERT: A 1915 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7547 (tm-30) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.3279 time to fit residues: 320.8270 Evaluate side-chains 621 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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: 0.9980 chunk 123 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** B1204 HIS B1838 GLN B1900 ASN ** A1523 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: 0.7393 moved from start: 1.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17454 Z= 0.160 Angle : 0.620 9.485 23282 Z= 0.334 Chirality : 0.040 0.160 2582 Planarity : 0.003 0.051 3158 Dihedral : 4.223 17.069 2318 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 2.88 (0.18), residues: 2150 helix: 1.94 (0.11), residues: 2108 sheet: None (None), residues: 0 loop : 1.33 (0.88), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B1379 HIS 0.013 0.001 HIS B1598 PHE 0.025 0.002 PHE A 945 TYR 0.020 0.002 TYR A1383 ARG 0.013 0.001 ARG A1332 *********************** 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 665 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 2.116 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: B 966 GLU cc_start: 0.7497 (tp30) cc_final: 0.6701 (tm-30) REVERT: B 987 ASN cc_start: 0.7009 (t0) cc_final: 0.6804 (t0) REVERT: B 1181 LYS cc_start: 0.8776 (tppt) cc_final: 0.8212 (tppt) REVERT: B 1182 LEU cc_start: 0.8178 (mp) cc_final: 0.7858 (mp) REVERT: B 1224 LYS cc_start: 0.8019 (tppp) cc_final: 0.7443 (tppp) REVERT: B 1246 MET cc_start: 0.8056 (ttp) cc_final: 0.7807 (ttp) REVERT: B 1249 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 1261 GLN cc_start: 0.8800 (tt0) cc_final: 0.8005 (tm-30) REVERT: B 1268 GLN cc_start: 0.8615 (tt0) cc_final: 0.8275 (tp40) REVERT: B 1271 LEU cc_start: 0.9109 (mm) cc_final: 0.8894 (tt) REVERT: B 1282 ASP cc_start: 0.8226 (m-30) cc_final: 0.7731 (t0) REVERT: B 1285 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8906 (tttm) REVERT: B 1286 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8795 (mtmt) REVERT: B 1291 GLU cc_start: 0.7630 (tp30) cc_final: 0.6876 (tp30) REVERT: B 1295 LEU cc_start: 0.7888 (pp) cc_final: 0.7457 (pp) REVERT: B 1301 GLU cc_start: 0.8407 (pp20) cc_final: 0.7478 (pp20) REVERT: B 1303 GLU cc_start: 0.8250 (pt0) cc_final: 0.7460 (pp20) REVERT: B 1312 ILE cc_start: 0.8265 (pt) cc_final: 0.8061 (tt) REVERT: B 1330 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8034 (mm-30) REVERT: B 1333 GLU cc_start: 0.8041 (tt0) cc_final: 0.7451 (pp20) REVERT: B 1353 GLU cc_start: 0.7664 (pm20) cc_final: 0.7389 (pm20) REVERT: B 1357 GLU cc_start: 0.8077 (tp30) cc_final: 0.7844 (tp30) REVERT: B 1358 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 1362 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7539 (mtmt) REVERT: B 1367 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7958 (tpp80) REVERT: B 1379 TRP cc_start: 0.6038 (t60) cc_final: 0.5506 (t60) REVERT: B 1392 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 1400 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8370 (mtmm) REVERT: B 1409 GLU cc_start: 0.7710 (pt0) cc_final: 0.7428 (pt0) REVERT: B 1418 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8153 (ptpp) REVERT: B 1457 ILE cc_start: 0.8997 (pt) cc_final: 0.8656 (mm) REVERT: B 1458 ASP cc_start: 0.7591 (t0) cc_final: 0.7253 (t0) REVERT: B 1478 SER cc_start: 0.8744 (m) cc_final: 0.8445 (p) REVERT: B 1496 TYR cc_start: 0.8888 (t80) cc_final: 0.8286 (t80) REVERT: B 1497 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7060 (tm-30) REVERT: B 1504 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 1516 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 1538 LYS cc_start: 0.8773 (pptt) cc_final: 0.8263 (ptmm) REVERT: B 1542 GLU cc_start: 0.8023 (tp30) cc_final: 0.7669 (tp30) REVERT: B 1549 GLN cc_start: 0.8707 (tt0) cc_final: 0.8260 (tm-30) REVERT: B 1556 GLU cc_start: 0.7908 (mp0) cc_final: 0.7494 (mp0) REVERT: B 1560 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8278 (tp30) REVERT: B 1562 GLU cc_start: 0.8115 (tt0) cc_final: 0.7846 (tt0) REVERT: B 1571 LEU cc_start: 0.8693 (mt) cc_final: 0.6809 (mt) REVERT: B 1590 GLU cc_start: 0.8413 (mp0) cc_final: 0.8209 (mp0) REVERT: B 1614 LYS cc_start: 0.8876 (tttt) cc_final: 0.8549 (tttt) REVERT: B 1627 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 1634 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 1638 ASP cc_start: 0.8121 (t0) cc_final: 0.7610 (t0) REVERT: B 1651 ILE cc_start: 0.9061 (mt) cc_final: 0.8842 (mt) REVERT: B 1653 LYS cc_start: 0.9128 (tttt) cc_final: 0.8690 (ttmm) REVERT: B 1667 GLU cc_start: 0.8287 (tp30) cc_final: 0.7680 (tp30) REVERT: B 1677 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 1678 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8203 (mp10) REVERT: B 1683 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 1694 GLU cc_start: 0.8211 (tt0) cc_final: 0.7742 (tt0) REVERT: B 1708 ARG cc_start: 0.8505 (mpt-90) cc_final: 0.8248 (mtm-85) REVERT: B 1713 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 1719 GLU cc_start: 0.7575 (pm20) cc_final: 0.7312 (pm20) REVERT: B 1737 LYS cc_start: 0.9350 (tmtt) cc_final: 0.9058 (tptp) REVERT: B 1741 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 1757 LYS cc_start: 0.8869 (tttp) cc_final: 0.8638 (tttp) REVERT: B 1759 SER cc_start: 0.9121 (p) cc_final: 0.8676 (p) REVERT: B 1760 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 1762 LYS cc_start: 0.8858 (mttp) cc_final: 0.8129 (mttp) REVERT: B 1764 LYS cc_start: 0.8614 (mmmt) cc_final: 0.7977 (mmmm) REVERT: B 1767 MET cc_start: 0.7515 (ppp) cc_final: 0.7153 (ppp) REVERT: B 1772 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8271 