Starting phenix.real_space_refine on Thu Mar 5 01:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_22975.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_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/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_22975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_22975.map" model { file = "/net/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_22975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kog_22975/03_2026/7kog_22975.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.13, per 1000 atoms: 0.18 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: 1.18 Conformation dependent library (CDL) restraints added in 552.8 milliseconds 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: 0.34 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: 2.63 Time building geometry restraints manager: 1.53 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: 0.03 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: 2.910 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: 0.570 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.620 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- 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= 0.277 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 : 10.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG B 897 TYR 0.061 0.007 TYR B1383 PHE 0.022 0.003 PHE B1341 TRP 0.011 0.003 TRP B1464 HIS 0.014 0.002 HIS B1193 Details of bonding type rmsd covalent geometry : bond 0.00546 (17454) covalent geometry : angle 1.02667 (23282) hydrogen bonds : bond 0.29754 ( 1625) hydrogen bonds : angle 9.74612 ( 4872) *********************** 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 to be fit. rotamer outliers: 13 poor density : 650 time to evaluate : 0.525 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: 0.5037 (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: 0.7920 (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: 0.7062 (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: 0.8074 (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: 0.1710 time to fit residues: 157.6552 Evaluate side-chains 473 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 469 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 B1841 HIS ** B1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN A 935 GLN A 947 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.123748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.102771 restraints weight = 49525.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.105567 restraints weight = 27945.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.107373 restraints weight = 17752.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.108551 restraints weight = 12281.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.109464 restraints weight = 9207.909| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17454 Z= 0.155 Angle : 0.668 10.384 23282 Z= 0.369 Chirality : 0.038 0.229 2582 Planarity : 0.005 0.059 3158 Dihedral : 4.837 26.015 2318 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2150 helix: -0.82 (0.10), residues: 2103 sheet: None (None), residues: 0 loop : 0.05 (0.78), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1380 TYR 0.010 0.002 TYR B1496 PHE 0.013 0.002 PHE A1341 TRP 0.010 0.003 TRP A1464 HIS 0.009 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00286 (17454) covalent geometry : angle 0.66812 (23282) hydrogen bonds : bond 0.05147 ( 1625) hydrogen bonds : angle 4.22361 ( 4872) *********************** 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 594 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 592 time to evaluate : 0.663 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 966 GLU cc_start: 0.7896 (tp30) cc_final: 0.7432 (tm-30) REVERT: B 980 ASP cc_start: 0.8225 (m-30) cc_final: 0.7766 (m-30) REVERT: B 1224 LYS cc_start: 0.7489 (tptm) cc_final: 0.7259 (tptm) REVERT: B 1231 HIS cc_start: 0.6090 (t70) cc_final: 0.5780 (t70) REVERT: B 1243 LEU cc_start: 0.7234 (tt) cc_final: 0.6679 (tt) REVERT: B 1345 GLU cc_start: 0.7642 (pt0) cc_final: 0.7066 (pt0) REVERT: B 1357 GLU cc_start: 0.7160 (tp30) cc_final: 0.6845 (tp30) REVERT: B 1415 LEU cc_start: 0.7505 (mm) cc_final: 0.7269 (mt) REVERT: B 1435 ASP cc_start: 0.6367 (t0) cc_final: 0.5921 (t0) REVERT: B 1468 VAL cc_start: 0.6712 (p) cc_final: 0.6481 (t) REVERT: B 1511 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7779 (mtmm) REVERT: B 1518 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8374 (mmtm) REVERT: B 1535 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 1560 GLU cc_start: 0.8350 (tt0) cc_final: 0.8081 (tt0) REVERT: B 1566 VAL cc_start: 0.7552 (t) cc_final: 0.7107 (t) REVERT: B 1590 GLU cc_start: 0.8682 (mp0) cc_final: 0.8274 (mp0) REVERT: B 1593 ASN cc_start: 0.7826 (t0) cc_final: 0.7360 (t0) REVERT: B 1597 ASN cc_start: 0.8520 (m-40) cc_final: 0.8208 (m-40) REVERT: B 1612 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 1614 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8407 (mtpp) REVERT: B 1638 ASP cc_start: 0.6947 (t0) cc_final: 0.6728 (t0) REVERT: B 1653 LYS cc_start: 0.8608 (tttt) cc_final: 0.8251 (ttpt) REVERT: B 1667 GLU cc_start: 0.7341 (tp30) cc_final: 0.6643 (tp30) REVERT: B 1668 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6240 (mm-30) REVERT: B 1670 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7512 (mtm110) REVERT: B 1681 ILE cc_start: 0.8078 (mm) cc_final: 0.7832 (mm) REVERT: B 1705 ARG cc_start: 0.8211 (ptm-80) cc_final: 0.7989 (ptm-80) REVERT: B 1708 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8543 (mtm-85) REVERT: B 1719 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: B 1741 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7225 (tm-30) REVERT: B 1760 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 1764 LYS cc_start: 0.8507 (mmmt) cc_final: 0.7343 (mmmm) REVERT: B 1792 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7906 (tppt) REVERT: B 1795 GLU cc_start: 0.8098 (pt0) cc_final: 0.7487 (pt0) REVERT: B 1824 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 1865 ASP cc_start: 0.8188 (m-30) cc_final: 0.7932 (m-30) REVERT: B 1871 ARG cc_start: 0.8108 (ptt90) cc_final: 0.7743 (ptt90) REVERT: B 1882 LYS cc_start: 0.8893 (tttp) cc_final: 0.8369 (ttmm) REVERT: B 1892 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 1894 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6847 (tm-30) REVERT: B 1903 LYS cc_start: 0.8927 (tptt) cc_final: 0.8633 (mptt) REVERT: B 1906 LYS cc_start: 0.9074 (tppt) cc_final: 0.8711 (tppt) REVERT: B 1908 GLN cc_start: 0.8105 (tt0) cc_final: 0.7826 (tp40) REVERT: B 1911 LEU cc_start: 0.8384 (tt) cc_final: 0.7515 (tp) REVERT: B 1923 GLN cc_start: 0.8429 (pp30) cc_final: 0.8183 (pp30) REVERT: A 924 GLU cc_start: 0.7327 (mp0) cc_final: 0.6766 (tp30) REVERT: A 952 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7819 (mt-10) REVERT: A 980 ASP cc_start: 0.8373 (m-30) cc_final: 0.8162 (m-30) REVERT: A 1092 ASP cc_start: 0.7800 (t0) cc_final: 0.7522 (t0) REVERT: A 1185 ASP cc_start: 0.8035 (m-30) cc_final: 0.7770 (m-30) REVERT: A 1273 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 1316 LEU cc_start: 0.7051 (mt) cc_final: 0.6518 (mt) REVERT: A 1320 LEU cc_start: 0.6049 (tt) cc_final: 0.5780 (tt) REVERT: A 1353 GLU cc_start: 0.6304 (tm-30) cc_final: 0.5961 (tm-30) REVERT: A 1356 GLU cc_start: 0.6949 (tp30) cc_final: 0.6309 (tp30) REVERT: A 1500 GLN cc_start: 0.7786 (tt0) cc_final: 0.7383 (mt0) REVERT: A 1501 GLU cc_start: 0.8262 (pt0) cc_final: 0.7855 (pt0) REVERT: A 1553 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 1570 GLN cc_start: 0.7820 (mt0) cc_final: 0.7583 (mp10) REVERT: A 1603 ASP cc_start: 0.7742 (t0) cc_final: 0.7473 (t0) REVERT: A 1622 MET cc_start: 0.6889 (mmm) cc_final: 0.6622 (mmm) REVERT: A 1623 LYS cc_start: 0.8048 (tppt) cc_final: 0.7728 (tppt) REVERT: A 1646 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 1741 GLU cc_start: 0.8343 (tp30) cc_final: 0.8096 (tp30) REVERT: A 1761 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 1762 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8940 (ttmt) REVERT: A 1775 ASP cc_start: 0.7940 (t0) cc_final: 0.7575 (t0) REVERT: A 1776 GLU cc_start: 0.7695 (tp30) cc_final: 0.6645 (tp30) REVERT: A 1782 ASP cc_start: 0.8165 (t0) cc_final: 0.7774 (t0) REVERT: A 1792 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8811 (mtpp) REVERT: A 1795 GLU cc_start: 0.7671 (tp30) cc_final: 0.7374 (tp30) REVERT: A 1797 GLN cc_start: 0.8281 (mm110) cc_final: 0.8041 (mm110) REVERT: A 1824 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 1839 ARG cc_start: 0.8351 (tmt170) cc_final: 0.8057 (tmt170) REVERT: A 1843 ASP cc_start: 0.7741 (t0) cc_final: 0.7477 (t0) REVERT: A 1846 LYS cc_start: 0.9103 (tttm) cc_final: 0.8745 (ttmm) REVERT: A 1858 LEU cc_start: 0.8559 (mp) cc_final: 0.8280 (mm) REVERT: A 1860 PHE cc_start: 0.8811 (t80) cc_final: 0.8499 (t80) REVERT: A 1864 GLU cc_start: 0.7722 (tp30) cc_final: 0.7513 (tp30) REVERT: A 1876 VAL cc_start: 0.9116 (m) cc_final: 0.8873 (p) REVERT: A 1882 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8999 (ttmm) REVERT: A 1892 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 1894 GLU cc_start: 0.7177 (pp20) cc_final: 0.6943 (pp20) REVERT: A 1909 GLN cc_start: 0.8356 (tp40) cc_final: 0.7830 (tm-30) REVERT: A 1910 GLU cc_start: 0.8252 (tt0) cc_final: 0.7721 (tt0) REVERT: A 1915 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7785 (tm-30) outliers start: 2 outliers final: 0 residues processed: 594 average time/residue: 0.1579 time to fit residues: 134.9750 Evaluate side-chains 484 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 174 optimal weight: 0.0000 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1037 GLN B1080 ASN ** B1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 GLN B1712 GLN B1718 HIS B1797 GLN B1900 ASN A 942 ASN A1199 ASN A1219 ASN A1233 GLN A1402 GLN A1783 HIS A1881 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.106659 restraints weight = 51067.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.109288 restraints weight = 29330.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.111015 restraints weight = 18878.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.112250 restraints weight = 13069.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.113075 restraints weight = 9584.224| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17454 Z= 0.154 Angle : 0.642 7.667 23282 Z= 0.354 Chirality : 0.040 0.164 2582 Planarity : 0.004 0.048 3158 Dihedral : 4.402 19.430 2318 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2150 helix: 0.76 (0.11), residues: 2099 sheet: None (None), residues: 0 loop : 0.84 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1905 TYR 0.022 0.003 TYR A1496 PHE 0.038 0.003 PHE B1281 TRP 0.012 0.003 TRP B1464 HIS 0.012 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00306 (17454) covalent geometry : angle 0.64199 (23282) hydrogen bonds : bond 0.04516 ( 1625) hydrogen bonds : angle 3.85668 ( 4872) *********************** 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 606 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 604 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 948 LYS cc_start: 0.8554 (pttp) cc_final: 0.8343 (pttp) REVERT: B 966 GLU cc_start: 0.7521 (tp30) cc_final: 0.7225 (tm-30) REVERT: B 1092 ASP cc_start: 0.6256 (m-30) cc_final: 0.5631 (t70) REVERT: B 1243 LEU cc_start: 0.7478 (tt) cc_final: 0.6875 (tt) REVERT: B 1261 GLN cc_start: 0.8605 (tt0) cc_final: 0.8398 (tt0) REVERT: B 1296 LEU cc_start: 0.7659 (tt) cc_final: 0.7213 (tp) REVERT: B 1324 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8479 (mtmm) REVERT: B 1334 ARG cc_start: 0.6871 (ptm160) cc_final: 0.6357 (ptm160) REVERT: B 1409 GLU cc_start: 0.7561 (pt0) cc_final: 0.7192 (pt0) REVERT: B 1439 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7624 (mp0) REVERT: B 1451 GLU cc_start: 0.7451 (pp20) cc_final: 0.7205 (pp20) REVERT: B 1458 ASP cc_start: 0.7468 (t0) cc_final: 0.7187 (t0) REVERT: B 1461 ILE cc_start: 0.7460 (pt) cc_final: 0.7233 (mm) REVERT: B 1481 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7386 (mp0) REVERT: B 1504 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 1538 LYS cc_start: 0.8569 (pptt) cc_final: 0.8265 (pptt) REVERT: B 1560 GLU cc_start: 0.8519 (tt0) cc_final: 0.8243 (tt0) REVERT: B 1565 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7187 (tmtt) REVERT: B 1588 GLU cc_start: 0.8430 (pm20) cc_final: 0.8053 (pp20) REVERT: B 1590 GLU cc_start: 0.8742 (mp0) cc_final: 0.8494 (mp0) REVERT: B 1593 ASN cc_start: 0.7718 (t0) cc_final: 0.7379 (t0) REVERT: B 1614 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8244 (mtpp) REVERT: B 1627 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 1638 ASP cc_start: 0.7418 (t0) cc_final: 0.6830 (t0) REVERT: B 1649 LYS cc_start: 0.8399 (tptp) cc_final: 0.8027 (mptp) REVERT: B 1653 LYS cc_start: 0.8933 (tttt) cc_final: 0.8512 (ttpp) REVERT: B 1667 GLU cc_start: 0.7910 (tp30) cc_final: 0.7672 (tp30) REVERT: B 1720 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8410 (tp40) REVERT: B 1737 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8811 (tptp) REVERT: B 1748 ASP cc_start: 0.7785 (m-30) cc_final: 0.7458 (m-30) REVERT: B 1750 ASP cc_start: 0.7375 (t0) cc_final: 0.7124 (t0) REVERT: B 1759 SER cc_start: 0.8545 (p) cc_final: 0.7989 (p) REVERT: B 1760 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 1762 LYS cc_start: 0.8480 (mttp) cc_final: 0.8220 (mttp) REVERT: B 1764 LYS cc_start: 0.8834 (mmmt) cc_final: 0.7548 (mmmm) REVERT: B 1765 LYS cc_start: 0.8962 (tttm) cc_final: 0.8715 (tttm) REVERT: B 1767 MET cc_start: 