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8128 (t0) cc_final: 0.7866 (t0) REVERT: B 1780 GLU cc_start: 0.7497 (tp30) cc_final: 0.7068 (tp30) REVERT: B 1786 THR cc_start: 0.8920 (p) cc_final: 0.8495 (t) REVERT: B 1789 LYS cc_start: 0.8945 (tppp) cc_final: 0.8643 (tppp) REVERT: B 1792 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8274 (tppt) REVERT: B 1818 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8547 (tppt) REVERT: B 1820 ILE cc_start: 0.8386 (mt) cc_final: 0.8102 (tp) REVERT: B 1824 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 1833 GLU cc_start: 0.8192 (tp30) cc_final: 0.7276 (tp30) REVERT: B 1840 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8357 (mtm-85) REVERT: B 1848 LEU cc_start: 0.9145 (tp) cc_final: 0.8826 (tt) REVERT: B 1853 ARG cc_start: 0.8543 (mmt90) cc_final: 0.8164 (tpp80) REVERT: B 1857 GLU cc_start: 0.8062 (pp20) cc_final: 0.7766 (pp20) REVERT: B 1865 ASP cc_start: 0.7983 (m-30) cc_final: 0.7718 (m-30) REVERT: B 1871 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7961 (ptt90) REVERT: B 1873 GLN cc_start: 0.8767 (tp40) cc_final: 0.8416 (tm-30) REVERT: B 1878 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7944 (mmmt) REVERT: B 1882 LYS cc_start: 0.9201 (tttp) cc_final: 0.8642 (tmtt) REVERT: B 1887 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8540 (tppt) REVERT: B 1889 GLN cc_start: 0.8701 (mt0) cc_final: 0.8253 (tp40) REVERT: B 1900 ASN cc_start: 0.7822 (t160) cc_final: 0.7618 (t0) REVERT: B 1903 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8653 (mmtt) REVERT: B 1906 LYS cc_start: 0.9139 (tppt) cc_final: 0.8761 (tppt) REVERT: B 1908 GLN cc_start: 0.8688 (tp-100) cc_final: 0.7957 (tp-100) REVERT: B 1910 GLU cc_start: 0.8196 (pp20) cc_final: 0.7981 (pp20) REVERT: B 1911 LEU cc_start: 0.8726 (tt) cc_final: 0.7981 (tt) REVERT: B 1915 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 1917 ARG cc_start: 0.8981 (mtp-110) cc_final: 0.8516 (ttm-80) REVERT: A 961 ASP cc_start: 0.6876 (t0) cc_final: 0.6650 (m-30) REVERT: A 1072 GLU cc_start: 0.8176 (pp20) cc_final: 0.7777 (tm-30) REVERT: A 1174 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8035 (mttp) REVERT: A 1176 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7002 (mm-30) REVERT: A 1179 MET cc_start: 0.7315 (ppp) cc_final: 0.6841 (ppp) REVERT: A 1188 GLU cc_start: 0.7171 (tp30) cc_final: 0.6650 (tp30) REVERT: A 1200 LEU cc_start: 0.7369 (mt) cc_final: 0.7141 (mt) REVERT: A 1202 LYS cc_start: 0.8959 (pptt) cc_final: 0.8650 (pptt) REVERT: A 1204 HIS cc_start: 0.6751 (t70) cc_final: 0.6490 (t70) REVERT: A 1215 ILE cc_start: 0.8062 (pt) cc_final: 0.7663 (pt) REVERT: A 1258 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8060 (mmmm) REVERT: A 1270 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8469 (ttmm) REVERT: A 1273 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 1276 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7463 (ttm-80) REVERT: A 1283 SER cc_start: 0.8509 (m) cc_final: 0.8295 (p) REVERT: A 1288 LEU cc_start: 0.8884 (mt) cc_final: 0.8645 (mm) REVERT: A 1297 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8422 (ttp-110) REVERT: A 1298 GLN cc_start: 0.8952 (mt0) cc_final: 0.8701 (mm110) REVERT: A 1299 LEU cc_start: 0.8170 (mt) cc_final: 0.7954 (tp) REVERT: A 1300 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8132 (tp30) REVERT: A 1329 GLU cc_start: 0.8175 (tp30) cc_final: 0.7579 (tp30) REVERT: A 1330 GLU cc_start: 0.8256 (tt0) cc_final: 0.7985 (mm-30) REVERT: A 1332 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8262 (mtm110) REVERT: A 1333 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 1344 LEU cc_start: 0.8307 (tp) cc_final: 0.8051 (tp) REVERT: A 1351 ILE cc_start: 0.8911 (pt) cc_final: 0.8694 (pt) REVERT: A 1352 ARG cc_start: 0.8605 (ttm170) cc_final: 0.8183 (ttp-110) REVERT: A 1353 GLU cc_start: 0.8009 (mp0) cc_final: 0.7663 (mp0) REVERT: A 1356 GLU cc_start: 0.8622 (tp30) cc_final: 0.8143 (tp30) REVERT: A 1357 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8167 (mm-30) REVERT: A 1358 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 1360 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6905 (tm-30) REVERT: A 1362 LYS cc_start: 0.8285 (ptmm) cc_final: 0.7807 (tttm) REVERT: A 1392 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1407 GLU cc_start: 0.7693 (pp20) cc_final: 0.7390 (pp20) REVERT: A 1409 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6840 (tm-30) REVERT: A 1417 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8099 (mm-40) REVERT: A 1426 LYS cc_start: 0.9152 (tttm) cc_final: 0.8900 (ttpp) REVERT: A 1427 GLN cc_start: 0.7982 (pp30) cc_final: 0.7484 (pp30) REVERT: A 1434 GLU cc_start: 0.8050 (mp0) cc_final: 0.7678 (mp0) REVERT: A 1448 ASN cc_start: 0.8225 (t0) cc_final: 0.7928 (t0) REVERT: A 1451 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7740 (mt-10) REVERT: A 1452 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8898 (tppt) REVERT: A 1457 ILE cc_start: 0.8326 (mm) cc_final: 0.7820 (mm) REVERT: A 1458 ASP cc_start: 0.7942 (p0) cc_final: 0.6969 (p0) REVERT: A 1463 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 1467 LYS cc_start: 0.8043 (mttm) cc_final: 0.7643 (ttmm) REVERT: A 1480 LYS cc_start: 0.8799 (tttp) cc_final: 0.8498 (tttp) REVERT: A 1481 GLU cc_start: 0.7286 (tp30) cc_final: 0.6629 (tp30) REVERT: A 1488 GLU cc_start: 0.6878 (tp30) cc_final: 0.6607 (tp30) REVERT: A 1501 GLU cc_start: 0.8573 (pt0) cc_final: 0.8294 (pt0) REVERT: A 1504 GLU cc_start: 0.7972 (pp20) cc_final: 0.7758 (pp20) REVERT: A 1511 LYS cc_start: 0.8879 (mmpt) cc_final: 0.8491 (mmmm) REVERT: A 1516 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 1537 