0.7903 (ppp) cc_final: 0.7654 (ppp) REVERT: B 1772 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8331 (ttm-80) REVERT: B 1781 GLN cc_start: 0.8072 (tp40) cc_final: 0.7650 (tp40) REVERT: B 1788 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 1792 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8276 (tppt) REVERT: B 1797 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8573 (tp40) REVERT: B 1824 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 1833 GLU cc_start: 0.7917 (tp30) cc_final: 0.7468 (tp30) REVERT: B 1837 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7252 (tp30) REVERT: B 1840 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8063 (ttm110) REVERT: B 1855 ILE cc_start: 0.8887 (tt) cc_final: 0.8657 (tt) REVERT: B 1860 PHE cc_start: 0.8550 (t80) cc_final: 0.8235 (t80) REVERT: B 1863 ASP cc_start: 0.7829 (m-30) cc_final: 0.6679 (t70) REVERT: B 1865 ASP cc_start: 0.8060 (m-30) cc_final: 0.7740 (m-30) REVERT: B 1866 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8055 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8478 (mmmm) REVERT: B 1873 GLN cc_start: 0.8916 (tp40) cc_final: 0.8688 (tp40) REVERT: B 1882 LYS cc_start: 0.9038 (tttp) cc_final: 0.8620 (tttm) REVERT: B 1888 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8085 (mtp85) REVERT: B 1889 GLN cc_start: 0.8739 (mt0) cc_final: 0.8430 (mt0) REVERT: B 1892 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 1894 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 1895 GLU cc_start: 0.8026 (mp0) cc_final: 0.7272 (mp0) REVERT: B 1903 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8688 (mmtt) REVERT: B 1906 LYS cc_start: 0.9060 (tppt) cc_final: 0.8550 (tppt) REVERT: B 1908 GLN cc_start: 0.7955 (tt0) cc_final: 0.7714 (tp40) REVERT: B 1922 GLU cc_start: 0.8343 (tp30) cc_final: 0.7877 (tm-30) REVERT: B 1923 GLN cc_start: 0.8439 (pp30) cc_final: 0.8154 (pp30) REVERT: A 1043 GLU cc_start: 0.8292 (tp30) cc_final: 0.7852 (mt-10) REVERT: A 1072 GLU cc_start: 0.8653 (pt0) cc_final: 0.8259 (mt-10) REVERT: A 1092 ASP cc_start: 0.7920 (t0) cc_final: 0.7606 (t0) REVERT: A 1179 MET cc_start: 0.5753 (ppp) cc_final: 0.5533 (ppp) REVERT: A 1185 ASP cc_start: 0.7868 (m-30) cc_final: 0.7606 (m-30) REVERT: A 1187 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 1228 ASP cc_start: 0.6553 (t70) cc_final: 0.6303 (t70) REVERT: A 1261 GLN cc_start: 0.7976 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 1282 ASP cc_start: 0.7071 (t0) cc_final: 0.6773 (t0) REVERT: A 1316 LEU cc_start: 0.7458 (mt) cc_final: 0.6816 (mt) REVERT: A 1329 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 1333 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 1345 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 1356 GLU cc_start: 0.7235 (tp30) cc_final: 0.6487 (tp30) REVERT: A 1392 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 1458 ASP cc_start: 0.7025 (p0) cc_final: 0.6825 (p0) REVERT: A 1467 LYS cc_start: 0.7038 (mttm) cc_final: 0.6769 (ttmm) REVERT: A 1480 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8636 (ttmm) REVERT: A 1488 GLU cc_start: 0.7358 (tp30) cc_final: 0.6369 (tp30) REVERT: A 1492 LEU cc_start: 0.8193 (mt) cc_final: 0.7358 (mt) REVERT: A 1511 LYS cc_start: 0.8652 (mptt) cc_final: 0.8425 (mmmm) REVERT: A 1516 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 1533 GLU cc_start: 0.8063 (pt0) cc_final: 0.7829 (pp20) REVERT: A 1542 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 1553 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7983 (mt-10) REVERT: A 1554 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 1559 LEU cc_start: 0.8073 (tp) cc_final: 0.7728 (tp) REVERT: A 1570 GLN cc_start: 0.8100 (mt0) cc_final: 0.7897 (mp10) REVERT: A 1614 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8001 (mtmm) REVERT: A 1623 LYS cc_start: 0.8091 (tppt) cc_final: 0.7642 (tppt) REVERT: A 1642 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8089 (mtmt) REVERT: A 1646 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 1660 ASP cc_start: 0.7950 (p0) cc_final: 0.7543 (p0) REVERT: A 1661 VAL cc_start: 0.8883 (m) cc_final: 0.8509 (t) REVERT: A 1662 GLN cc_start: 0.8607 (tt0) cc_final: 0.8379 (tt0) REVERT: A 1690 GLN cc_start: 0.8468 (tt0) cc_final: 0.8087 (tp40) REVERT: A 1711 GLU cc_start: 0.7764 (pt0) cc_final: 0.7515 (pt0) REVERT: A 1720 GLN cc_start: 0.8197 (tp40) cc_final: 0.7905 (tp40) REVERT: A 1729 THR cc_start: 0.8754 (p) cc_final: 0.8482 (t) REVERT: A 1741 GLU cc_start: 0.8298 (tp30) cc_final: 0.7966 (tp30) REVERT: A 1754 ASN cc_start: 0.8176 (t0) cc_final: 0.7890 (t0) REVERT: A 1757 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8608 (ttpt) REVERT: A 1775 ASP cc_start: 0.7869 (t0) cc_final: 0.7548 (t0) REVERT: A 1776 GLU cc_start: 0.7813 (tp30) cc_final: 0.6896 (tp30) REVERT: A 1777 LEU cc_start: 0.9046 (tt) cc_final: 0.8817 (tp) REVERT: A 1782 ASP cc_start: 0.8184 (t0) cc_final: 0.7893 (t0) REVERT: A 1789 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8791 (ttmm) REVERT: A 1792 LYS cc_start: 0.9258 (ttmt) cc_final: 0.8839 (ttmm) REVERT: A 1795 GLU cc_start: 0.7711 (tp30) cc_final: 0.7077 (tp30) REVERT: A 1797 GLN cc_start: 0.8353 (mm110) cc_final: 0.8110 (mm110) REVERT: A 1807 GLU cc_start: 0.8008 (pp20) cc_final: 0.7740 (pp20) REVERT: A 1809 GLU cc_start: 0.8522 (pt0) cc_final: 0.8219 (pt0) REVERT: A 1818 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8381 (mmtt) REVERT: A 1822 LYS cc_start: 0.8576 (tttm) cc_final: 0.8277 (ttpp) REVERT: A 1824 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 1828 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7908 (ptt-90) REVERT: A 1839 ARG cc_start: 0.8303 (tmt170) cc_final: 0.8012 (tmt170) REVERT: A 1843 ASP cc_start: 0.7679 (t0) cc_final: 0.7445 (t0) REVERT: A 1846 LYS cc_start: 0.9181 (tttm) cc_final: 0.8861 (ttmm) REVERT: A 1850 LYS cc_start: 0.8909 (ptpt) cc_final: 0.8584 (ptpt) REVERT: A 1853 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7765 (ttm110) REVERT: A 1858 LEU cc_start: 0.8599 (mp) cc_final: 0.8371 (mm) REVERT: A 1860 PHE cc_start: 0.8979 (t80) cc_final: 0.8684 (t80) REVERT: A 1864 GLU cc_start: 0.7932 (tp30) cc_final: 0.6645 (tp30) REVERT: A 1865 ASP cc_start: 0.8002 (t0) cc_final: 0.7645 (t0) REVERT: A 1868 ASN cc_start: 0.8705 (m110) cc_final: 0.6770 (m-40) REVERT: A 1870 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 1876 VAL cc_start: 0.9123 (m) cc_final: 0.8799 (p) REVERT: A 1881 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8124 (tp40) REVERT: A 1882 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8979 (ttmm) REVERT: A 1884 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8631 (ttpp) REVERT: A 1889 GLN cc_start: 0.8032 (pp30) cc_final: 0.7767 (pp30) REVERT: A 1892 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 1909 GLN cc_start: 0.8496 (tp40) cc_final: 0.7996 (tm-30) REVERT: A 1915 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7636 (tm-30) outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.1575 time to fit residues: 136.3086 Evaluate side-chains 511 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 510 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 118 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1037 GLN B1115 GLN B1168 GLN ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1802 GLN B1900 ASN A1089 GLN A1237 ASN A1263 GLN ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1900 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.109224 restraints weight = 49597.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.111955 restraints weight = 28887.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.113810 restraints weight = 18691.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.115061 restraints weight = 12959.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.115899 restraints weight = 9531.126| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 1.0056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17454 Z= 0.163 Angle : 0.649 8.634 23282 Z= 0.358 Chirality : 0.042 0.183 2582 Planarity : 0.003 0.035 3158 Dihedral : 4.400 17.533 2318 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2150 helix: 1.23 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : 1.15 (0.90), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1090 TYR 0.037 0.003 TYR A1383 PHE 0.025 0.003 PHE B1281 TRP 0.051 0.005 TRP A1379 HIS 0.007 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00308 (17454) covalent geometry : angle 0.64869 (23282) hydrogen bonds : bond 0.04346 ( 1625) hydrogen bonds : angle 3.81090 ( 4872) *********************** 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 620 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 617 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1006 MET cc_start: 0.7622 (ptp) cc_final: 0.7382 (ptp) REVERT: B 1249 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 1255 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7670 (ptmm) REVERT: B 1261 GLN cc_start: 0.8928 (tt0) cc_final: 0.7951 (tm-30) REVERT: B 1264 VAL cc_start: 0.7774 (p) cc_final: 0.7018 (t) REVERT: B 1291 GLU cc_start: 0.7183 (tp30) cc_final: 0.6294 (tp30) REVERT: B 1292 ASN cc_start: 0.8076 (m110) cc_final: 0.7874 (m110) REVERT: B 1295 LEU cc_start: 0.6836 (mt) cc_final: 0.6393 (mt) REVERT: B 1300 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 1303 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: B 1395 GLU cc_start: 0.7123 (pp20) cc_final: 0.6605 (tm-30) REVERT: B 1416 ASN cc_start: 0.8167 (t0) cc_final: 0.7891 (t0) REVERT: B 1420 ILE cc_start: 0.8923 (pt) cc_final: 0.8463 (pt) REVERT: B 1423 GLU cc_start: 0.8351 (pt0) cc_final: 0.7985 (pt0) REVERT: B 1435 ASP cc_start: 0.7632 (t0) cc_final: 0.7175 (t0) REVERT: B 1436 LEU cc_start: 0.8375 (mt) cc_final: 0.7802 (mt) REVERT: B 1439 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7785 (mp0) REVERT: B 1458 ASP cc_start: 0.7393 (t0) cc_final: 0.7078 (t0) REVERT: B 1471 LEU cc_start: 0.8785 (mt) cc_final: 0.8535 (mm) REVERT: B 1481 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7738 (mp0) REVERT: B 1509 GLU cc_start: 0.8385 (tt0) cc_final: 0.8045 (tt0) REVERT: B 1515 ASP cc_start: 0.7548 (p0) cc_final: 0.6727 (p0) REVERT: B 1516 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 1523 GLN cc_start: 0.8327 (mt0) cc_final: 0.8103 (mt0) REVERT: B 1538 LYS cc_start: 0.8853 (pptt) cc_final: 0.8530 (pptt) REVERT: B 1565 LYS cc_start: 0.7829 (tmtt) cc_final: 0.7496 (tmtt) REVERT: B 1590 GLU cc_start: 0.8803 (mp0) cc_final: 0.8441 (mp0) REVERT: B 1593 ASN cc_start: 0.8085 (t0) cc_final: 0.7755 (t0) REVERT: B 1606 GLN cc_start: 0.8337 (mm110) cc_final: 0.8113 (tt0) REVERT: B 1614 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8266 (mtpp) REVERT: B 1627 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7103 (tm-30) REVERT: B 1629 ASP cc_start: 0.8051 (t70) cc_final: 0.7621 (t0) REVERT: B 1633 LEU cc_start: 0.8698 (mm) cc_final: 0.8452 (mm) REVERT: B 1638 ASP cc_start: 0.7717 (t0) cc_final: 0.7295 (t0) REVERT: B 1641 ASN cc_start: 0.8761 (m-40) cc_final: 0.8560 (t0) REVERT: B 1653 LYS cc_start: 0.8932 (tttt) cc_final: 0.8324 (ttmm) REVERT: B 1654 TYR cc_start: 0.8342 (m-80) cc_final: 0.8062 (m-80) REVERT: B 1667 GLU cc_start: 0.8013 (tp30) cc_final: 0.7731 (tp30) REVERT: B 1677 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 1720 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8057 (tp40) REVERT: B 1737 LYS cc_start: 0.9305 (tmtt) cc_final: 0.8860 (tptp) REVERT: B 1744 THR cc_start: 0.8581 (p) cc_final: 0.8272 (p) REVERT: B 1748 ASP cc_start: 0.7810 (m-30) cc_final: 0.7327 (m-30) REVERT: B 1750 ASP cc_start: 0.7447 (t0) cc_final: 0.7219 (t0) REVERT: B 1757 LYS cc_start: 0.8848 (tttp) cc_final: 0.8505 (ttpp) REVERT: B 1760 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 1764 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8328 (mmmm) REVERT: B 1772 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8368 (ttm-80) REVERT: B 1789 LYS cc_start: 0.8855 (tppp) cc_final: 0.8574 (tppp) REVERT: B 1818 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8423 (mmmm) REVERT: B 1824 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 1826 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8708 (mmm-85) REVERT: B 1828 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8333 (mtp85) REVERT: B 1833 GLU cc_start: 0.7953 (tp30) cc_final: 0.7072 (tp30) REVERT: B 1837 GLU cc_start: 0.8373 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 1840 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.7938 (ttm110) REVERT: B 1848 LEU cc_start: 0.9102 (tp) cc_final: 0.8749 (tt) REVERT: B 1853 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8007 (tpp80) REVERT: B 1860 PHE cc_start: 0.8527 (t80) cc_final: 0.8177 (t80) REVERT: B 1865 ASP cc_start: 0.8025 (m-30) cc_final: 0.7680 (m-30) REVERT: B 1866 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8262 (tmm-80) REVERT: B 1870 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 1871 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7636 (ptt90) REVERT: B 1873 GLN cc_start: 0.8768 (tp40) cc_final: 0.8247 (tm-30) REVERT: B 1882 LYS cc_start: 0.9114 (tttp) cc_final: 0.8806 (tttm) REVERT: B 1884 LYS cc_start: 0.8633 (tppp) cc_final: 0.8411 (tppp) REVERT: B 1888 ARG cc_start: 0.8370 (mtp85) cc_final: 0.8161 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8608 (mt0) cc_final: 0.8224 (tp40) REVERT: B 1896 ILE cc_start: 0.8934 (mt) cc_final: 0.8733 (mt) REVERT: B 1903 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8604 (mmtt) REVERT: B 1906 LYS cc_start: 0.9108 (tppt) cc_final: 0.8796 (tppt) REVERT: B 1910 GLU cc_start: 0.8055 (pp20) cc_final: 0.7854 (pp20) REVERT: B 1911 LEU cc_start: 0.8538 (tt) cc_final: 0.7846 (tt) REVERT: B 1915 GLU cc_start: 0.8143 (pt0) cc_final: 0.7800 (pt0) REVERT: A 928 MET cc_start: 0.6947 (mmp) cc_final: 0.6716 (mmp) REVERT: A 944 MET cc_start: 0.7146 (ptt) cc_final: 0.6810 (ptt) REVERT: A 959 LYS cc_start: 0.8684 (ptpt) cc_final: 0.8375 (mttm) REVERT: A 980 ASP cc_start: 0.8312 (m-30) cc_final: 0.8091 (m-30) REVERT: A 1016 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 1043 GLU cc_start: 0.8366 (tp30) cc_final: 0.7761 (mt-10) REVERT: A 1179 MET cc_start: 0.6508 (ppp) cc_final: 0.6136 (ppp) REVERT: A 1187 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 1226 GLU cc_start: 0.6393 (tm-30) cc_final: 0.6058 (tm-30) REVERT: A 1273 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6879 (mm-30) REVERT: A 1276 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7834 (ptp-110) REVERT: A 1282 ASP cc_start: 0.7140 (t0) cc_final: 0.6736 (t0) REVERT: A 1297 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8399 (mtp85) REVERT: A 1298 GLN cc_start: 0.8195 (mp10) cc_final: 0.7975 (mm110) REVERT: A 1300 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8032 (mm-30) REVERT: A 1345 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 1353 GLU cc_start: 0.8335 (mp0) cc_final: 0.7871 (mp0) REVERT: A 1356 GLU cc_start: 0.7797 (tp30) cc_final: 0.6953 (tp30) REVERT: A 1358 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 1419 VAL cc_start: 0.8850 (m) cc_final: 0.8475 (p) REVERT: A 1424 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7740 (mmmm) REVERT: A 1427 GLN cc_start: 0.7437 (pp30) cc_final: 0.6969 (pp30) REVERT: A 1434 GLU cc_start: 0.8118 (mp0) cc_final: 0.7709 (mp0) REVERT: A 1439 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6338 (tm-30) REVERT: A 1440 VAL cc_start: 0.8680 (m) cc_final: 0.8389 (p) REVERT: A 1451 GLU cc_start: 0.7656 (pt0) cc_final: 0.7228 (pt0) REVERT: A 1453 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8429 (mtpp) REVERT: A 1458 ASP cc_start: 0.7585 (p0) cc_final: 0.7209 (p0) REVERT: A 1463 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 1465 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7176 (mmtm) REVERT: A 1467 LYS cc_start: 0.7691 (mttm) cc_final: 0.7268 (ttmm) REVERT: A 1475 LEU cc_start: 0.8742 (tp) cc_final: 0.8469 (tt) REVERT: A 1480 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8374 (mmmm) REVERT: A 1482 CYS cc_start: 0.8275 (m) cc_final: 0.8019 (p) REVERT: A 1488 GLU cc_start: 0.7392 (tp30) cc_final: 0.6424 (tp30) REVERT: A 1506 VAL cc_start: 0.8111 (m) cc_final: 0.7255 (p) REVERT: A 1510 ASN cc_start: 0.7986 (m-40) cc_final: 0.7767 (m-40) REVERT: A 1511 LYS cc_start: 0.8937 (mptt) cc_final: 0.8661 (mmmm) REVERT: A 1523 GLN cc_start: 0.7900 (mt0) cc_final: 0.7497 (tt0) REVERT: A 1542 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6979 (tm-30) REVERT: A 1563 GLU cc_start: 0.8012 (tp30) cc_final: 0.7634 (tp30) REVERT: A 1567 LEU cc_start: 0.9088 (mt) cc_final: 0.8846 (mm) REVERT: A 1570 GLN cc_start: 0.8437 (mt0) cc_final: 0.7910 (mm-40) REVERT: A 1576 VAL cc_start: 0.8884 (m) cc_final: 0.8680 (p) REVERT: A 1598 HIS cc_start: 0.8751 (t70) cc_final: 0.8230 (t-170) REVERT: A 1623 LYS cc_start: 0.8258 (tppt) cc_final: 0.7752 (tppt) REVERT: A 1624 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8645 (tppt) REVERT: A 1634 GLU cc_start: 0.8057 (pt0) cc_final: 0.7755 (pt0) REVERT: A 1637 LEU cc_start: 0.8735 (mt) cc_final: 0.8411 (mm) REVERT: A 1642 LYS cc_start: 0.8470 (mtmt) cc_final: 0.7867 (mtpp) REVERT: A 1646 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 1662 GLN cc_start: 0.8577 (tt0) cc_final: 0.8268 (tp40) REVERT: A 1705 ARG cc_start: 0.8322 (ttt90) cc_final: 0.7966 (ttm110) REVERT: A 1711 GLU cc_start: 0.7905 (pt0) cc_final: 0.7180 (pt0) REVERT: A 1712 GLN cc_start: 0.8834 (mm110) cc_final: 0.8223 (mm-40) REVERT: A 1723 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 1729 THR cc_start: 0.8821 (p) cc_final: 0.8615 (t) REVERT: A 1737 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8736 (ttpp) REVERT: A 1741 GLU cc_start: 0.8267 (tp30) cc_final: 0.7952 (tp30) REVERT: A 1754 ASN cc_start: 0.8456 (t0) cc_final: 0.8216 (t0) REVERT: A 1757 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8620 (ttpt) REVERT: A 1776 GLU cc_start: 0.7949 (tp30) cc_final: 0.7193 (tp30) REVERT: A 1778 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7916 (mtt-85) REVERT: A 1780 GLU cc_start: 0.8065 (tt0) cc_final: 0.7680 (tt0) REVERT: A 1782 ASP cc_start: 0.8097 (t0) cc_final: 0.7834 (t0) REVERT: A 1783 HIS cc_start: 0.9145 (t70) cc_final: 0.8873 (t-170) REVERT: A 1789 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8839 (ttmm) REVERT: A 1792 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8975 (ttmm) REVERT: A 1795 GLU cc_start: 0.7705 (tp30) cc_final: 0.7458 (tp30) REVERT: A 1796 THR cc_start: 0.8900 (p) cc_final: 0.8655 (t) REVERT: A 1807 GLU cc_start: 0.7815 (pp20) cc_final: 0.7564 (pp20) REVERT: A 1809 GLU cc_start: 0.8455 (pt0) cc_final: 0.8040 (pt0) REVERT: A 1818 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8470 (mmtt) REVERT: A 1822 LYS cc_start: 0.8591 (tttm) cc_final: 0.8207 (ttpp) REVERT: A 1824 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 1839 ARG cc_start: 0.8306 (tmt170) cc_final: 0.7901 (tmt170) REVERT: A 1846 LYS cc_start: 0.9193 (tttm) cc_final: 0.8790 (ttmm) REVERT: A 1850 LYS cc_start: 0.8855 (ptpt) cc_final: 0.8484 (ptpt) REVERT: A 1853 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7763 (ttm110) REVERT: A 1860 PHE cc_start: 0.9054 (t80) cc_final: 0.8787 (t80) REVERT: A 1864 GLU cc_start: 0.7925 (tp30) cc_final: 0.7316 (tp30) REVERT: A 1865 ASP cc_start: 0.8126 (t0) cc_final: 0.7810 (t0) REVERT: A 1868 ASN cc_start: 0.8689 (m110) cc_final: 0.7961 (m-40) REVERT: A 1870 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 1882 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8925 (ttmm) REVERT: A 1889 GLN cc_start: 0.7896 (pp30) cc_final: 0.7556 (pp30) REVERT: A 1892 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 1909 GLN cc_start: 0.8617 (tp40) cc_final: 0.8110 (tm-30) REVERT: A 1910 GLU cc_start: 0.8494 (tt0) cc_final: 0.7808 (tt0) REVERT: A 1915 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7634 (tm-30) outliers start: 3 outliers final: 0 residues processed: 619 average time/residue: 0.1571 time to fit residues: 138.6909 Evaluate side-chains 541 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 540 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 208 optimal weight: 0.3980 chunk 159 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1080 ASN ** B1172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1245 GLN B1644 ASN B1783 HIS B1900 ASN A1263 GLN A1889 GLN A1900 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.123377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103092 restraints weight = 49309.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.105873 restraints weight = 28651.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.107783 restraints weight = 18647.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.109124 restraints weight = 12938.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.110053 restraints weight = 9451.222| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 1.1151 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= 0.146 Angle : 0.611 7.379 23282 Z= 0.337 Chirality : 0.041 0.140 2582 Planarity : 0.003 0.056 3158 Dihedral : 4.285 16.153 2318 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.18), residues: 2150 helix: 1.57 (0.11), residues: 2108 sheet: None (None), residues: 0 loop : 0.60 (0.86), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1840 TYR 0.027 0.003 TYR A1886 PHE 0.019 0.002 PHE B1281 TRP 0.026 0.003 TRP A1379 HIS 0.008 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00288 (17454) covalent geometry : angle 0.61108 (23282) hydrogen bonds : bond 0.04110 ( 1625) hydrogen bonds : angle 3.70029 ( 4872) *********************** 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 635 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 632 time to evaluate : 0.613 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 1047 GLU cc_start: 0.8343 (mp0) cc_final: 0.8112 (pm20) REVERT: B 1194 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 1211 MET cc_start: 0.8197 (ptp) cc_final: 0.7613 (ptp) REVERT: B 1243 LEU cc_start: 0.8379 (tt) cc_final: 0.7991 (tt) REVERT: B 1245 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7789 (pp30) REVERT: B 1246 MET cc_start: 0.7596 (ppp) cc_final: 0.7298 (ppp) REVERT: B 1249 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 1250 LYS cc_start: 0.8737 (ptmt) cc_final: 0.8461 (ptpt) REVERT: B 1254 GLU cc_start: 0.8052 (tp30) cc_final: 0.7697 (tp30) REVERT: B 1261 GLN cc_start: 0.9013 (tt0) cc_final: 0.7158 (tm-30) REVERT: B 1264 VAL cc_start: 0.8291 (p) cc_final: 0.7949 (p) REVERT: B 1288 LEU cc_start: 0.7825 (tp) cc_final: 0.7411 (mm) REVERT: B 1291 GLU cc_start: 0.7484 (tp30) cc_final: 0.6807 (tp30) REVERT: B 1292 ASN cc_start: 0.8285 (m110) cc_final: 0.8075 (m110) REVERT: B 1300 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 1303 GLU cc_start: 0.7894 (pt0) cc_final: 0.7211 (pp20) REVERT: B 1317 THR cc_start: 0.8660 (p) cc_final: 0.8433 (t) REVERT: B 1349 ASP cc_start: 0.7425 (m-30) cc_final: 0.7162 (m-30) REVERT: B 1355 LEU cc_start: 0.8154 (tp) cc_final: 0.7818 (tp) REVERT: B 1358 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 1395 GLU cc_start: 0.7163 (pp20) cc_final: 0.6683 (tm-30) REVERT: B 1400 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8308 (mtmm) REVERT: B 1409 GLU cc_start: 0.7660 (pt0) cc_final: 0.7326 (pt0) REVERT: B 1423 GLU cc_start: 0.8420 (pt0) cc_final: 0.8053 (pt0) REVERT: B 1455 LYS cc_start: 0.8279 (mptt) cc_final: 0.7997 (mptt) REVERT: B 1457 ILE cc_start: 0.8815 (pt) cc_final: 0.8334 (mm) REVERT: B 1460 ILE cc_start: 0.8657 (tt) cc_final: 0.8350 (tt) REVERT: B 1464 TRP cc_start: 0.7956 (m100) cc_final: 0.6781 (m100) REVERT: B 1471 LEU cc_start: 0.8827 (mt) cc_final: 0.8551 (mm) REVERT: B 1479 GLN cc_start: 0.8695 (mm110) cc_final: 0.8388 (mm110) REVERT: B 1481 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7657 (mp0) REVERT: B 1497 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 1498 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 1504 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 1509 GLU cc_start: 0.8313 (tt0) cc_final: 0.8016 (tt0) REVERT: B 1515 ASP cc_start: 0.7627 (p0) cc_final: 0.6622 (p0) REVERT: B 1516 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 1535 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 1536 LYS cc_start: 0.8866 (tttm) cc_final: 0.8475 (tttm) REVERT: B 1538 LYS cc_start: 0.8931 (pptt) cc_final: 0.8612 (pptt) REVERT: B 1546 ASP cc_start: 0.8611 (m-30) cc_final: 0.8176 (m-30) REVERT: B 1549 GLN cc_start: 0.8441 (pp30) cc_final: 0.7966 (pp30) REVERT: B 1562 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7904 (tt0) REVERT: B 1565 LYS cc_start: 0.8065 (tmtt) cc_final: 0.7673 (tmtt) REVERT: B 1573 LEU cc_start: 0.8624 (pp) cc_final: 0.8419 (tt) REVERT: B 1577 ARG cc_start: 0.8277 (ttp-170) cc_final: 0.7972 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7368 (pp30) cc_final: 0.6729 (pp30) REVERT: B 1588 GLU cc_start: 0.8222 (pm20) cc_final: 0.7912 (pm20) REVERT: B 1592 GLU cc_start: 0.8321 (mp0) cc_final: 0.7855 (mp0) REVERT: B 1597 ASN cc_start: 0.8755 (m-40) cc_final: 0.7115 (m-40) REVERT: B 1600 ARG cc_start: 0.8470 (mtm110) cc_final: 0.8218 (ptt-90) REVERT: B 1606 GLN cc_start: 0.8424 (mm110) cc_final: 0.8206 (tt0) REVERT: B 1614 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8455 (mtpp) REVERT: B 1627 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 1634 GLU cc_start: 0.8129 (tp30) cc_final: 0.7312 (tp30) REVERT: B 1638 ASP cc_start: 0.7906 (t0) cc_final: 0.7442 (t0) REVERT: B 1646 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 1651 ILE cc_start: 0.9085 (mt) cc_final: 0.8595 (mt) REVERT: B 1653 LYS cc_start: 0.9089 (tttt) cc_final: 0.8722 (ttpp) REVERT: B 1655 GLN cc_start: 0.8918 (mt0) cc_final: 0.8480 (mm-40) REVERT: B 1657 GLN cc_start: 0.7708 (tp40) cc_final: 0.7330 (tp40) REVERT: B 1670 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7941 (ttp80) REVERT: B 1677 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 1678 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8202 (mp10) REVERT: B 1683 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 1720 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8409 (tp40) REVERT: B 1736 ARG cc_start: 0.8869 (mpt-90) cc_final: 0.8454 (mpt-90) REVERT: B 1737 LYS cc_start: 0.9369 (tmtt) cc_final: 0.8991 (tptp) REVERT: B 1739 GLU cc_start: 0.8373 (tt0) cc_final: 0.8123 (tp30) REVERT: B 1741 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 1744 THR cc_start: 0.8756 (p) cc_final: 0.8526 (p) REVERT: B 1757 LYS cc_start: 0.8872 (tttp) cc_final: 0.8467 (ttpp) REVERT: B 1759 SER cc_start: 0.8861 (p) cc_final: 0.8392 (p) REVERT: B 1760 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 1762 LYS cc_start: 0.8643 (mttp) cc_final: 0.8335 (mttp) REVERT: B 1764 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8564 (mmmm) REVERT: B 1772 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8387 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8111 (t0) cc_final: 0.7867 (t0) REVERT: B 1799 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8924 (mmmt) REVERT: B 1818 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8490 (mmmm) REVERT: B 1820 ILE cc_start: 0.8348 (mt) cc_final: 0.8071 (tp) REVERT: B 1824 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 1826 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8676 (mmm-85) REVERT: B 1828 