GLN cc_start: 0.8684 (pp30) cc_final: 0.8376 (pp30) REVERT: A 1542 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7117 (tm-30) REVERT: A 1548 LEU cc_start: 0.8699 (tp) cc_final: 0.8410 (tt) REVERT: A 1561 GLN cc_start: 0.7937 (pp30) cc_final: 0.7314 (pp30) REVERT: A 1563 GLU cc_start: 0.8235 (tp30) cc_final: 0.7884 (tp30) REVERT: A 1565 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8416 (mttp) REVERT: A 1567 LEU cc_start: 0.9005 (mt) cc_final: 0.8738 (mm) REVERT: A 1570 GLN cc_start: 0.8222 (mt0) cc_final: 0.7981 (mm-40) REVERT: A 1572 GLU cc_start: 0.7791 (tp30) cc_final: 0.7227 (tp30) REVERT: A 1590 GLU cc_start: 0.8414 (tt0) cc_final: 0.8212 (tt0) REVERT: A 1614 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8814 (mmmm) REVERT: A 1618 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 1622 MET cc_start: 0.7798 (mtp) cc_final: 0.7451 (mtp) REVERT: A 1623 LYS cc_start: 0.8571 (tppt) cc_final: 0.8131 (tppt) REVERT: A 1642 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8151 (ttmm) REVERT: A 1649 LYS cc_start: 0.9158 (tttp) cc_final: 0.8704 (ttmm) REVERT: A 1659 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8444 (ttmm) REVERT: A 1660 ASP cc_start: 0.8326 (p0) cc_final: 0.8074 (p0) REVERT: A 1662 GLN cc_start: 0.8676 (tt0) cc_final: 0.8132 (tp40) REVERT: A 1679 LEU cc_start: 0.8888 (tp) cc_final: 0.8318 (tp) REVERT: A 1681 ILE cc_start: 0.8276 (tt) cc_final: 0.8033 (tt) REVERT: A 1683 GLU cc_start: 0.7603 (pp20) cc_final: 0.7140 (pp20) REVERT: A 1687 ASN cc_start: 0.8155 (p0) cc_final: 0.7603 (t0) REVERT: A 1695 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 1712 GLN cc_start: 0.8801 (mm110) cc_final: 0.8509 (mm-40) REVERT: A 1741 GLU cc_start: 0.8220 (tp30) cc_final: 0.8001 (tp30) REVERT: A 1746 HIS cc_start: 0.8774 (t70) cc_final: 0.8564 (t70) REVERT: A 1754 ASN cc_start: 0.8436 (t0) cc_final: 0.8200 (t0) REVERT: A 1757 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8551 (ttmt) REVERT: A 1758 ASN cc_start: 0.8484 (t0) cc_final: 0.8135 (t0) REVERT: A 1762 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9089 (ttmt) REVERT: A 1776 GLU cc_start: 0.7893 (tp30) cc_final: 0.7500 (tp30) REVERT: A 1778 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8047 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8010 (t0) cc_final: 0.7808 (t0) REVERT: A 1783 HIS cc_start: 0.9185 (t-90) cc_final: 0.8981 (t-170) REVERT: A 1792 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9017 (ttmm) REVERT: A 1794 LEU cc_start: 0.8760 (mt) cc_final: 0.8521 (mm) REVERT: A 1797 GLN cc_start: 0.8497 (tp-100) cc_final: 0.7839 (tp-100) REVERT: A 1818 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8234 (mmmm) REVERT: A 1822 LYS cc_start: 0.8565 (tttm) cc_final: 0.8282 (ttpp) REVERT: A 1824 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 1825 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 1828 ARG cc_start: 0.8399 (ptt-90) cc_final: 0.8024 (ptt-90) REVERT: A 1840 ARG cc_start: 0.8070 (mpp80) cc_final: 0.7691 (mtm110) REVERT: A 1846 LYS cc_start: 0.9196 (tttm) cc_final: 0.8920 (ttmm) REVERT: A 1850 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8237 (ptmt) REVERT: A 1853 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.7758 (ttm110) REVERT: A 1858 LEU cc_start: 0.8523 (mp) cc_final: 0.8311 (mm) REVERT: A 1864 GLU cc_start: 0.7932 (tp30) cc_final: 0.6995 (tp30) REVERT: A 1865 ASP cc_start: 0.7999 (t0) cc_final: 0.7611 (t0) REVERT: A 1868 ASN cc_start: 0.8539 (m110) cc_final: 0.7501 (m-40) REVERT: A 1870 GLU cc_start: 0.8016 (tp30) cc_final: 0.7282 (tp30) REVERT: A 1878 LYS cc_start: 0.9009 (tppt) cc_final: 0.8772 (mmmm) REVERT: A 1882 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8923 (ttmm) REVERT: A 1884 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8802 (ttpp) REVERT: A 1888 ARG cc_start: 0.7778 (ttp80) cc_final: 0.6833 (ttp80) REVERT: A 1889 GLN cc_start: 0.7660 (pp30) cc_final: 0.7107 (pp30) REVERT: A 1892 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 1894 GLU cc_start: 0.7078 (pp20) cc_final: 0.6732 (pp20) REVERT: A 1909 GLN cc_start: 0.8650 (tp40) cc_final: 0.8348 (tm-30) REVERT: A 1910 GLU cc_start: 0.8497 (tt0) cc_final: 0.8060 (tt0) REVERT: A 1915 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.3390 time to fit residues: 319.8768 Evaluate side-chains 624 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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: 0.8980 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 173 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 993 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1838 GLN B1900 ASN A1261 GLN A1523 GLN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1881 GLN A1900 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 1.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17454 Z= 0.159 Angle : 0.625 8.848 23282 Z= 0.336 Chirality : 0.040 0.181 2582 Planarity : 0.003 0.055 3158 Dihedral : 4.220 16.733 2318 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % 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: 2.96 (0.18), residues: 2150 helix: 1.99 (0.11), residues: 2112 sheet: None (None), residues: 0 loop : 0.99 (0.99), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP B1379 HIS 0.012 0.001 HIS B1598 PHE 0.020 0.002 PHE A1860 TYR 0.013 0.002 TYR A1496 ARG 0.013 0.001 ARG A1332 *********************** 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 660 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 659 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1181 LYS cc_start: 0.8825 (tppt) cc_final: 0.8271 (tppt) REVERT: B 1182 LEU cc_start: 0.8218 (mp) cc_final: 0.7944 (mp) REVERT: B 1224 LYS cc_start: 0.8046 (tppp) cc_final: 