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8253 (mtp85) REVERT: B 1833 GLU cc_start: 0.8110 (tp30) cc_final: 0.7256 (tp30) REVERT: B 1837 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8172 (tp30) REVERT: B 1838 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8759 (mm-40) REVERT: B 1853 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8194 (tpp80) REVERT: B 1854 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8364 (mtp85) REVERT: B 1860 PHE cc_start: 0.8564 (t80) cc_final: 0.8126 (t80) REVERT: B 1863 ASP cc_start: 0.7681 (m-30) cc_final: 0.7230 (m-30) REVERT: B 1865 ASP cc_start: 0.8027 (m-30) cc_final: 0.7760 (m-30) REVERT: B 1866 ARG cc_start: 0.8586 (ttp-170) cc_final: 0.8062 (tmm-80) REVERT: B 1871 ARG cc_start: 0.8116 (ptt90) cc_final: 0.7796 (ptt90) REVERT: B 1873 GLN cc_start: 0.8892 (tp40) cc_final: 0.8377 (tm-30) REVERT: B 1878 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7844 (mmmt) REVERT: B 1881 GLN cc_start: 0.8520 (pm20) cc_final: 0.8272 (pm20) REVERT: B 1882 LYS cc_start: 0.9193 (tttp) cc_final: 0.8571 (tmtt) REVERT: B 1888 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8213 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8737 (mt0) cc_final: 0.8294 (tp40) REVERT: B 1896 ILE cc_start: 0.8963 (mt) cc_final: 0.8762 (mt) REVERT: B 1903 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8628 (mmtt) REVERT: B 1906 LYS cc_start: 0.9160 (tppt) cc_final: 0.8769 (tppt) REVERT: B 1908 GLN cc_start: 0.8481 (tp40) cc_final: 0.8088 (tp-100) REVERT: B 1910 GLU cc_start: 0.8119 (pp20) cc_final: 0.7857 (pp20) REVERT: B 1911 LEU cc_start: 0.8554 (tt) cc_final: 0.7951 (tt) REVERT: B 1915 GLU cc_start: 0.8314 (pt0) cc_final: 0.7920 (pt0) REVERT: B 1917 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8472 (ttp-110) REVERT: A 952 GLU cc_start: 0.8496 (pt0) cc_final: 0.7711 (tp30) REVERT: A 980 ASP cc_start: 0.8287 (m-30) cc_final: 0.8079 (m-30) REVERT: A 1016 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 1041 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7064 (pm20) REVERT: A 1170 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 1179 MET cc_start: 0.6598 (ppp) cc_final: 0.6188 (ppp) REVERT: A 1188 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6234 (tm-30) REVERT: A 1202 LYS cc_start: 0.8710 (pptt) cc_final: 0.8436 (pptt) REVERT: A 1250 LYS cc_start: 0.8562 (pptt) cc_final: 0.8325 (pptt) REVERT: A 1270 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8528 (mmtp) REVERT: A 1273 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 1276 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7783 (ptp-110) REVERT: A 1282 ASP cc_start: 0.7512 (t0) cc_final: 0.7134 (t0) REVERT: A 1300 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 1319 GLN cc_start: 0.8211 (mt0) cc_final: 0.7983 (mt0) REVERT: A 1333 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 1345 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 1353 GLU cc_start: 0.8425 (mp0) cc_final: 0.7954 (mp0) REVERT: A 1356 GLU cc_start: 0.8115 (tp30) cc_final: 0.7456 (tp30) REVERT: A 1358 GLU cc_start: 0.8155 (mm-30) cc_final: 0.6989 (mm-30) REVERT: A 1393 GLU cc_start: 0.7695 (pp20) cc_final: 0.7048 (pp20) REVERT: A 1407 GLU cc_start: 0.7894 (pp20) cc_final: 0.7659 (pp20) REVERT: A 1409 GLU cc_start: 0.7030 (tm-30) cc_final: 0.5486 (tm-30) REVERT: A 1413 GLU cc_start: 0.7344 (pm20) cc_final: 0.6839 (pm20) REVERT: A 1434 GLU cc_start: 0.8304 (mp0) cc_final: 0.8056 (mm-30) REVERT: A 1439 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6692 (tm-30) REVERT: A 1442 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7793 (tmm-80) REVERT: A 1451 GLU cc_start: 0.7905 (pt0) cc_final: 0.7601 (pt0) REVERT: A 1458 ASP cc_start: 0.7802 (p0) cc_final: 0.6947 (p0) REVERT: A 1463 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 1465 LYS cc_start: 0.7787 (mmpt) cc_final: 0.7249 (tppt) REVERT: A 1488 GLU cc_start: 0.7451 (tp30) cc_final: 0.6548 (tp30) REVERT: A 1492 LEU cc_start: 0.8639 (mt) cc_final: 0.8092 (mm) REVERT: A 1501 GLU cc_start: 0.8462 (pt0) cc_final: 0.8175 (pt0) REVERT: A 1504 GLU cc_start: 0.7812 (mp0) cc_final: 0.7501 (mp0) REVERT: A 1511 LYS cc_start: 0.8871 (mptt) cc_final: 0.8454 (mmmm) REVERT: A 1523 GLN cc_start: 0.7880 (mt0) cc_final: 0.7425 (tt0) REVERT: A 1542 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 1556 GLU cc_start: 0.7925 (pp20) cc_final: 0.7402 (pp20) REVERT: A 1561 GLN cc_start: 0.7457 (pp30) cc_final: 0.7017 (pp30) REVERT: A 1563 GLU cc_start: 0.8125 (tp30) cc_final: 0.7677 (tp30) REVERT: A 1567 LEU cc_start: 0.9069 (mt) cc_final: 0.8815 (mm) REVERT: A 1570 GLN cc_start: 0.8370 (mt0) cc_final: 0.8054 (mm-40) REVERT: A 1589 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 1598 HIS cc_start: 0.8444 (t70) cc_final: 0.8161 (t70) REVERT: A 1599 GLN cc_start: 0.8579 (tt0) cc_final: 0.8141 (tp40) REVERT: A 1624 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8655 (tppt) REVERT: A 1625 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8532 (mtpp) REVERT: A 1637 LEU cc_start: 0.8790 (mt) cc_final: 0.8389 (tt) REVERT: A 1642 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7913 (mtpp) REVERT: A 1644 ASN cc_start: 0.8312 (p0) cc_final: 0.8066 (t0) REVERT: A 1646 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 1649 LYS cc_start: 0.9101 (tttp) cc_final: 0.8643 (ttpp) REVERT: A 1660 ASP cc_start: 0.8236 (p0) cc_final: 0.7951 (p0) REVERT: A 1662 GLN cc_start: 0.8641 (tt0) cc_final: 0.8098 (tp40) REVERT: A 1692 GLU cc_start: 0.8159 (tp30) cc_final: 0.7911 (tp30) REVERT: A 1705 ARG cc_start: 0.8381 (ttt90) cc_final: 0.7937 (ttm-80) REVERT: A 1712 GLN cc_start: 0.8840 (mm110) cc_final: 0.8557 (mm-40) REVERT: A 1737 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8737 (ttpp) REVERT: A 1754 ASN cc_start: 0.8541 (t0) cc_final: 0.8284 (t0) REVERT: A 1757 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8596 (ttpt) REVERT: A 1758 ASN cc_start: 0.8418 (t0) cc_final: 0.8067 (t0) REVERT: A 1776 GLU cc_start: 0.8042 (tp30) cc_final: 0.7661 (tp30) REVERT: A 1778 ARG cc_start: 0.8384 (mtt-85) cc_final: 0.7932 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8105 (t0) cc_final: 0.7831 (t0) REVERT: A 1789 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8828 (ttmm) REVERT: A 1792 LYS cc_start: 0.9274 (ttmt) cc_final: 0.8905 (ttmm) REVERT: A 1807 GLU cc_start: 0.7828 (pp20) cc_final: 0.7595 (pp20) REVERT: A 1809 GLU cc_start: 0.8382 (pt0) cc_final: 0.7982 (pt0) REVERT: A 1822 LYS cc_start: 0.8606 (tttm) cc_final: 0.8362 (ttpp) REVERT: A 1824 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 1839 ARG cc_start: 0.8405 (tmt170) cc_final: 0.8015 (tmt170) REVERT: A 1840 ARG cc_start: 0.8060 (mpp80) cc_final: 0.7655 (mtm-85) REVERT: A 1846 LYS cc_start: 0.9232 (tttm) cc_final: 0.8995 (ttmm) REVERT: A 1849 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8094 (tpp-160) REVERT: A 1853 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7715 (ttm110) REVERT: A 1858 LEU cc_start: 0.8496 (mp) cc_final: 0.8269 (mm) REVERT: A 1860 PHE cc_start: 0.9087 (t80) cc_final: 0.8842 (t80) REVERT: A 1864 GLU cc_start: 0.7974 (tp30) cc_final: 0.7356 (tp30) REVERT: A 1865 ASP cc_start: 0.8125 (t0) cc_final: 0.7747 (t0) REVERT: A 1868 ASN cc_start: 0.8696 (m110) cc_final: 0.8065 (m-40) REVERT: A 1870 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 1882 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8918 (ttmm) REVERT: A 1884 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8850 (ttpp) REVERT: A 1892 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 1909 GLN cc_start: 0.8608 (tp40) cc_final: 0.8299 (tm-30) REVERT: A 1910 GLU cc_start: 0.8496 (tt0) cc_final: 0.7991 (tt0) REVERT: A 1915 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 3 outliers final: 1 residues processed: 634 average time/residue: 0.1537 time to fit residues: 139.2816 Evaluate side-chains 583 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 580 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 184 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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** B1479 GLN B1570 GLN B1783 HIS B1900 ASN ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 HIS A1900 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.122581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.101814 restraints weight = 48584.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.104514 restraints weight = 28691.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.106363 restraints weight = 18792.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.107484 restraints weight = 13164.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.108510 restraints weight = 9914.948| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 1.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17454 Z= 0.142 Angle : 0.620 8.263 23282 Z= 0.339 Chirality : 0.041 0.140 2582 Planarity : 0.003 0.019 3158 Dihedral : 4.261 15.521 2318 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.18), residues: 2150 helix: 1.74 (0.11), residues: 2107 sheet: None (None), residues: 0 loop : 0.78 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1804 TYR 0.025 0.003 TYR A1383 PHE 0.015 0.002 PHE B1281 TRP 0.022 0.003 TRP A1379 HIS 0.011 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00279 (17454) covalent geometry : angle 0.61955 (23282) hydrogen bonds : bond 0.04082 ( 1625) hydrogen bonds : angle 3.68067 ( 4872) *********************** 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 647 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 646 time to evaluate : 0.693 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 1224 LYS cc_start: 0.7924 (tppp) cc_final: 0.7344 (tppp) REVERT: B 1248 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7844 (mmt180) REVERT: B 1249 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 1250 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8382 (ptmt) REVERT: B 1261 GLN cc_start: 0.8894 (tt0) cc_final: 0.7528 (tm-30) REVERT: B 1265 ASN cc_start: 0.8443 (m110) cc_final: 0.7371 (m110) REVERT: B 1268 GLN cc_start: 0.8335 (pt0) cc_final: 0.7868 (tt0) REVERT: B 1271 LEU cc_start: 0.9216 (mt) cc_final: 0.8947 (tp) REVERT: B 1288 LEU cc_start: 0.8137 (tp) cc_final: 0.7835 (mt) REVERT: B 1292 ASN cc_start: 0.8413 (m110) cc_final: 0.8207 (m110) REVERT: B 1303 GLU cc_start: 0.8107 (pt0) cc_final: 0.7370 (pp20) REVERT: B 1320 LEU cc_start: 0.8860 (mm) cc_final: 0.8583 (tt) REVERT: B 1349 ASP cc_start: 0.7342 (m-30) cc_final: 0.7128 (m-30) REVERT: B 1355 LEU cc_start: 0.8564 (tp) cc_final: 0.8306 (tp) REVERT: B 1357 GLU cc_start: 0.7735 (tp30) cc_final: 0.7055 (tp30) REVERT: B 1358 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 1367 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7772 (tpp80) REVERT: B 1384 GLU cc_start: 0.4971 (mt-10) cc_final: 0.3163 (mt-10) REVERT: B 1395 GLU cc_start: 0.7186 (pp20) cc_final: 0.6780 (tm-30) REVERT: B 1400 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8468 (mtmm) REVERT: B 1423 GLU cc_start: 0.8491 (pt0) cc_final: 0.8168 (pt0) REVERT: B 1431 THR cc_start: 0.8692 (m) cc_final: 0.8295 (t) REVERT: B 1455 LYS cc_start: 0.8343 (mptt) cc_final: 0.8001 (mptt) REVERT: B 1457 ILE cc_start: 0.8840 (pt) cc_final: 0.8399 (mm) REVERT: B 1458 ASP cc_start: 0.7456 (t0) cc_final: 0.7235 (t0) REVERT: B 1460 ILE cc_start: 0.8689 (tt) cc_final: 0.8223 (tt) REVERT: B 1461 ILE cc_start: 0.7742 (mm) cc_final: 0.7443 (mm) REVERT: B 1464 TRP cc_start: 0.7763 (m100) cc_final: 0.6401 (m100) REVERT: B 1471 LEU cc_start: 0.8812 (mt) cc_final: 0.8605 (mm) REVERT: B 1479 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8219 (mm110) REVERT: B 1481 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7674 (mp0) REVERT: B 1492 LEU cc_start: 0.8583 (mp) cc_final: 0.8358 (mm) REVERT: B 1498 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7476 (tm-30) REVERT: B 1504 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 1509 GLU cc_start: 0.8329 (tt0) cc_final: 0.8062 (tt0) REVERT: B 1516 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 1536 LYS cc_start: 0.8902 (tttm) cc_final: 0.8583 (tttm) REVERT: B 1538 LYS cc_start: 0.8962 (pptt) cc_final: 0.8738 (pptt) REVERT: B 1540 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7465 (ttp80) REVERT: B 1544 GLU cc_start: 0.8367 (pt0) cc_final: 0.7838 (pt0) REVERT: B 1549 GLN cc_start: 0.8302 (pp30) cc_final: 0.7855 (tm-30) REVERT: B 1556 GLU cc_start: 0.7847 (mp0) cc_final: 0.7495 (mp0) REVERT: B 1562 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8007 (tt0) REVERT: B 1582 ARG cc_start: 0.8202 (ptt90) cc_final: 0.7888 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7353 (pp30) cc_final: 0.6753 (pp30) REVERT: B 1586 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6373 (mm-30) REVERT: B 1587 LYS cc_start: 0.8518 (tttp) cc_final: 0.8145 (ttpp) REVERT: B 1590 GLU cc_start: 0.8627 (mp0) cc_final: 0.8221 (mp0) REVERT: B 1593 ASN cc_start: 0.8077 (t0) cc_final: 0.7435 (t0) REVERT: B 1597 ASN cc_start: 0.8742 (m-40) cc_final: 0.6863 (m-40) REVERT: B 1614 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8403 (mtpp) REVERT: B 1622 MET cc_start: 0.7657 (ppp) cc_final: 0.7111 (ppp) REVERT: B 1627 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 1634 GLU cc_start: 0.8083 (tp30) cc_final: 0.7279 (tp30) REVERT: B 1638 ASP cc_start: 0.7952 (t0) cc_final: 0.7457 (t0) REVERT: B 1644 ASN cc_start: 0.8537 (m-40) cc_final: 0.8189 (t0) REVERT: B 1646 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 1651 ILE cc_start: 0.9094 (mt) cc_final: 0.8870 (mt) REVERT: B 1653 LYS cc_start: 0.9087 (tttt) cc_final: 0.8690 (ttmm) REVERT: B 1655 GLN cc_start: 0.8895 (mt0) cc_final: 0.8552 (mm-40) REVERT: B 1657 GLN cc_start: 