0.7635 (tppp) REVERT: B 1246 MET cc_start: 0.8019 (ttp) cc_final: 0.7552 (ttp) REVERT: B 1249 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 1254 GLU cc_start: 0.8446 (tt0) cc_final: 0.8186 (tt0) REVERT: B 1261 GLN cc_start: 0.8819 (tt0) cc_final: 0.7943 (tm-30) REVERT: B 1268 GLN cc_start: 0.8674 (tt0) cc_final: 0.8345 (tp40) REVERT: B 1282 ASP cc_start: 0.8206 (m-30) cc_final: 0.7660 (t70) REVERT: B 1285 LYS cc_start: 0.9148 (ptmt) cc_final: 0.8906 (tttm) REVERT: B 1286 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8870 (mtmt) REVERT: B 1303 GLU cc_start: 0.8260 (pt0) cc_final: 0.7431 (pp20) REVERT: B 1325 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8068 (mtp-110) REVERT: B 1333 GLU cc_start: 0.8328 (tt0) cc_final: 0.7908 (pp20) REVERT: B 1347 ASP cc_start: 0.7824 (p0) cc_final: 0.7597 (p0) REVERT: B 1357 GLU cc_start: 0.8079 (tp30) cc_final: 0.7866 (tp30) REVERT: B 1358 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 1362 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7672 (mtmt) REVERT: B 1367 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7902 (tpp80) REVERT: B 1386 GLU cc_start: 0.7066 (tp30) cc_final: 0.6732 (mm-30) REVERT: B 1392 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7309 (mm-30) REVERT: B 1400 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8391 (mtmm) REVERT: B 1402 GLN cc_start: 0.8581 (mt0) cc_final: 0.8371 (mt0) REVERT: B 1418 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8240 (ptpp) REVERT: B 1439 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7930 (mm-30) REVERT: B 1457 ILE cc_start: 0.8972 (pt) cc_final: 0.8693 (mm) REVERT: B 1460 ILE cc_start: 0.8487 (tt) cc_final: 0.8202 (tt) REVERT: B 1478 SER cc_start: 0.8759 (m) cc_final: 0.8434 (p) REVERT: B 1496 TYR cc_start: 0.8863 (t80) cc_final: 0.8615 (t80) REVERT: B 1497 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 1498 GLU cc_start: 0.7989 (pp20) cc_final: 0.7646 (pp20) REVERT: B 1504 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 1516 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 1529 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7805 (ttt-90) REVERT: B 1542 GLU cc_start: 0.8191 (tp30) cc_final: 0.7885 (tp30) REVERT: B 1544 GLU cc_start: 0.8400 (pt0) cc_final: 0.8089 (pt0) REVERT: B 1549 GLN cc_start: 0.8735 (tt0) cc_final: 0.8298 (tm-30) REVERT: B 1556 GLU cc_start: 0.7932 (mp0) cc_final: 0.7511 (mp0) REVERT: B 1577 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7478 (ptp-170) REVERT: B 1582 ARG cc_start: 0.8241 (ptt90) cc_final: 0.7729 (ppt90) REVERT: B 1585 GLN cc_start: 0.7170 (pp30) cc_final: 0.6503 (pp30) REVERT: B 1586 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 1590 GLU cc_start: 0.8391 (mp0) cc_final: 0.8109 (mp0) REVERT: B 1614 LYS cc_start: 0.8853 (tttt) cc_final: 0.8561 (tttt) REVERT: B 1627 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 1633 LEU cc_start: 0.8883 (mm) cc_final: 0.8420 (mm) REVERT: B 1634 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 1638 ASP cc_start: 0.8140 (t0) cc_final: 0.7676 (t0) REVERT: B 1653 LYS cc_start: 0.9167 (tttt) cc_final: 0.8548 (ttmm) REVERT: B 1657 GLN cc_start: 0.7862 (tp40) cc_final: 0.7478 (tp40) REVERT: B 1659 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8141 (ttmm) REVERT: B 1667 GLU cc_start: 0.8257 (tp30) cc_final: 0.7666 (tp30) REVERT: B 1677 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 1678 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8160 (mp10) REVERT: B 1683 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 1694 GLU cc_start: 0.8248 (tt0) cc_final: 0.8035 (tt0) REVERT: B 1708 ARG cc_start: 0.8491 (mpt-90) cc_final: 0.8244 (mtm-85) REVERT: B 1713 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 1719 GLU cc_start: 0.7588 (pm20) cc_final: 0.7302 (pm20) REVERT: B 1737 LYS cc_start: 0.9328 (tmtt) cc_final: 0.9062 (tptp) REVERT: B 1741 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7663 (tm-30) REVERT: B 1759 SER cc_start: 0.9093 (p) cc_final: 0.8670 (p) REVERT: B 1760 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7181 (tm-30) REVERT: B 1762 LYS cc_start: 0.8846 (mttp) cc_final: 0.8154 (mttp) REVERT: B 1772 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8294 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8122 (t0) cc_final: 0.7868 (t0) REVERT: B 1780 GLU cc_start: 0.7427 (tp30) cc_final: 0.7052 (tp30) REVERT: B 1786 THR cc_start: 0.8936 (p) cc_final: 0.8530 (t) REVERT: B 1792 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8186 (tppt) REVERT: B 1818 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8541 (tppt) REVERT: B 1820 ILE cc_start: 0.8390 (mt) cc_final: 0.8113 (tp) REVERT: B 1824 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 1833 GLU cc_start: 0.8199 (tp30) cc_final: 0.7300 (tp30) REVERT: B 1840 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8329 (mtm-85) REVERT: B 1848 LEU cc_start: 0.9150 (tp) cc_final: 0.8836 (tt) REVERT: B 1853 ARG cc_start: 0.8541 (mmt90) cc_final: 0.8162 (tpp80) REVERT: B 1857 GLU cc_start: 0.8046 (pp20) cc_final: 0.7845 (pp20) REVERT: B 1858 LEU cc_start: 0.8742 (mt) cc_final: 0.8528 (mt) REVERT: B 1865 ASP cc_start: 0.7984 (m-30) cc_final: 0.7723 (m-30) REVERT: B 1867 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8584 (mmmm) REVERT: B 1870 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 1871 ARG cc_start: 0.8252 (ptt90) cc_final: 0.7885 (ptt90) REVERT: B 1873 GLN cc_start: 0.8773 (tp40) cc_final: 0.8424 (tm-30) REVERT: B 1878 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7975 (mmmt) REVERT: B 1881 GLN cc_start: 0.8388 (pm20) cc_final: 0.8188 (pm20) REVERT: B 1882 LYS cc_start: 0.9164 (tttp) cc_final: 0.8580 (tmtt) REVERT: B 