0.7798 (tp40) cc_final: 0.7450 (tp40) REVERT: B 1667 GLU cc_start: 0.7979 (tp30) cc_final: 0.6383 (tp30) REVERT: B 1670 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7765 (ttp80) REVERT: B 1677 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 1678 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8123 (mp10) REVERT: B 1683 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 1691 ASN cc_start: 0.7693 (p0) cc_final: 0.5332 (p0) REVERT: B 1720 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8381 (tp40) REVERT: B 1737 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9070 (tptp) REVERT: B 1741 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 1757 LYS cc_start: 0.8865 (tttp) cc_final: 0.8449 (ttpp) REVERT: B 1759 SER cc_start: 0.8862 (p) cc_final: 0.8498 (p) REVERT: B 1760 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 1762 LYS cc_start: 0.8673 (mttp) cc_final: 0.8410 (mttp) REVERT: B 1764 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8524 (mmmm) REVERT: B 1772 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8405 (ttm-80) REVERT: B 1789 LYS cc_start: 0.8895 (tppp) cc_final: 0.8541 (tppp) REVERT: B 1818 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8516 (tppt) REVERT: B 1820 ILE cc_start: 0.8334 (mt) cc_final: 0.8083 (tp) REVERT: B 1824 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 1828 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8212 (mtp85) REVERT: B 1833 GLU cc_start: 0.8047 (tp30) cc_final: 0.7188 (tp30) REVERT: B 1837 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 1838 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8664 (mm-40) REVERT: B 1840 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8112 (ttm-80) REVERT: B 1848 LEU cc_start: 0.8995 (tp) cc_final: 0.8792 (tt) REVERT: B 1852 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7996 (tp30) REVERT: B 1853 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8168 (tpp80) REVERT: B 1863 ASP cc_start: 0.7675 (m-30) cc_final: 0.7281 (m-30) REVERT: B 1865 ASP cc_start: 0.8009 (m-30) cc_final: 0.7702 (m-30) REVERT: B 1866 ARG cc_start: 0.8609 (ttp-170) cc_final: 0.7804 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8521 (mmmm) REVERT: B 1870 GLU cc_start: 0.7890 (mt-10) cc_final: 0.6381 (mt-10) REVERT: B 1871 ARG cc_start: 0.8225 (ptt90) cc_final: 0.7792 (ptt90) REVERT: B 1873 GLN cc_start: 0.8797 (tp40) cc_final: 0.8338 (tm-30) REVERT: B 1878 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7808 (mmmt) REVERT: B 1882 LYS cc_start: 0.9176 (tttp) cc_final: 0.8744 (tttm) REVERT: B 1888 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8301 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8723 (mt0) cc_final: 0.8288 (tp40) REVERT: B 1903 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8632 (mmtt) REVERT: B 1906 LYS cc_start: 0.9188 (tppt) cc_final: 0.8840 (tppt) REVERT: B 1908 GLN cc_start: 0.8508 (tp40) cc_final: 0.8066 (tp-100) REVERT: B 1911 LEU cc_start: 0.8557 (tt) cc_final: 0.7938 (tt) REVERT: B 1915 GLU cc_start: 0.8274 (pt0) cc_final: 0.7888 (pt0) REVERT: B 1917 ARG cc_start: 0.9050 (mtp-110) cc_final: 0.8568 (ttp-110) REVERT: A 952 GLU cc_start: 0.8483 (pt0) cc_final: 0.7547 (mt-10) REVERT: A 1016 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8379 (mt-10) REVERT: A 1092 ASP cc_start: 0.8059 (t0) cc_final: 0.7842 (t0) REVERT: A 1170 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8475 (mt-10) REVERT: A 1202 LYS cc_start: 0.8811 (pptt) cc_final: 0.8472 (pptt) REVERT: A 1215 ILE cc_start: 0.7936 (pt) cc_final: 0.7628 (pt) REVERT: A 1221 LEU cc_start: 0.7460 (tt) cc_final: 0.6942 (tp) REVERT: A 1250 LYS cc_start: 0.8588 (pptt) cc_final: 0.8248 (pptt) REVERT: A 1261 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8427 (tp40) REVERT: A 1273 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 1276 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7557 (ttm110) REVERT: A 1297 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8441 (ttm-80) REVERT: A 1300 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8207 (mm-30) REVERT: A 1329 GLU cc_start: 0.8236 (tp30) cc_final: 0.7740 (tp30) REVERT: A 1344 LEU cc_start: 0.8264 (tp) cc_final: 0.8018 (tp) REVERT: A 1353 GLU cc_start: 0.8511 (mp0) cc_final: 0.8015 (mp0) REVERT: A 1356 GLU cc_start: 0.8192 (tp30) cc_final: 0.7813 (tp30) REVERT: A 1357 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 1379 TRP cc_start: 0.6914 (m100) cc_final: 0.6670 (m100) REVERT: A 1399 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8228 (mtm110) REVERT: A 1407 GLU cc_start: 0.7874 (pp20) cc_final: 0.7531 (pp20) REVERT: A 1409 GLU cc_start: 0.7193 (tm-30) cc_final: 0.5650 (tm-30) REVERT: A 1413 GLU cc_start: 0.7347 (pm20) cc_final: 0.6711 (pm20) REVERT: A 1423 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 1424 LYS cc_start: 0.8682 (tptm) cc_final: 0.8275 (tppt) REVERT: A 1425 THR cc_start: 0.9030 (p) cc_final: 0.8776 (t) REVERT: A 1434 GLU cc_start: 0.8258 (mp0) cc_final: 0.7990 (mm-30) REVERT: A 1439 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 1442 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7758 (tmm-80) REVERT: A 1458 ASP cc_start: 0.7881 (p0) cc_final: 0.7275 (p0) REVERT: A 1463 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 1465 LYS cc_start: 0.7742 (mmpt) cc_final: 0.6990 (tppt) REVERT: A 1469 ASP cc_start: 0.7370 (t0) cc_final: 0.6893 (t0) REVERT: A 1488 GLU cc_start: 0.7558 (tp30) cc_final: 0.6527 (tp30) REVERT: A 1489 LEU cc_start: 0.8834 (tt) cc_final: 0.8420 (tp) REVERT: A 1492 LEU cc_start: 0.8641 (mt) cc_final: 0.7897 (mm) REVERT: A 1511 LYS cc_start: 0.8876 (mptt) cc_final: 0.8471 (mmmm) REVERT: A 1516 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7027 (mm-30) REVERT: A 1542 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 1561 GLN cc_start: 0.7655 (pp30) cc_final: 0.7190 (pp30) REVERT: A 1563 GLU cc_start: 0.8359 (tp30) cc_final: 0.7938 (tp30) REVERT: A 1570 GLN cc_start: 0.8414 (mt0) cc_final: 0.8069 (mm-40) REVERT: A 1589 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 1599 GLN cc_start: 0.8430 (tt0) cc_final: 0.8136 (tp40) REVERT: A 1623 LYS cc_start: 0.8469 (tppt) cc_final: 0.7952 (tppt) REVERT: A 1649 LYS cc_start: 0.9113 (tttp) cc_final: 0.8587 (ttpp) REVERT: A 1662 GLN cc_start: 0.8548 (tt0) cc_final: 0.8090 (tp40) REVERT: A 1692 GLU cc_start: 0.8190 (tp30) cc_final: 0.7937 (tp30) REVERT: A 1712 GLN cc_start: 0.8811 (mm110) cc_final: 0.8505 (mm-40) REVERT: A 1732 SER cc_start: 0.8596 (t) cc_final: 0.8264 (p) REVERT: A 1737 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8756 (ttpp) REVERT: A 1741 GLU cc_start: 0.8161 (tp30) cc_final: 0.7892 (tp30) REVERT: A 1749 LEU cc_start: 0.8855 (tp) cc_final: 0.8649 (tp) REVERT: A 1754 ASN cc_start: 0.8542 (t0) cc_final: 0.8243 (t0) REVERT: A 1757 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8578 (ttpt) REVERT: A 1758 ASN cc_start: 0.8430 (t0) cc_final: 0.8067 (t0) REVERT: A 1762 LYS cc_start: 0.9264 (ttmt) cc_final: 0.9038 (ttmt) REVERT: A 1767 MET cc_start: 0.8228 (mmp) cc_final: 0.7956 (tpp) REVERT: A 1778 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8066 (t0) cc_final: 0.7829 (t0) REVERT: A 1792 LYS cc_start: 0.9255 (ttmt) cc_final: 0.8739 (tppp) REVERT: A 1807 GLU cc_start: 0.7824 (pp20) cc_final: 0.7591 (pp20) REVERT: A 1822 LYS cc_start: 0.8591 (tttm) cc_final: 0.8355 (ttpp) REVERT: A 1824 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 1834 LEU cc_start: 0.8713 (tt) cc_final: 0.8463 (tp) REVERT: A 1839 ARG cc_start: 0.8426 (tmt170) cc_final: 0.8009 (tmt170) REVERT: A 1840 ARG cc_start: 0.7993 (mpp80) cc_final: 0.7721 (mtm110) REVERT: A 1846 LYS cc_start: 0.9197 (tttm) cc_final: 0.8922 (ttmm) REVERT: A 1849 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.8086 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8771 (ptpt) cc_final: 0.8500 (ptpt) REVERT: A 1853 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7696 (ttm110) REVERT: A 1858 LEU cc_start: 0.8496 (mp) cc_final: 0.8285 (mm) REVERT: A 1860 PHE cc_start: 0.9096 (t80) cc_final: 0.8880 (t80) REVERT: A 1864 GLU cc_start: 0.7974 (tp30) cc_final: 0.7458 (tp30) REVERT: A 1865 ASP cc_start: 0.8121 (t0) cc_final: 0.7746 (t0) REVERT: A 1868 ASN cc_start: 0.8702 (m110) cc_final: 0.8201 (m-40) REVERT: A 1870 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 1878 LYS cc_start: 0.8968 (tppt) cc_final: 0.8633 (mmmm) REVERT: A 1882 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8990 (ttmm) REVERT: A 1884 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8762 (ttpp) REVERT: A 1892 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 1894 GLU cc_start: 0.7054 (pp20) cc_final: 0.6785 (pp20) REVERT: A 1909 GLN cc_start: 0.8664 (tp40) cc_final: 0.7904 (tm-30) REVERT: A 1910 GLU cc_start: 0.8481 (tt0) cc_final: 0.7735 (tt0) REVERT: A 1913 GLU cc_start: 0.7717 (pt0) cc_final: 0.6569 (pt0) REVERT: A 1915 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 1 outliers final: 1 residues processed: 647 average time/residue: 0.1572 time to fit residues: 145.4094 Evaluate side-chains 591 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 940 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1900 ASN A1298 GLN A1900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.121170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.100070 restraints weight = 48312.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.102739 restraints weight = 28604.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.104556 restraints weight = 18774.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.105813 restraints weight = 13210.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.106726 restraints weight = 9829.317| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 1.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17454 Z= 0.147 Angle : 0.644 9.119 23282 Z= 0.354 Chirality : 0.042 0.182 2582 Planarity : 0.003 0.051 3158 Dihedral : 4.278 16.372 2318 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.05 % Allowed : 1.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.18), residues: 2150 helix: 1.80 (0.11), residues: 2102 sheet: None (None), residues: 0 loop : 1.17 (0.97), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1491 TYR 0.023 0.002 TYR A1383 PHE 0.021 0.002 PHE A 945 TRP 0.029 0.004 TRP B1379 HIS 0.015 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00290 (17454) covalent geometry : angle 0.64416 (23282) hydrogen bonds : bond 0.04090 ( 1625) hydrogen bonds : angle 3.74593 ( 4872) *********************** 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 664 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 0.689 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 1057 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: B 1181 LYS cc_start: 0.8719 (tppt) cc_final: 0.8231 (tppt) REVERT: B 1182 LEU cc_start: 0.8219 (mp) cc_final: 0.8004 (mp) REVERT: B 1224 LYS cc_start: 0.7961 (tppp) cc_final: 0.7200 (tppp) REVERT: B 1248 ARG cc_start: 0.8303 (mmt180) cc_final: 0.7959 (mmt180) REVERT: B 1249 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 1250 LYS cc_start: 0.8899 (ptmt) cc_final: 0.8353 (ptmm) REVERT: B 1254 GLU cc_start: 0.8377 (tp30) cc_final: 0.7277 (tp30) REVERT: B 1261 GLN cc_start: 0.8929 (tt0) cc_final: 0.8018 (tm-30) REVERT: B 1264 VAL cc_start: 0.8814 (p) cc_final: 0.8534 (m) REVERT: B 1266 GLU cc_start: 0.7948 (pp20) cc_final: 0.7728 (pp20) REVERT: B 1268 GLN cc_start: 0.8467 (pt0) cc_final: 0.8149 (tt0) REVERT: B 1271 LEU cc_start: 0.9241 (mt) cc_final: 0.8878 (tt) REVERT: B 1300 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 1303 GLU cc_start: 0.8206 (pt0) cc_final: 0.7460 (pp20) REVERT: B 1355 LEU cc_start: 0.8699 (tp) cc_final: 0.8494 (tp) REVERT: B 1358 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 1366 GLN cc_start: 0.7778 (mm110) cc_final: 0.7537 (mm-40) REVERT: B 1367 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7908 (tpp80) REVERT: B 1382 LYS cc_start: 0.8521 (pptt) cc_final: 0.8311 (pptt) REVERT: B 1400 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8469 (mtmm) REVERT: B 1455 LYS cc_start: 0.8371 (mptt) cc_final: 0.8170 (mptt) REVERT: B 1457 ILE cc_start: 0.8996 (pt) cc_final: 0.8622 (mm) REVERT: B 1461 ILE cc_start: 0.7767 (mm) cc_final: 0.7518 (mm) REVERT: B 1464 TRP cc_start: 0.7868 (m100) cc_final: 0.7014 (m100) REVERT: B 1479 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8225 (mm110) REVERT: B 1481 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7767 (mp0) REVERT: B 1492 LEU cc_start: 0.8615 (mp) cc_final: 0.8337 (mm) REVERT: B 1497 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7045 (tm-30) REVERT: B 1498 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 1504 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 1516 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 1523 GLN cc_start: 0.8203 (mt0) cc_final: 0.7965 (mt0) REVERT: B 1538 LYS cc_start: 0.8885 (pptt) cc_final: 0.8296 (ptmm) REVERT: B 1542 GLU cc_start: 0.7775 (tp30) cc_final: 0.7257 (tp30) REVERT: B 1544 GLU cc_start: 0.8398 (pt0) cc_final: 0.7607 (pt0) REVERT: B 1547 GLU cc_start: 0.8234 (pp20) cc_final: 0.7763 (pp20) REVERT: B 1549 GLN cc_start: 0.8425 (pp30) cc_final: 0.7994 (tm-30) REVERT: B 1556 GLU cc_start: 0.7735 (mp0) cc_final: 0.7444 (mp0) REVERT: B 1562 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8078 (tt0) REVERT: B 1565 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8046 (tmtt) REVERT: B 1582 ARG cc_start: 0.8296 (ptt90) cc_final: 0.7865 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7512 (pp30) cc_final: 0.6687 (tm-30) REVERT: B 1588 GLU cc_start: 0.8278 (pm20) cc_final: 0.7855 (pm20) REVERT: B 1592 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 1593 ASN cc_start: 0.8218 (t0) cc_final: 0.7703 (t0) REVERT: B 1597 ASN cc_start: 0.8669 (m-40) cc_final: 0.8105 (m-40) REVERT: B 1598 HIS cc_start: 0.8634 (p90) cc_final: 0.8328 (p90) REVERT: B 1627 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 1634 GLU cc_start: 0.8126 (tp30) cc_final: 0.7348 (tp30) REVERT: B 1638 ASP cc_start: 0.8011 (t0) cc_final: 0.7549 (t0) REVERT: B 1644 ASN cc_start: 0.8509 (m-40) cc_final: 0.8193 (t0) REVERT: B 1651 ILE cc_start: 0.9110 (mt) cc_final: 0.8883 (mt) REVERT: B 1653 LYS cc_start: 0.9242 (tttt) cc_final: 0.8753 (ttmm) REVERT: B 1655 GLN cc_start: 0.8934 (mt0) cc_final: 0.8640 (mm-40) REVERT: B 1657 GLN cc_start: 0.7817 (tp40) cc_final: 0.7447 (tp40) REVERT: B 1667 GLU cc_start: 0.8064 (tp30) cc_final: 0.7570 (tp30) REVERT: B 1677 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 1678 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8139 (mp10) REVERT: B 1683 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 1720 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8181 (tp40) REVERT: B 1737 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9071 (tptp) REVERT: B 1741 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 1757 LYS cc_start: 0.8870 (tttp) cc_final: 0.8400 (ttpp) REVERT: B 1759 SER cc_start: 0.8993 (p) cc_final: 0.8772 (p) REVERT: B 1760 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 1762 LYS cc_start: 0.8683 (mttp) cc_final: 0.8427 (mttp) REVERT: B 1764 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8585 (mmmm) REVERT: B 1772 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8416 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8154 (t0) cc_final: 0.7884 (t0) REVERT: B 1780 GLU cc_start: 0.7566 (tp30) cc_final: 0.7149 (tp30) REVERT: B 1818 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8563 (tppt) REVERT: B 1820 ILE cc_start: 0.8399 (mt) cc_final: 0.8112 (tp) REVERT: B 1824 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8045 (mt-10) REVERT: B 1833 GLU cc_start: 0.8111 (tp30) cc_final: 0.7259 (tp30) REVERT: B 1837 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 1838 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8748 (mm-40) REVERT: B 1840 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.7803 (ttm-80) REVERT: B 1848 LEU cc_start: 0.8978 (tp) cc_final: 0.8623 (tt) REVERT: B 1853 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8210 (tpp80) REVERT: B 1865 ASP cc_start: 0.8055 (m-30) cc_final: 0.7665 (m-30) REVERT: B 1866 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.7814 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8411 (mmmm) REVERT: B 1870 GLU cc_start: 0.7828 (mt-10) cc_final: 0.6268 (mt-10) REVERT: B 1871 ARG cc_start: 0.8312 (ptt90) cc_final: 0.7839 (ptt90) REVERT: B 1873 GLN cc_start: 0.8763 (tp40) cc_final: 0.8426 (tm-30) REVERT: B 1878 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7915 (mmmt) REVERT: B 1882 LYS cc_start: 0.9220 (tttp) cc_final: 0.8685 (tmtt) REVERT: B 1884 LYS cc_start: 0.8842 (tppp) cc_final: 0.8532 (tppp) REVERT: B 1888 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8357 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8774 (mt0) cc_final: 0.8303 (tp40) REVERT: B 1903 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8658 (mmtt) REVERT: B 1906 LYS cc_start: 0.9148 (tppt) cc_final: 0.8793 (tppt) REVERT: B 1908 GLN cc_start: 0.8600 (tp40) cc_final: 0.8166 (tp-100) REVERT: B 1910 GLU cc_start: 0.8122 (pp20) cc_final: 0.7879 (pp20) REVERT: B 1911 LEU cc_start: 0.8558 (tt) cc_final: 0.8056 (tt) REVERT: B 1915 GLU cc_start: 0.8317 (pt0) cc_final: 0.7949 (pt0) REVERT: B 1917 ARG cc_start: 0.9071 (mtp-110) cc_final: 0.8612 (ttm-80) REVERT: A 928 MET cc_start: 0.7001 (mmp) cc_final: 0.6790 (mmp) REVERT: A 952 GLU cc_start: 0.8618 (pt0) cc_final: 0.7590 (mt-10) REVERT: A 961 ASP cc_start: 0.7254 (t0) cc_final: 0.6588 (m-30) REVERT: A 1009 GLU cc_start: 0.7527 (pm20) cc_final: 0.6986 (mm-30) REVERT: A 1012 GLN cc_start: 0.7869 (tt0) cc_final: 0.7528 (tt0) REVERT: A 1188 GLU cc_start: 0.7325 (tp30) cc_final: 0.7034 (tp30) REVERT: A 1215 ILE cc_start: 0.7933 (pt) cc_final: 0.7603 (pt) REVERT: A 1250 LYS cc_start: 0.8631 (pptt) cc_final: 0.8258 (pptt) REVERT: A 1261 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8610 (tp40) REVERT: A 1263 GLN cc_start: 0.8794 (mt0) cc_final: 0.8548 (mt0) REVERT: A 1267 ILE cc_start: 0.8575 (pt) cc_final: 0.8369 (pt) REVERT: A 1270 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8463 (mtmm) REVERT: A 1273 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 1276 ARG cc_start: 0.8171 (mtp-110) cc_final: 0.7530 (ttm-80) REVERT: A 1288 LEU cc_start: 0.8765 (mt) cc_final: 0.8444 (mm) REVERT: A 1291 GLU cc_start: 0.7786 (pt0) cc_final: 0.7462 (pt0) REVERT: A 1297 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8522 (ttm-80) REVERT: A 1299 LEU cc_start: 0.8589 (mm) cc_final: 0.7987 (tp) REVERT: A 1300 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8035 (tp30) REVERT: A 1338 LEU cc_start: 0.8876 (mt) cc_final: 0.8660 (mm) REVERT: A 1344 LEU cc_start: 0.8377 (tp) cc_final: 0.8081 (tp) REVERT: A 1345 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 1350 ASN cc_start: 0.7453 (t0) cc_final: 0.7175 (t0) REVERT: A 1352 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8364 (ttm110) REVERT: A 1353 GLU cc_start: 0.8375 (mp0) cc_final: 0.7856 (mp0) REVERT: A 1356 GLU cc_start: 0.8208 (tp30) cc_final: 0.7665 (tp30) REVERT: A 1357 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8018 (mm-30) REVERT: A 1360 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 1407 GLU cc_start: 0.7944 (pp20) cc_final: 0.7598 (pp20) REVERT: A 1409 GLU cc_start: 0.7438 (tm-30) cc_final: 0.5976 (tm-30) REVERT: A 1413 GLU cc_start: 0.7176 (pm20) cc_final: 0.6618 (pm20) REVERT: A 1417 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7932 (mm-40) REVERT: A 1418 LYS cc_start: 0.8966 (tttp) cc_final: 0.8742 (tppp) REVERT: A 1424 LYS cc_start: 0.8703 (tptm) cc_final: 0.8379 (tppt) REVERT: A 1425 THR cc_start: 0.9065 (p) cc_final: 0.8846 (t) REVERT: A 1432 GLU cc_start: 0.7503 (mp0) cc_final: 0.7280 (mp0) REVERT: A 1434 GLU cc_start: 0.8411 (mp0) cc_final: 0.8103 (mm-30) REVERT: A 1439 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 1442 ARG cc_start: 0.8226 (ptm160) cc_final: 0.7846 (tmm-80) REVERT: A 1451 GLU cc_start: 0.7883 (pt0) cc_final: 0.7574 (pt0) REVERT: A 1458 ASP cc_start: 0.7961 (p0) cc_final: 0.7466 (p0) REVERT: A 1463 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 1465 LYS cc_start: 0.7703 (mmpt) cc_final: 0.7023 (tppt) REVERT: A 1469 ASP cc_start: 0.7489 (t0) cc_final: 0.7246 (t0) REVERT: A 1481 GLU cc_start: 0.7986 (tp30) cc_final: 0.7663 (tp30) REVERT: A 1488 GLU cc_start: 0.7533 (tp30) cc_final: 0.7025 (tp30) REVERT: A 1492 LEU cc_start: 0.8707 (mt) cc_final: 0.8426 (mm) REVERT: A 1501 GLU cc_start: 0.8568 (pt0) cc_final: 0.8306 (pt0) REVERT: A 1504 GLU cc_start: 0.7844 (mp0) cc_final: 0.7285 (mp0) REVERT: A 1508 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8258 (mtp85) REVERT: A 1511 LYS cc_start: 0.8882 (mptt) cc_final: 0.8510 (mmmm) REVERT: A 1516 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 1542 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 1560 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 1561 GLN cc_start: 0.7728 (pp30) cc_final: 0.7313 (pp30) REVERT: A 1563 GLU cc_start: 0.8436 (tp30) cc_final: 0.8002 (tp30) REVERT: A 1570 GLN cc_start: 0.8474 (mt0) cc_final: 0.8137 (mm-40) REVERT: A 1575 GLN cc_start: 0.8294 (mt0) cc_final: 0.7612 (mt0) REVERT: A 1579 GLU cc_start: 0.7869 (mp0) cc_final: 0.7257 (mp0) REVERT: A 1589 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 1597 ASN cc_start: 0.8862 (m-40) cc_final: 0.8627 (t0) REVERT: A 1599 GLN cc_start: 0.8458 (tt0) cc_final: 0.8136 (tp40) REVERT: A 1618 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 1622 MET cc_start: 0.7523 (tpp) cc_final: 0.6535 (tpp) REVERT: A 1623 LYS cc_start: 0.8594 (tppt) cc_final: 0.8068 (tppt) REVERT: A 1642 LYS cc_start: 0.8590 (ttpp) cc_final: 0.7762 (ttmm) REVERT: A 1646 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 1649 LYS cc_start: 0.9197 (tttp) cc_final: 0.8762 (ttmm) REVERT: A 1662 GLN cc_start: 0.8571 (tt0) cc_final: 0.8166 (tp40) REVERT: A 1672 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7370 (ttp80) REVERT: A 1692 GLU cc_start: 0.8212 (tp30) cc_final: 0.7918 (tp30) REVERT: A 1712 GLN cc_start: 0.8833 (mm110) cc_final: 0.8524 (mm-40) REVERT: A 1735 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8495 (tptp) REVERT: A 1737 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8788 (ttpp) REVERT: A 1739 GLU cc_start: 0.8242 (pt0) cc_final: 0.7857 (pt0) REVERT: A 1741 GLU cc_start: 0.8231 (tp30) cc_final: 0.7970 (tp30) REVERT: A 1752 LEU cc_start: 0.9064 (tp) cc_final: 0.8825 (tt) REVERT: A 1754 ASN cc_start: 0.8516 (t0) cc_final: 0.8197 (t0) REVERT: A 1757 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8536 (ttpt) REVERT: A 1758 ASN cc_start: 0.8440 (t0) cc_final: 0.8087 (t0) REVERT: A 1762 LYS cc_start: 0.9294 (ttmt) cc_final: 0.9068 (ttmt) REVERT: A 1776 GLU cc_start: 0.7975 (tp30) cc_final: 0.7657 (tp30) REVERT: A 1778 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.7907 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8125 (t0) cc_final: 0.7888 (t0) REVERT: A 1783 HIS cc_start: 0.9061 (t-90) cc_final: 0.8821 (t-170) REVERT: A 1792 LYS cc_start: 0.9286 (ttmt) cc_final: 0.8714 (tppp) REVERT: A 1822 LYS cc_start: 0.8624 (tttm) cc_final: 0.8392 (ttpp) REVERT: A 1846 LYS cc_start: 0.9216 (tttm) cc_final: 0.8931 (ttmm) REVERT: A 1849 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8445 (ptpt) REVERT: A 1853 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.7795 (ttm110) REVERT: A 1858 LEU cc_start: 0.8553 (mp) cc_final: 0.8336 (mm) REVERT: A 1860 PHE cc_start: 0.9123 (t80) cc_final: 0.8896 (t80) REVERT: A 1864 GLU cc_start: 0.8022 (tp30) cc_final: 0.7373 (tp30) REVERT: A 1865 ASP cc_start: 0.8156 (t0) cc_final: 0.7806 (t0) REVERT: A 1868 ASN cc_start: 0.8703 (m110) cc_final: 0.8064 (m-40) REVERT: A 1870 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 1878 LYS cc_start: 0.9036 (tppt) cc_final: 0.8771 (mmmm) REVERT: A 1881 GLN cc_start: 0.8643 (tp40) cc_final: 0.8443 (tp40) REVERT: A 1882 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8973 (ttmm) REVERT: A 1884 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8958 (ttpp) REVERT: A 1889 GLN cc_start: 0.7761 (pp30) cc_final: 0.7506 (pp30) REVERT: A 1892 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 1909 GLN cc_start: 0.8696 (tp40) cc_final: 0.8099 (tm-30) REVERT: A 1910 GLU cc_start: 0.8570 (tt0) cc_final: 0.8000 (tt0) REVERT: A 1915 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7647 (tm-30) outliers start: 1 outliers final: 0 residues processed: 664 average time/residue: 0.1498 time to fit residues: 143.5480 Evaluate side-chains 603 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 101 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS B1537 GLN B1869 HIS B1900 ASN A1881 GLN A1900 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.121382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.098945 restraints weight = 47419.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.101680 restraints weight = 27934.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.103539 restraints weight = 18370.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.104870 restraints weight = 12964.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.105758 restraints weight = 9660.719| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 1.3225 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= 0.132 Angle : 0.625 7.217 23282 Z= 0.339 Chirality : 0.041 0.183 2582 Planarity : 0.003 0.054 3158 Dihedral : 4.257 16.488 2318 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.18), residues: 2150 helix: 1.99 (0.11), residues: 2105 sheet: None (None), residues: 0 loop : 2.22 (1.05), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1491 TYR 0.020 0.002 TYR A1383 PHE 0.017 0.002 PHE A 945 TRP 0.053 0.004 TRP B1379 HIS 0.010 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00258 (17454) covalent geometry : angle 0.62519 (23282) hydrogen bonds : bond 0.03981 ( 1625) hydrogen bonds : angle 3.62215 ( 4872) *********************** 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 661 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 661 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1181 LYS cc_start: 0.8731 (tppt) cc_final: 0.8195 (tppt) REVERT: B 1182 LEU cc_start: 0.8246 (mp) cc_final: 0.7996 (mp) REVERT: B 1217 GLN cc_start: 0.6778 (pm20) cc_final: 0.6342 (pm20) REVERT: B 1248 ARG cc_start: 0.8378 (mmt180) cc_final: 0.8008 (mmt180) REVERT: B 1249 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 1250 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8432 (ptmm) REVERT: B 1254 GLU cc_start: 0.8427 (tp30) cc_final: 0.7426 (tp30) REVERT: B 1261 GLN cc_start: 0.8938 (tt0) cc_final: 0.8219 (tm-30) REVERT: B 1268 GLN cc_start: 0.8408 (pt0) cc_final: 0.8182 (tt0) REVERT: B 1271 LEU cc_start: 0.9121 (mt) cc_final: 0.8911 (tt) REVERT: B 1282 ASP cc_start: 0.8306 (m-30) cc_final: 0.7831 (t0) REVERT: B 1286 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8817 (mtmt) REVERT: B 1291 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 1300 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 1301 GLU cc_start: 0.8386 (pp20) cc_final: 0.8150 (pp20) REVERT: B 1303 GLU cc_start: 0.8174 (pt0) cc_final: 0.7388 (pp20) REVERT: B 1345 GLU cc_start: 0.7982 (pt0) cc_final: 0.7397 (pt0) REVERT: B 1358 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 1367 