1889 GLN cc_start: 0.8702 (mt0) cc_final: 0.8167 (tp40) REVERT: B 1903 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8639 (mmtt) REVERT: B 1906 LYS cc_start: 0.9137 (tppt) cc_final: 0.8767 (tppt) REVERT: B 1908 GLN cc_start: 0.8666 (tp-100) cc_final: 0.7932 (tp-100) REVERT: B 1910 GLU cc_start: 0.8194 (pp20) cc_final: 0.7968 (pp20) REVERT: B 1911 LEU cc_start: 0.8731 (tt) cc_final: 0.7994 (tt) REVERT: B 1915 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 1174 LYS cc_start: 0.8712 (mtmm) cc_final: 0.7927 (mttp) REVERT: A 1179 MET cc_start: 0.7341 (ppp) cc_final: 0.7131 (ppp) REVERT: A 1188 GLU cc_start: 0.7202 (tp30) cc_final: 0.6651 (tp30) REVERT: A 1192 GLN cc_start: 0.8004 (pt0) cc_final: 0.7772 (pt0) REVERT: A 1200 LEU cc_start: 0.7512 (mt) cc_final: 0.7264 (mt) REVERT: A 1202 LYS cc_start: 0.9035 (pptt) cc_final: 0.8804 (pptt) REVERT: A 1246 MET cc_start: 0.7723 (ppp) cc_final: 0.6560 (ppp) REVERT: A 1250 LYS cc_start: 0.8665 (tttm) cc_final: 0.8386 (tttm) REVERT: A 1258 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8118 (mmmm) REVERT: A 1276 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7543 (ttm-80) REVERT: A 1282 ASP cc_start: 0.7449 (t70) cc_final: 0.7217 (t70) REVERT: A 1283 SER cc_start: 0.8501 (m) cc_final: 0.8191 (p) REVERT: A 1297 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8403 (ttm-80) REVERT: A 1329 GLU cc_start: 0.8155 (tp30) cc_final: 0.7887 (tp30) REVERT: A 1333 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 1344 LEU cc_start: 0.8405 (tp) cc_final: 0.8158 (tp) REVERT: A 1356 GLU cc_start: 0.8626 (tp30) cc_final: 0.8275 (tp30) REVERT: A 1357 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8182 (mm-30) REVERT: A 1358 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 1360 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 1392 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 1405 LEU cc_start: 0.8676 (tt) cc_final: 0.8470 (tt) REVERT: A 1407 GLU cc_start: 0.7687 (pp20) cc_final: 0.7390 (pp20) REVERT: A 1409 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 1417 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8071 (mm-40) REVERT: A 1426 LYS cc_start: 0.9111 (tttm) cc_final: 0.8897 (ttpp) REVERT: A 1427 GLN cc_start: 0.8071 (pp30) cc_final: 0.7593 (pp30) REVERT: A 1432 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 1434 GLU cc_start: 0.8164 (mp0) cc_final: 0.7588 (mp0) REVERT: A 1439 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6623 (tm-30) REVERT: A 1448 ASN cc_start: 0.8260 (t0) cc_final: 0.7886 (t0) REVERT: A 1452 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8999 (tppt) REVERT: A 1457 ILE cc_start: 0.8330 (mm) cc_final: 0.7825 (mm) REVERT: A 1458 ASP cc_start: 0.7913 (p0) cc_final: 0.7002 (p0) REVERT: A 1463 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6913 (tm-30) REVERT: A 1467 LYS cc_start: 0.8033 (mttm) cc_final: 0.7661 (tppp) REVERT: A 1480 LYS cc_start: 0.8784 (tttp) cc_final: 0.8500 (tttp) REVERT: A 1481 GLU cc_start: 0.7303 (tp30) cc_final: 0.6631 (tp30) REVERT: A 1488 GLU cc_start: 0.6857 (tp30) cc_final: 0.6273 (tp30) REVERT: A 1504 GLU cc_start: 0.7975 (pp20) cc_final: 0.7701 (pp20) REVERT: A 1511 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8555 (mmmm) REVERT: A 1516 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7177 (mm-30) REVERT: A 1523 GLN cc_start: 0.8002 (tt0) cc_final: 0.7534 (tt0) REVERT: A 1542 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7104 (tm-30) REVERT: A 1547 GLU cc_start: 0.8662 (pp20) cc_final: 0.8211 (tm-30) REVERT: A 1548 LEU cc_start: 0.8754 (tp) cc_final: 0.8403 (tt) REVERT: A 1560 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 1561 GLN cc_start: 0.8067 (pp30) cc_final: 0.7535 (pp30) REVERT: A 1563 GLU cc_start: 0.8240 (tp30) cc_final: 0.7924 (tp30) REVERT: A 1565 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8478 (mttp) REVERT: A 1567 LEU cc_start: 0.9031 (mt) cc_final: 0.8724 (mm) REVERT: A 1572 GLU cc_start: 0.7928 (tp30) cc_final: 0.7553 (tp30) REVERT: A 1573 LEU cc_start: 0.9141 (tt) cc_final: 0.8873 (tt) REVERT: A 1597 ASN cc_start: 0.8808 (m-40) cc_final: 0.8450 (t0) REVERT: A 1614 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8875 (mmmm) REVERT: A 1623 LYS cc_start: 0.8571 (tppt) cc_final: 0.8103 (tppt) REVERT: A 1629 ASP cc_start: 0.8001 (t70) cc_final: 0.7651 (t70) REVERT: A 1642 LYS cc_start: 0.8532 (mtpt) cc_final: 0.7883 (ttmm) REVERT: A 1646 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 1649 LYS cc_start: 0.9172 (tttp) cc_final: 0.8705 (ttmm) REVERT: A 1660 ASP cc_start: 0.8299 (p0) cc_final: 0.8046 (p0) REVERT: A 1662 GLN cc_start: 0.8634 (tt0) cc_final: 0.8148 (tp40) REVERT: A 1679 LEU cc_start: 0.8883 (tp) cc_final: 0.8341 (tp) REVERT: A 1681 ILE cc_start: 0.8266 (tt) cc_final: 0.7993 (tt) REVERT: A 1683 GLU cc_start: 0.7600 (pp20) cc_final: 0.7127 (pp20) REVERT: A 1687 ASN cc_start: 0.8183 (p0) cc_final: 0.7631 (t0) REVERT: A 1712 GLN cc_start: 0.8774 (mm110) cc_final: 0.8476 (mm-40) REVERT: A 1741 GLU cc_start: 0.8168 (tp30) cc_final: 0.7922 (tp30) REVERT: A 1746 HIS cc_start: 0.8788 (t70) cc_final: 0.8555 (t70) REVERT: A 1757 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8581 (ttmt) REVERT: A 1758 ASN cc_start: 0.8475 (t0) cc_final: 0.8124 (t0) REVERT: A 1762 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9112 (ttmt) REVERT: A 1778 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8060 (t0) cc_final: 0.7832 (t0) REVERT: A 1792 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9095 (tppp) REVERT: A 1794 LEU cc_start: 0.8798 (mt) cc_final: 0.8504 (mt) REVERT: A 1795 GLU cc_start: 0.7860 (tp30) cc_final: 0.7238 (tp30) REVERT: A 1797 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 