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.7975 (tpp80) REVERT: B 1393 GLU cc_start: 0.7755 (pp20) cc_final: 0.7317 (pp20) REVERT: B 1395 GLU cc_start: 0.7793 (tp30) cc_final: 0.7336 (tm-30) REVERT: B 1396 GLU cc_start: 0.7605 (pp20) cc_final: 0.7219 (pp20) REVERT: B 1400 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8478 (mtmm) REVERT: B 1455 LYS cc_start: 0.8375 (mptt) cc_final: 0.8099 (mptt) REVERT: B 1457 ILE cc_start: 0.8950 (pt) cc_final: 0.8612 (mm) REVERT: B 1478 SER cc_start: 0.8748 (m) cc_final: 0.8499 (p) REVERT: B 1481 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7776 (mp0) REVERT: B 1492 LEU cc_start: 0.8597 (mp) cc_final: 0.8287 (mm) REVERT: B 1497 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 1498 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 1504 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 1509 GLU cc_start: 0.8357 (tt0) cc_final: 0.8149 (tt0) REVERT: B 1516 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 1540 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7887 (ttp80) REVERT: B 1542 GLU cc_start: 0.7922 (tp30) cc_final: 0.7391 (tp30) REVERT: B 1544 GLU cc_start: 0.8393 (pt0) cc_final: 0.7891 (pt0) REVERT: B 1547 GLU cc_start: 0.8227 (pp20) cc_final: 0.7996 (pp20) REVERT: B 1549 GLN cc_start: 0.8289 (pp30) cc_final: 0.7978 (tm-30) REVERT: B 1556 GLU cc_start: 0.7787 (mp0) cc_final: 0.7423 (mp0) REVERT: B 1562 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8091 (tt0) REVERT: B 1565 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8237 (tttt) REVERT: B 1571 LEU cc_start: 0.8598 (mt) cc_final: 0.8150 (mt) REVERT: B 1582 ARG cc_start: 0.8467 (ptt90) cc_final: 0.8133 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7616 (pp30) cc_final: 0.6712 (tm-30) REVERT: B 1586 GLU cc_start: 0.7274 (tp30) cc_final: 0.6492 (tp30) REVERT: B 1588 GLU cc_start: 0.8281 (pm20) cc_final: 0.7706 (pm20) REVERT: B 1593 ASN cc_start: 0.8272 (t0) cc_final: 0.7716 (t0) REVERT: B 1602 LEU cc_start: 0.8840 (tp) cc_final: 0.8545 (tt) REVERT: B 1627 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 1634 GLU cc_start: 0.8200 (tp30) cc_final: 0.7442 (tp30) REVERT: B 1638 ASP cc_start: 0.8120 (t0) cc_final: 0.7631 (t0) REVERT: B 1644 ASN cc_start: 0.8412 (m-40) cc_final: 0.8196 (t0) REVERT: B 1651 ILE cc_start: 0.9115 (mt) cc_final: 0.8865 (mt) REVERT: B 1653 LYS cc_start: 0.9190 (tttt) cc_final: 0.8919 (ttpp) REVERT: B 1657 GLN cc_start: 0.7811 (tp40) cc_final: 0.7544 (tp40) REVERT: B 1659 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8154 (ttmm) REVERT: B 1667 GLU cc_start: 0.8084 (tp30) cc_final: 0.7603 (tp30) REVERT: B 1668 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 1677 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 1678 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8145 (mp10) REVERT: B 1683 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 1694 GLU cc_start: 0.8192 (tt0) cc_final: 0.7713 (tt0) REVERT: B 1708 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.7785 (mtm-85) REVERT: B 1720 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8212 (tp-100) REVERT: B 1737 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9080 (tptp) REVERT: B 1741 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 1757 LYS cc_start: 0.8872 (tttp) cc_final: 0.8425 (ttpp) REVERT: B 1760 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 1762 LYS cc_start: 0.8673 (mttp) cc_final: 0.8415 (mttp) REVERT: B 1764 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8555 (mmmm) REVERT: B 1772 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8429 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8216 (t0) cc_final: 0.7949 (t0) REVERT: B 1780 GLU cc_start: 0.7494 (tp30) cc_final: 0.7224 (tp30) REVERT: B 1781 GLN cc_start: 0.8270 (tp40) cc_final: 0.8020 (tp40) REVERT: B 1786 THR cc_start: 0.8885 (p) cc_final: 0.8460 (t) REVERT: B 1788 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 1789 LYS cc_start: 0.8908 (tppp) cc_final: 0.8561 (tppp) REVERT: B 1818 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8546 (tppt) REVERT: B 1820 ILE cc_start: 0.8324 (mt) cc_final: 0.8076 (tp) REVERT: B 1824 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 1833 GLU cc_start: 0.8148 (tp30) cc_final: 0.7243 (tp30) REVERT: B 1837 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 1838 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8720 (mm-40) REVERT: B 1840 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.7803 (ttm-80) REVERT: B 1852 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7984 (tp30) REVERT: B 1853 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8223 (tpp80) REVERT: B 1863 ASP cc_start: 0.7713 (m-30) cc_final: 0.7261 (m-30) REVERT: B 1865 ASP cc_start: 0.7970 (m-30) cc_final: 0.7640 (m-30) REVERT: B 1866 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.7815 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8395 (mmmm) REVERT: B 1870 GLU cc_start: 0.7901 (mt-10) cc_final: 0.6424 (mt-10) REVERT: B 1871 ARG cc_start: 0.8235 (ptt90) cc_final: 0.7698 (ptt90) REVERT: B 1873 GLN cc_start: 0.8757 (tp40) cc_final: 0.8382 (tm-30) REVERT: B 1878 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7926 (mmmt) REVERT: B 1882 LYS cc_start: 0.9221 (tttp) cc_final: 0.8624 (tmtt) REVERT: B 1884 LYS cc_start: 0.8834 (tppp) cc_final: 0.8556 (tppp) REVERT: B 1888 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8298 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8811 (mt0) cc_final: 0.8318 (tp40) REVERT: B 1892 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 1903 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8661 (mmtt) REVERT: B 1906 LYS cc_start: 0.8998 (tppt) cc_final: 0.8778 (tppt) REVERT: B 1908 GLN cc_start: 0.8586 (tp40) cc_final: 0.8212 (tp-100) REVERT: B 1915 GLU cc_start: 0.8305 (pt0) cc_final: 0.7916 (pt0) REVERT: B 1917 ARG cc_start: 0.9048 (mtp-110) cc_final: 0.8524 (ttp-110) REVERT: A 952 GLU cc_start: 0.8650 (pt0) cc_final: 0.7743 (mt-10) REVERT: A 1009 GLU cc_start: 0.7602 (pm20) cc_final: 0.7175 (mm-30) REVERT: A 1012 GLN cc_start: 0.8031 (tt0) cc_final: 0.7510 (tt0) REVERT: A 1040 ASP cc_start: 0.7429 (m-30) cc_final: 0.7162 (m-30) REVERT: A 1188 GLU cc_start: 0.7400 (tp30) cc_final: 0.7049 (tp30) REVERT: A 1202 LYS cc_start: 0.9068 (pptt) cc_final: 0.8772 (pptt) REVERT: A 1215 ILE cc_start: 0.7975 (pt) cc_final: 0.7663 (pt) REVERT: A 1250 LYS cc_start: 0.8702 (pptt) cc_final: 0.8300 (pptt) REVERT: A 1261 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8601 (tp40) REVERT: A 1270 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8551 (mtmm) REVERT: A 1273 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 1276 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7338 (ttm-80) REVERT: A 1297 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8529 (ttm-80) REVERT: A 1299 LEU cc_start: 0.8504 (mm) cc_final: 0.7729 (tt) REVERT: A 1300 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8117 (tp30) REVERT: A 1329 GLU cc_start: 0.8388 (tp30) cc_final: 0.7977 (tp30) REVERT: A 1338 LEU cc_start: 0.8948 (mt) cc_final: 0.8675 (mm) REVERT: A 1345 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7998 (mt-10) REVERT: A 1350 ASN cc_start: 0.7684 (t0) cc_final: 0.7445 (t0) REVERT: A 1353 GLU cc_start: 0.8367 (mp0) cc_final: 0.7679 (mp0) REVERT: A 1356 GLU cc_start: 0.8287 (tp30) cc_final: 0.7766 (tp30) REVERT: A 1357 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 1358 GLU cc_start: 0.8136 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 1360 GLU cc_start: 0.7472 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 1392 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7881 (mt-10) REVERT: A 1407 GLU cc_start: 0.7897 (pp20) cc_final: 0.7621 (pp20) REVERT: A 1409 GLU cc_start: 0.7413 (tm-30) cc_final: 0.5998 (tm-30) REVERT: A 1413 GLU cc_start: 0.6989 (pm20) cc_final: 0.6704 (pm20) REVERT: A 1417 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7966 (mm-40) REVERT: A 1423 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 1424 LYS cc_start: 0.8789 (tptm) cc_final: 0.8293 (tppt) REVERT: A 1432 GLU cc_start: 0.7699 (mp0) cc_final: 0.7238 (pm20) REVERT: A 1434 GLU cc_start: 0.8163 (mp0) cc_final: 0.7938 (mp0) REVERT: A 1439 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6959 (tm-30) REVERT: A 1442 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7886 (tmm-80) REVERT: A 1451 GLU cc_start: 0.7884 (pt0) cc_final: 0.7528 (pt0) REVERT: A 1452 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8786 (tppt) REVERT: A 1458 ASP cc_start: 0.7974 (p0) cc_final: 0.7481 (p0) REVERT: A 1463 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 1481 GLU cc_start: 0.8029 (tp30) cc_final: 0.7736 (tp30) REVERT: A 1488 GLU cc_start: 0.7480 (tp30) cc_final: 0.6604 (tp30) REVERT: A 1492 LEU cc_start: 0.8687 (mt) cc_final: 0.8096 (mm) REVERT: A 1501 GLU cc_start: 0.8572 (pt0) cc_final: 0.8252 (pt0) REVERT: A 1504 GLU cc_start: 0.7813 (mp0) cc_final: 0.7360 (mp0) REVERT: A 1511 LYS cc_start: 0.8837 (mptt) cc_final: 0.8476 (mmmm) REVERT: A 1540 ARG cc_start: 0.8100 (tmt-80) cc_final: 0.7859 (tmt-80) REVERT: A 1542 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 1560 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 1561 GLN cc_start: 0.7776 (pp30) cc_final: 0.7353 (pp30) REVERT: A 1563 GLU cc_start: 0.8522 (tp30) cc_final: 0.8059 (tp30) REVERT: A 1570 GLN cc_start: 0.8244 (mt0) cc_final: 0.7962 (mm-40) REVERT: A 1575 GLN cc_start: 0.8121 (mt0) cc_final: 0.7528 (mt0) REVERT: A 1579 GLU cc_start: 0.7884 (mp0) cc_final: 0.7261 (mp0) REVERT: A 1589 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 1590 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 1597 ASN cc_start: 0.8843 (m-40) cc_final: 0.8596 (t0) REVERT: A 1599 GLN cc_start: 0.8439 (tt0) cc_final: 0.8131 (tp40) REVERT: A 1622 MET cc_start: 0.7612 (tpp) cc_final: 0.6921 (tpp) REVERT: A 1623 LYS cc_start: 0.8639 (tppt) cc_final: 0.8342 (tppt) REVERT: A 1642 LYS cc_start: 0.8557 (ttpp) cc_final: 0.7949 (mtpp) REVERT: A 1646 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 1649 LYS cc_start: 0.9197 (tttp) cc_final: 0.8746 (ttmm) REVERT: A 1655 GLN cc_start: 0.8606 (mm110) cc_final: 0.8359 (mm-40) REVERT: A 1662 GLN cc_start: 0.8575 (tt0) cc_final: 0.8143 (tp40) REVERT: A 1667 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 1672 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7427 (ttp80) REVERT: A 1692 GLU cc_start: 0.8221 (tp30) cc_final: 0.7716 (tp30) REVERT: A 1712 GLN cc_start: 0.8831 (mm110) cc_final: 0.8529 (mm-40) REVERT: A 1735 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8713 (tptp) REVERT: A 1737 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8734 (ttpp) REVERT: A 1741 GLU cc_start: 0.8320 (tp30) cc_final: 0.7951 (tp30) REVERT: A 1744 THR cc_start: 0.8604 (m) cc_final: 0.8394 (p) REVERT: A 1755 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 1757 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8560 (ttpt) REVERT: A 1758 ASN cc_start: 0.8519 (t0) cc_final: 0.8152 (t0) REVERT: A 1762 LYS cc_start: 0.9309 (ttmt) cc_final: 0.9068 (ttmt) REVERT: A 1776 GLU cc_start: 0.8010 (tp30) cc_final: 0.7731 (tp30) REVERT: A 1778 ARG cc_start: 0.8431 (mtt-85) cc_final: 0.8031 (mtt-85) REVERT: A 1782 ASP cc_start: 0.8171 (t0) cc_final: 0.7924 (t0) REVERT: A 1783 HIS cc_start: 0.9148 (t-90) cc_final: 0.8895 (t-170) REVERT: A 1792 LYS cc_start: 0.9274 (ttmt) cc_final: 0.8715 (tppp) REVERT: A 1822 LYS cc_start: 0.8577 (tttm) cc_final: 0.8230 (ttpp) REVERT: A 1824 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 1825 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 1840 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7699 (mtm110) REVERT: A 1846 LYS cc_start: 0.9207 (tttm) cc_final: 0.8977 (ttmm) REVERT: A 1853 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7755 (ttm110) REVERT: A 1860 PHE cc_start: 0.9070 (t80) cc_final: 0.8865 (t80) REVERT: A 1864 GLU cc_start: 0.8064 (tp30) cc_final: 0.7004 (tp30) REVERT: A 1865 ASP cc_start: 0.8187 (t0) cc_final: 0.7810 (t0) REVERT: A 1868 ASN cc_start: 0.8622 (m110) cc_final: 0.7528 (m-40) REVERT: A 1870 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 1871 ARG cc_start: 0.8475 (tpt90) cc_final: 0.8266 (tpt90) REVERT: A 1878 LYS cc_start: 0.9033 (tppt) cc_final: 0.8790 (mmmm) REVERT: A 1882 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8911 (ttmm) REVERT: A 1884 LYS cc_start: 0.9224 (ttpp) cc_final: 0.8970 (ttpp) REVERT: A 1889 GLN cc_start: 0.7861 (pp30) cc_final: 0.7632 (pp30) REVERT: A 1892 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 1894 GLU cc_start: 0.7121 (pp20) cc_final: 0.6865 (pp20) REVERT: A 1909 GLN cc_start: 0.8690 (tp40) cc_final: 0.8194 (tm-30) REVERT: A 1910 GLU cc_start: 0.8540 (tt0) cc_final: 0.7976 (tt0) REVERT: A 1915 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 1922 GLU cc_start: 0.8110 (mp0) cc_final: 0.7597 (pp20) outliers start: 0 outliers final: 0 residues processed: 661 average time/residue: 0.1505 time to fit residues: 143.4081 Evaluate side-chains 609 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 32 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 205 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1305 GLN ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS B1869 HIS ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1802 GLN A1900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.121254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.100302 restraints weight = 48426.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.102972 restraints weight = 28879.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.104789 restraints weight = 19046.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.106090 restraints weight = 13472.