1802 GLN cc_start: 0.8992 (tp40) cc_final: 0.8328 (tm-30) REVERT: A 1818 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8236 (mmmm) REVERT: A 1822 LYS cc_start: 0.8583 (tttm) cc_final: 0.8301 (ttpp) REVERT: A 1824 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 1825 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 1828 ARG cc_start: 0.8363 (ptt-90) cc_final: 0.7988 (ptt-90) REVERT: A 1840 ARG cc_start: 0.8069 (mpp80) cc_final: 0.7718 (mtm110) REVERT: A 1846 LYS cc_start: 0.9198 (tttm) cc_final: 0.8918 (ttmm) REVERT: A 1850 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8281 (ptmt) REVERT: A 1853 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.7761 (ttm110) REVERT: A 1864 GLU cc_start: 0.7946 (tp30) cc_final: 0.7450 (tp30) REVERT: A 1865 ASP cc_start: 0.8024 (t0) cc_final: 0.7650 (t0) REVERT: A 1868 ASN cc_start: 0.8595 (m110) cc_final: 0.8190 (m-40) REVERT: A 1878 LYS cc_start: 0.9032 (tppt) cc_final: 0.8771 (mmmm) REVERT: A 1888 ARG cc_start: 0.7952 (tmm160) cc_final: 0.7123 (ttp80) REVERT: A 1889 GLN cc_start: 0.7657 (pp30) cc_final: 0.7306 (pp30) REVERT: A 1892 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7260 (mt-10) REVERT: A 1909 GLN cc_start: 0.8615 (tp40) cc_final: 0.8327 (tm-30) REVERT: A 1910 GLU cc_start: 0.8486 (tt0) cc_final: 0.8005 (tt0) REVERT: A 1915 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 1 outliers final: 1 residues processed: 660 average time/residue: 0.3312 time to fit residues: 314.6429 Evaluate side-chains 613 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 612 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1900 ASN ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS A1900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.4154 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= 0.192 Angle : 0.676 9.368 23282 Z= 0.362 Chirality : 0.042 0.213 2582 Planarity : 0.003 0.054 3158 Dihedral : 4.242 16.780 2318 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % 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: 2.81 (0.18), residues: 2150 helix: 1.90 (0.11), residues: 2105 sheet: None (None), residues: 0 loop : 1.02 (0.90), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1379 HIS 0.012 0.001 HIS B1598 PHE 0.010 0.001 PHE A1341 TYR 0.018 0.003 TYR A1383 ARG 0.010 0.001 ARG B1540 ********************** 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 666 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 664 time to evaluate : 1.930 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 1139 LYS cc_start: 0.8779 (pttp) cc_final: 0.8039 (ptmm) REVERT: B 1150 GLU cc_start: 0.8188 (mp0) cc_final: 0.7726 (mp0) REVERT: B 1181 LYS cc_start: 0.8919 (tppt) cc_final: 0.8312 (tppt) REVERT: B 1182 LEU cc_start: 0.8400 (mp) cc_final: 0.8200 (mp) REVERT: B 1224 LYS cc_start: 0.8291 (tppp) cc_final: 0.7986 (tppp) REVERT: B 1246 MET cc_start: 0.8017 (ttp) cc_final: 0.7665 (ttp) REVERT: B 1249 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 1254 GLU cc_start: 0.8462 (tt0) cc_final: 0.8247 (tt0) REVERT: B 1261 GLN cc_start: 0.8911 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 1268 GLN cc_start: 0.8848 (tt0) cc_final: 0.8640 (tp40) REVERT: B 1282 ASP cc_start: 0.8157 (m-30) cc_final: 0.7584 (t70) REVERT: B 1286 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8867 (mtmt) REVERT: B 1303 GLU cc_start: 0.8246 (pt0) cc_final: 0.7330 (pp20) REVERT: B 1325 ARG cc_start: 0.8361 (ptm-80) cc_final: 0.8100 (mtp-110) REVERT: B 1358 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 1362 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7812 (mtmt) REVERT: B 1367 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7929 (tpp80) REVERT: B 1392 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 1400 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8566 (ttmm) REVERT: B 1402 GLN cc_start: 0.8636 (mt0) cc_final: 0.8432 (mt0) REVERT: B 1418 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8271 (ptpp) REVERT: B 1457 ILE cc_start: 0.9031 (pt) cc_final: 0.8696 (mm) REVERT: B 1478 SER cc_start: 0.8765 (m) cc_final: 0.8446 (p) REVERT: B 1480 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8495 (mtpp) REVERT: B 1496 TYR cc_start: 0.8845 (t80) cc_final: 0.8624 (t80) REVERT: B 1497 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 1498 GLU cc_start: 0.8044 (pp20) cc_final: 0.7710 (pp20) REVERT: B 1504 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 1516 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 1540 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7994 (ttp80) REVERT: B 1542 GLU cc_start: 0.8178 (tp30) cc_final: 0.7862 (tp30) REVERT: B 1544 GLU cc_start: 0.8375 (pt0) cc_final: 0.8011 (pt0) REVERT: B 1549 GLN cc_start: 0.8771 (tt0) cc_final: 0.8298 (tm-30) REVERT: B 1556 GLU cc_start: 0.7822 (mp0) cc_final: 0.7389 (mp0) REVERT: B 1560 GLU cc_start: 0.8154 (tp30) cc_final: 0.7704 (mm-30) REVERT: B 1571 LEU cc_start: 0.8557 (mt) cc_final: 0.7643 (mt) REVERT: B 1577 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7641 (ptp-170) REVERT: B 1582 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7809 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7498 (pp30) cc_final: 0.6971 (pp30) REVERT: B 1590 GLU cc_start: 0.8584 (mp0) cc_final: 0.8236 (mp0) REVERT: B 1592 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 1627 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 1633 LEU cc_start: 0.8880 (mm) cc_final: 0.8483 (mm) REVERT: B 1634 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 1638 ASP cc_start: 0.8161 (t0) cc_final: 0.7712 (t0) REVERT: B 1651 ILE cc_start: 0.9074 (mt) cc_final: 0.8818 (mt) REVERT: B 1653 LYS cc_start: 0.9164 (tttt) cc_final: 0.8606 (ttmm) REVERT: B 1657 GLN cc_start: 0.7874 (tp40) cc_final: 0.7489 (tp40) REVERT: B 1667 GLU cc_start: 0.8280 (tp30) cc_final: 0.7705 (tp30) REVERT: B 1677 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 1683 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 1694 GLU cc_start: 0.8289 (tt0) cc_final: 0.8059 (tt0) REVERT: B 1708 ARG cc_start: 0.8488 (mpt-90) cc_final: 0.8243 (mtm-85) REVERT: B 1713 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 1719 GLU cc_start: 0.7588 (pm20) cc_final: 0.7327 (pm20) REVERT: B 1737 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9076 (tptp) REVERT: B 1741 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 1759 SER cc_start: 0.9081 (p) cc_final: 0.8681 (p) REVERT: B 1762 LYS cc_start: 0.8864 (mttp) cc_final: 0.8144 (mttp) REVERT: B 1772 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8396 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8123 (t0) cc_final: 0.7913 (t0) REVERT: B 1780 GLU cc_start: 0.7607 (tp30) cc_final: 0.7352 (tp30) REVERT: B 1786 THR cc_start: 0.8899 (p) cc_final: 0.8505 (t) REVERT: B 1789 LYS cc_start: 0.8953 (tppp) cc_final: 0.8632 (tppp) REVERT: B 1792 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8215 (tppt) REVERT: B 1818 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8532 (tppt) REVERT: B 1820 ILE cc_start: 0.8472 (mt) cc_final: 0.8180 (tp) REVERT: B 1824 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 1833 GLU cc_start: 0.8204 (tp30) cc_final: 0.7312 (tp30) REVERT: B 1840 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8555 (ttm110) REVERT: B 1848 LEU cc_start: 0.9126 (tp) cc_final: 0.8802 (tt) REVERT: B 1853 ARG cc_start: 0.8563 (mmt90) cc_final: 0.8166 (tpp80) REVERT: B 1857 GLU cc_start: 0.8028 (pp20) cc_final: 0.7827 (pp20) REVERT: B 1858 LEU cc_start: 0.8777 (mt) cc_final: 0.8569 (mt) REVERT: B 1865 ASP cc_start: 0.8020 (m-30) cc_final: 0.7750 (m-30) REVERT: B 1871 ARG cc_start: 0.8260 (ptt90) cc_final: 0.7851 (ptt90) REVERT: B 1873 GLN cc_start: 0.8782 (tp40) cc_final: 0.8437 (tm-30) REVERT: B 1878 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7875 (mmmt) REVERT: B 1882 LYS cc_start: 0.9236 (tttp) cc_final: 0.8771 (tttm) REVERT: B 1888 ARG cc_start: 0.8374 (ttt180) cc_final: 0.7913 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8707 (mt0) cc_final: 0.8212 (tp40) REVERT: B 1890 ILE cc_start: 0.8850 (tp) cc_final: 0.8625 (tp) REVERT: B 1903 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8663 (mmtt) REVERT: B 1906 LYS cc_start: 0.9118 (tppt) cc_final: 0.8752 (tppt) REVERT: B 1908 GLN cc_start: 0.8672 (tp-100) cc_final: 0.7941 (tp-100) REVERT: B 1910 GLU cc_start: 0.8209 (pp20) cc_final: 0.7975 (pp20) REVERT: B 1911 LEU cc_start: 0.8697 (tt) cc_final: 0.7974 (tt) REVERT: B 1915 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 1113 GLN cc_start: 0.7937 (mt0) cc_final: 0.7536 (mt0) REVERT: A 1174 LYS cc_start: 0.8674 (mtmm) cc_final: 0.7874 (mttp) REVERT: A 1188 GLU cc_start: 0.7262 (tp30) cc_final: 0.6407 (tp30) REVERT: A 1200 LEU cc_start: 0.7619 (mt) cc_final: 0.7337 (mt) REVERT: A 1202 LYS cc_start: 0.9162 (pptt) cc_final: 0.8827 (pptt) REVERT: A 1215 ILE cc_start: 0.8114 (pt) cc_final: 0.7786 (pt) REVERT: A 1243 LEU cc_start: 0.6840 (mt) cc_final: 0.6373 (tp) REVERT: A 1249 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 1258 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8084 (mmmm) REVERT: A 1267 ILE cc_start: 0.8871 (pt) cc_final: 0.8339 (mm) REVERT: A 1273 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 1276 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.7821 (mtp-110) REVERT: A 1279 ASN cc_start: 0.8746 (m-40) cc_final: 0.8279 (t0) REVERT: A 1283 SER cc_start: 0.8575 (m) cc_final: 0.8306 (p) REVERT: A 1291 GLU cc_start: 0.8066 (pt0) cc_final: 0.7722 (pt0) REVERT: A 1297 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8469 (ttm-80) REVERT: A 1298 GLN cc_start: 0.8927 (mm110) cc_final: 0.8724 (mm110) REVERT: A 1329 GLU cc_start: 0.8395 (tp30) cc_final: 0.7727 (tp30) REVERT: A 1332 ARG cc_start: 0.8517 (mtm110) cc_final: 0.8158 (mtm110) REVERT: A 1344 LEU cc_start: 0.8454 (tp) cc_final: 0.8179 (tp) REVERT: A 1352 ARG cc_start: 0.8953 (ttp-110) cc_final: 0.8746 (ttm110) REVERT: A 1356 GLU cc_start: 0.8616 (tp30) cc_final: 0.8160 (tp30) REVERT: A 1357 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 1358 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8066 (mm-30) REVERT: A 1360 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 1362 LYS cc_start: 0.8458 (tttm) cc_final: 0.8207 (ttmm) REVERT: A 1368 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7996 (pp30) REVERT: A 1392 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 1405 LEU cc_start: 0.8721 (tt) cc_final: 0.8498 (tt) REVERT: A 1407 GLU cc_start: 0.7723 (pp20) cc_final: 0.7421 (pp20) REVERT: A 1409 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 1415 LEU cc_start: 0.9059 (mt) cc_final: 0.8859 (mm) REVERT: A 1417 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8148 (mm-40) REVERT: A 1426 LYS cc_start: 0.9197 (tttm) cc_final: 0.8971 (ttpp) REVERT: A 1427 GLN cc_start: 0.8087 (pp30) cc_final: 0.7556 (pp30) REVERT: A 1434 GLU cc_start: 0.8187 (mp0) cc_final: 0.7638 (mp0) REVERT: A 1448 ASN cc_start: 0.8235 (t0) cc_final: 0.7896 (t0) REVERT: A 1451 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 1452 LYS cc_start: 0.9243 (mmmm) cc_final: 0.9013 (tppt) REVERT: A 1457 ILE cc_start: 0.8363 (mm) cc_final: 0.7883 (mm) REVERT: A 1463 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 1467 LYS cc_start: 0.8153 (mttm) cc_final: 0.7784 (tppp) REVERT: A 1480 LYS cc_start: 0.8821 (tttp) cc_final: 0.8513 (tttp) REVERT: A 1481 GLU cc_start: 0.7297 (tp30) cc_final: 0.6647 (tp30) REVERT: A 1488 GLU cc_start: 0.7021 (tp30) cc_final: 0.6803 (tp30) REVERT: A 1511 LYS cc_start: 0.8879 (mmpt) cc_final: 0.8524 (mmmm) REVERT: A 1523 GLN cc_start: 0.8022 (tt0) cc_final: 0.7616 (tt0) REVERT: A 1542 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7012 (tm-30) REVERT: A 1560 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 1561 GLN cc_start: 0.8072 (pp30) cc_final: 0.7575 (pp30) REVERT: A 1563 GLU cc_start: 0.8235 (tp30) cc_final: 0.7823 (tp30) REVERT: A 1565 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8526 (mttt) REVERT: A 1567 LEU cc_start: 0.9094 (mt) cc_final: 0.8821 (mm) REVERT: A 1572 GLU cc_start: 0.7878 (tp30) cc_final: 0.7425 (tp30) REVERT: A 1573 LEU cc_start: 0.9262 (tt) cc_final: 0.8984 (mt) REVERT: A 1597 ASN cc_start: 0.8817 (m-40) cc_final: 0.8463 (t0) REVERT: A 1614 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8860 (mmmm) REVERT: A 1623 LYS cc_start: 0.8602 (tppt) cc_final: 0.8151 (tppt) REVERT: A 1642 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8091 (mtpp) REVERT: A 1646 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 1649 LYS cc_start: 0.9193 (tttp) cc_final: 0.8727 (ttmm) REVERT: A 1656 GLN cc_start: 0.8798 (mm110) cc_final: 0.8493 (tp40) REVERT: A 1662 GLN cc_start: 0.8651 (tt0) cc_final: 0.8184 (tp40) REVERT: A 1679 LEU cc_start: 0.8916 (tp) cc_final: 0.8368 (tp) REVERT: A 1681 ILE cc_start: 0.8298 (tt) cc_final: 0.8064 (tt) REVERT: A 1683 GLU cc_start: 0.7616 (pp20) cc_final: 0.7140 (pp20) REVERT: A 1687 ASN cc_start: 0.8135 (p0) cc_final: 0.7670 (t0) REVERT: A 1712 GLN cc_start: 0.8802 (mm110) cc_final: 0.8504 (mm-40) REVERT: A 1741 GLU cc_start: 0.8182 (tp30) cc_final: 0.7947 (tp30) REVERT: A 1746 HIS cc_start: 0.8799 (t70) cc_final: 0.8543 (t70) REVERT: A 1754 ASN cc_start: 0.8454 (t0) cc_final: 0.8242 (t0) REVERT: A 1755 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 1757 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8556 (ttmt) REVERT: A 1762 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9071 (ttmt) REVERT: A 1778 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.7988 (mtt-85) REVERT: A 1788 GLU cc_start: 0.7782 (tp30) cc_final: 0.7303 (tp30) REVERT: A 1792 LYS cc_start: 0.9394 (ttmt) cc_final: 0.8996 (ttmm) REVERT: A 1794 LEU cc_start: 0.8779 (mt) cc_final: 0.8544 (mm) REVERT: A 1795 GLU cc_start: 0.7911 (tp30) cc_final: 0.7246 (tp30) REVERT: A 1797 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7959 (tp-100) REVERT: A 1802 GLN cc_start: 0.8986 (tp40) cc_final: 0.8298 (tm-30) REVERT: A 1818 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8235 (mmmm) REVERT: A 1822 LYS cc_start: 0.8645 (tttm) cc_final: 0.8358 (ttpp) REVERT: A 1824 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 1825 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 1828 ARG cc_start: 0.8396 (ptt-90) cc_final: 0.8016 (ptt-90) REVERT: A 1840 ARG cc_start: 0.8138 (mpp80) cc_final: 0.7814 (mtm110) REVERT: A 1846 LYS cc_start: 0.9212 (tttm) cc_final: 0.8925 (ttmm) REVERT: A 1853 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7768 (ttm110) REVERT: A 1860 PHE cc_start: 0.9039 (t80) cc_final: 0.8797 (t80) REVERT: A 1864 GLU cc_start: 0.7994 (tp30) cc_final: 0.7517 (tp30) REVERT: A 1865 ASP cc_start: 0.8080 (t0) cc_final: 0.7692 (t0) REVERT: A 1868 ASN cc_start: 0.8639 (m110) cc_final: 0.8219 (m-40) REVERT: A 1871 ARG cc_start: 0.8599 (tpm170) cc_final: 0.7874 (tpm170) REVERT: A 1874 ASP cc_start: 0.8025 (m-30) cc_final: 0.7040 (m-30) REVERT: A 1878 LYS cc_start: 0.9053 (tppt) cc_final: 0.8758 (mmmm) REVERT: A 1881 GLN cc_start: 0.8631 (tp40) cc_final: 0.8411 (tp40) REVERT: A 1888 ARG cc_start: 0.7894 (tmm160) cc_final: 0.6878 (ttp80) REVERT: A 1889 GLN cc_start: 0.7713 (pp30) cc_final: 0.7208 (pp30) REVERT: A 1892 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 1894 GLU cc_start: 0.7081 (pp20) cc_final: 0.6816 (pp20) REVERT: A 1909 GLN cc_start: 0.8651 (tp40) cc_final: 0.8335 (tm-30) REVERT: A 1910 GLU cc_start: 0.8503 (tt0) cc_final: 0.8003 (tt0) REVERT: A 1915 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7645 (tm-30) outliers start: 2 outliers final: 1 residues processed: 666 average time/residue: 0.3366 time to fit residues: 321.5335 Evaluate side-chains 620 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 618 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 0.5980 chunk 156 optimal weight: 0.0670 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1662 GLN B1838 GLN ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 ASN ** A1598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1881 GLN A1900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.119092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.096785 restraints weight = 46358.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.099552 restraints weight = 27209.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.101429 restraints weight = 17773.169| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 1.4348 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= 0.156 Angle : 0.637 7.619 23282 Z= 0.339 Chirality : 0.040 0.159 2582 Planarity : 0.003 0.048 3158 Dihedral : 4.274 17.123 2318 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.18), residues: 2150 helix: 2.01 (0.11), residues: 2111 sheet: None (None), residues: 0 loop : 1.29 (0.98), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B1464 HIS 0.012 0.001 HIS B1598 PHE 0.007 0.001 PHE B1928 TYR 0.012 0.002 TYR B1383 ARG 0.010 0.001 ARG A1491 =============================================================================== Job complete usr+sys time: 6009.14 seconds wall clock time: 108 minutes 17.92 seconds (6497.92 seconds total)