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.106969 restraints weight = 10014.586| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 1.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17454 Z= 0.143 Angle : 0.660 9.268 23282 Z= 0.356 Chirality : 0.042 0.212 2582 Planarity : 0.003 0.042 3158 Dihedral : 4.252 16.162 2318 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.18), residues: 2150 helix: 1.98 (0.11), residues: 2107 sheet: None (None), residues: 0 loop : 1.59 (1.02), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1491 TYR 0.021 0.002 TYR A1383 PHE 0.056 0.002 PHE A 945 TRP 0.047 0.005 TRP B1379 HIS 0.014 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00287 (17454) covalent geometry : angle 0.65994 (23282) hydrogen bonds : bond 0.04055 ( 1625) hydrogen bonds : angle 3.68292 ( 4872) *********************** 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 656 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.636 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: B 1181 LYS cc_start: 0.8815 (tppt) cc_final: 0.8189 (tppt) REVERT: B 1182 LEU cc_start: 0.8287 (mp) cc_final: 0.8004 (mp) REVERT: B 1222 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8502 (ttpt) REVERT: B 1241 HIS cc_start: 0.8393 (m90) cc_final: 0.8085 (m90) REVERT: B 1246 MET cc_start: 0.8261 (ppp) cc_final: 0.7468 (ppp) REVERT: B 1247 CYS cc_start: 0.8294 (p) cc_final: 0.8085 (p) REVERT: B 1248 ARG cc_start: 0.8323 (mmt180) cc_final: 0.7959 (mmt180) REVERT: B 1249 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 1250 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8404 (ptmm) REVERT: B 1261 GLN cc_start: 0.8961 (tt0) cc_final: 0.8493 (tp40) REVERT: B 1265 ASN cc_start: 0.8375 (m110) cc_final: 0.8001 (m-40) REVERT: B 1266 GLU cc_start: 0.8001 (pp20) cc_final: 0.7767 (pp20) REVERT: B 1268 GLN cc_start: 0.8403 (pt0) cc_final: 0.8158 (tt0) REVERT: B 1282 ASP cc_start: 0.8295 (m-30) cc_final: 0.7867 (t70) REVERT: B 1285 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8808 (ttmm) REVERT: B 1291 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 1303 GLU cc_start: 0.8200 (pt0) cc_final: 0.7351 (pp20) REVERT: B 1321 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8350 (mt-10) REVERT: B 1325 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.8072 (mtp-110) REVERT: B 1358 GLU cc_start: 0.7783 (tm-30) cc_final: 0.5763 (tm-30) REVERT: B 1367 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7971 (tpp80) REVERT: B 1388 VAL cc_start: 0.7836 (m) cc_final: 0.7621 (t) REVERT: B 1393 GLU cc_start: 0.7690 (pp20) cc_final: 0.7268 (pp20) REVERT: B 1395 GLU cc_start: 0.7844 (tp30) cc_final: 0.7445 (tm-30) REVERT: B 1396 GLU cc_start: 0.7632 (pp20) cc_final: 0.7256 (pp20) REVERT: B 1400 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8506 (mtmm) REVERT: B 1431 THR cc_start: 0.8633 (m) cc_final: 0.8364 (t) REVERT: B 1455 LYS cc_start: 0.8340 (mptt) cc_final: 0.8091 (mptt) REVERT: B 1457 ILE cc_start: 0.8936 (pt) cc_final: 0.8628 (mm) REVERT: B 1478 SER cc_start: 0.8793 (m) cc_final: 0.8447 (p) REVERT: B 1481 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7745 (mp0) REVERT: B 1497 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7117 (tm-30) REVERT: B 1498 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7302 (tm-30) REVERT: B 1504 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 1516 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 1542 GLU cc_start: 0.7948 (tp30) cc_final: 0.7390 (tp30) REVERT: B 1544 GLU cc_start: 0.8449 (pt0) cc_final: 0.8107 (pt0) REVERT: B 1549 GLN cc_start: 0.8290 (pp30) cc_final: 0.8022 (tm-30) REVERT: B 1556 GLU cc_start: 0.7733 (mp0) cc_final: 0.7349 (mp0) REVERT: B 1560 GLU cc_start: 0.8870 (tt0) cc_final: 0.8446 (mm-30) REVERT: B 1562 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8104 (tt0) REVERT: B 1565 LYS cc_start: 0.8651 (tmtt) cc_final: 0.8307 (tmtt) REVERT: B 1577 ARG cc_start: 0.8055 (ptp-170) cc_final: 0.7442 (ptp-170) REVERT: B 1582 ARG cc_start: 0.8438 (ptt90) cc_final: 0.8112 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7715 (pp30) cc_final: 0.6896 (tm-30) REVERT: B 1588 GLU cc_start: 0.8154 (pm20) cc_final: 0.7778 (pm20) REVERT: B 1593 ASN cc_start: 0.8229 (t0) cc_final: 0.7904 (t0) REVERT: B 1597 ASN cc_start: 0.8563 (m-40) cc_final: 0.8356 (m-40) REVERT: B 1598 HIS cc_start: 0.8567 (p90) cc_final: 0.8290 (p90) REVERT: B 1602 LEU cc_start: 0.8845 (tp) cc_final: 0.8562 (tt) REVERT: B 1614 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8113 (mtpp) REVERT: B 1627 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 1634 GLU cc_start: 0.8177 (tp30) cc_final: 0.7445 (tp30) REVERT: B 1638 ASP cc_start: 0.8066 (t0) cc_final: 0.7598 (t0) REVERT: B 1644 ASN cc_start: 0.8400 (m-40) cc_final: 0.8158 (t0) REVERT: B 1651 ILE cc_start: 0.9085 (mt) cc_final: 0.8817 (mt) REVERT: B 1653 LYS cc_start: 0.9193 (tttt) cc_final: 0.8695 (ttmm) REVERT: B 1657 GLN cc_start: 0.7755 (tp40) cc_final: 0.7483 (tp40) REVERT: B 1659 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8044 (ttmm) REVERT: B 1667 GLU cc_start: 0.8034 (tp30) cc_final: 0.7543 (tp30) REVERT: B 1677 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 1678 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8166 (mp10) REVERT: B 1683 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 1694 GLU cc_start: 0.8123 (tt0) cc_final: 0.7732 (tt0) REVERT: B 1720 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8095 (tp40) REVERT: B 1737 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9090 (tptp) REVERT: B 1741 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 1760 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7172 (tm-30) REVERT: B 1762 LYS cc_start: 0.8700 (mttp) cc_final: 0.8493 (mttp) REVERT: B 1764 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8589 (mmmm) REVERT: B 1772 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8357 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8111 (t0) cc_final: 0.7878 (t0) REVERT: B 1780 GLU cc_start: 0.7402 (tp30) cc_final: 0.7114 (tp30) REVERT: B 1781 GLN cc_start: 0.8201 (tp40) cc_final: 0.7959 (tp40) REVERT: B 1786 THR cc_start: 0.8867 (p) cc_final: 0.8441 (t) REVERT: B 1789 LYS cc_start: 0.8866 (tppp) cc_final: 0.8641 (tppp) REVERT: B 1818 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8567 (tppt) REVERT: B 1820 ILE cc_start: 0.8428 (mt) cc_final: 0.8149 (tp) REVERT: B 1824 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 1833 GLU cc_start: 0.8144 (tp30) cc_final: 0.7290 (tp30) REVERT: B 1837 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 1838 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8721 (mm-40) REVERT: B 1853 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8262 (tpp80) REVERT: B 1865 ASP cc_start: 0.8093 (m-30) cc_final: 0.7633 (m-30) REVERT: B 1867 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8611 (mmmm) REVERT: B 1871 ARG cc_start: 0.8265 (ptt90) cc_final: 0.7944 (ptt90) REVERT: B 1873 GLN cc_start: 0.8700 (tp40) cc_final: 0.8389 (tm-30) REVERT: B 1878 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7799 (mmmt) REVERT: B 1881 GLN cc_start: 0.8384 (pm20) cc_final: 0.8167 (pm20) REVERT: B 1882 LYS cc_start: 0.9219 (tttp) cc_final: 0.8669 (tmtt) REVERT: B 1884 LYS cc_start: 0.8809 (tppp) cc_final: 0.8475 (tppp) REVERT: B 1888 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8268 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8758 (mt0) cc_final: 0.8234 (tp40) REVERT: B 1892 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 1903 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8643 (mmtt) REVERT: B 1906 LYS cc_start: 0.9138 (tppt) cc_final: 0.8837 (tppt) REVERT: B 1908 GLN cc_start: 0.8607 (tp40) cc_final: 0.8148 (tp-100) REVERT: B 1911 LEU cc_start: 0.8581 (tt) cc_final: 0.7973 (tt) REVERT: B 1915 GLU cc_start: 0.8323 (pt0) cc_final: 0.7977 (pt0) REVERT: B 1917 ARG cc_start: 0.9046 (mtp-110) cc_final: 0.8610 (ttp-110) REVERT: A 949 LYS cc_start: 0.7698 (mptt) cc_final: 0.7395 (tptt) REVERT: A 952 GLU cc_start: 0.8520 (pt0) cc_final: 0.7749 (mt-10) REVERT: A 1040 ASP cc_start: 0.7506 (m-30) cc_final: 0.7246 (m-30) REVERT: A 1176 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7162 (mm-30) REVERT: A 1179 MET cc_start: 0.6854 (ppp) cc_final: 0.6463 (ppp) REVERT: A 1202 LYS cc_start: 0.9178 (pptt) cc_final: 0.8849 (pptt) REVERT: A 1215 ILE cc_start: 0.8047 (pt) cc_final: 0.7636 (pt) REVERT: A 1250 LYS cc_start: 0.8940 (pptt) cc_final: 0.8555 (pptt) REVERT: A 1261 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8666 (tp40) REVERT: A 1270 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8454 (mtmm) REVERT: A 1273 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 1275 ASN cc_start: 0.9025 (m110) cc_final: 0.8806 (m110) REVERT: A 1276 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7431 (ttm-80) REVERT: A 1291 GLU cc_start: 0.7853 (pt0) cc_final: 0.7511 (pt0) REVERT: A 1297 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8525 (ttm-80) REVERT: A 1299 LEU cc_start: 0.8519 (mm) cc_final: 0.7759 (tt) REVERT: A 1300 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8067 (tp30) REVERT: A 1329 GLU cc_start: 0.8222 (tp30) cc_final: 0.7718 (tp30) REVERT: A 1330 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 1338 LEU cc_start: 0.8973 (mt) cc_final: 0.8739 (mm) REVERT: A 1345 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 1350 ASN cc_start: 0.7747 (t0) cc_final: 0.7485 (t0) REVERT: A 1352 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8174 (mtm-85) REVERT: A 1353 GLU cc_start: 0.8333 (mp0) cc_final: 0.7618 (mp0) REVERT: A 1356 GLU cc_start: 0.8274 (tp30) cc_final: 0.7755 (tp30) REVERT: A 1357 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 1358 GLU cc_start: 0.8086 (mm-30) cc_final: 0.6690 (mm-30) REVERT: A 1360 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 1362 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8511 (ttmm) REVERT: A 1379 TRP cc_start: 0.7219 (m100) cc_final: 0.6751 (m100) REVERT: A 1392 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 1409 GLU cc_start: 0.7461 (tm-30) cc_final: 0.5987 (tm-30) REVERT: A 1413 GLU cc_start: 0.7192 (pm20) cc_final: 0.6649 (pm20) REVERT: A 1417 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8014 (mm-40) REVERT: A 1424 LYS cc_start: 0.8824 (tptm) cc_final: 0.8376 (tppt) REVERT: A 1429 LEU cc_start: 0.9020 (tt) cc_final: 0.8754 (tt) REVERT: A 1432 GLU cc_start: 0.7760 (mp0) cc_final: 0.7140 (mp0) REVERT: A 1434 GLU cc_start: 0.8193 (mp0) cc_final: 0.7813 (mp0) REVERT: A 1451 GLU cc_start: 0.7866 (pt0) cc_final: 0.7514 (pt0) REVERT: A 1452 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8811 (tppt) REVERT: A 1458 ASP cc_start: 0.7996 (p0) cc_final: 0.7500 (p0) REVERT: A 1463 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 1467 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8033 (ttmm) REVERT: A 1481 GLU cc_start: 0.7963 (tp30) cc_final: 0.7598 (tp30) REVERT: A 1488 GLU cc_start: 0.7490 (tp30) cc_final: 0.6721 (tp30) REVERT: A 1492 LEU cc_start: 0.8684 (mt) cc_final: 0.8180 (mm) REVERT: A 1501 GLU cc_start: 0.8555 (pt0) cc_final: 0.8273 (pt0) REVERT: A 1504 GLU cc_start: 0.7840 (mp0) cc_final: 0.7331 (mp0) REVERT: A 1511 LYS cc_start: 0.8880 (mptt) cc_final: 0.8529 (mmmm) REVERT: A 1540 ARG cc_start: 0.8178 (tmt-80) cc_final: 0.7921 (tmt-80) REVERT: A 1542 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 1559 LEU cc_start: 0.8529 (tp) cc_final: 0.8301 (tp) REVERT: A 1560 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 1561 GLN cc_start: 0.7846 (pp30) cc_final: 0.7518 (pp30) REVERT: A 1563 GLU cc_start: 0.8455 (tp30) cc_final: 0.8052 (tp30) REVERT: A 1570 GLN cc_start: 0.8189 (mt0) cc_final: 0.7950 (mm-40) REVERT: A 1572 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8021 (mm-30) REVERT: A 1589 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7815 (mm-30) REVERT: A 1597 ASN cc_start: 0.8860 (m-40) cc_final: 0.8612 (t0) REVERT: A 1599 GLN cc_start: 0.8440 (tt0) cc_final: 0.8145 (tp40) REVERT: A 1622 MET cc_start: 0.7579 (tpp) cc_final: 0.6683 (tpp) REVERT: A 1623 LYS cc_start: 0.8631 (tppt) cc_final: 0.8047 (tppt) REVERT: A 1642 LYS cc_start: 0.8628 (ttpp) cc_final: 0.7897 (ttmm) REVERT: A 1646 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 1649 LYS cc_start: 0.9201 (tttp) cc_final: 0.8739 (ttmm) REVERT: A 1662 GLN cc_start: 0.8617 (tt0) cc_final: 0.8126 (tp40) REVERT: A 1692 GLU cc_start: 0.8172 (tp30) cc_final: 0.7829 (tp30) REVERT: A 1712 GLN cc_start: 0.8827 (mm110) cc_final: 0.8521 (mm-40) REVERT: A 1741 GLU cc_start: 0.8212 (tp30) cc_final: 0.7999 (tp30) REVERT: A 1754 ASN cc_start: 0.8448 (t0) cc_final: 0.8158 (t0) REVERT: A 1757 LYS cc_start: 0.8839 (ttpt) cc_final: 0.8634 (ttpt) REVERT: A 1762 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9107 (ttmt) REVERT: A 1778 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.8017 (mtt-85) REVERT: A 1783 HIS cc_start: 0.9132 (t-90) cc_final: 0.8895 (t-170) REVERT: A 1792 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8907 (tppp) REVERT: A 1802 GLN cc_start: 0.8892 (tp40) cc_final: 0.8557 (tm-30) REVERT: A 1822 LYS cc_start: 0.8621 (tttm) cc_final: 0.8385 (ttpp) REVERT: A 1824 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 1840 ARG cc_start: 0.8083 (mpp80) cc_final: 0.7736 (mtm110) REVERT: A 1846 LYS cc_start: 0.9194 (tttm) cc_final: 0.8878 (ttmm) REVERT: A 1849 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8107 (tpp-160) REVERT: A 1850 LYS cc_start: 0.8715 (ptpt) cc_final: 0.8380 (ptpt) REVERT: A 1853 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.7729 (ttm110) REVERT: A 1860 PHE cc_start: 0.9101 (t80) cc_final: 0.8899 (t80) REVERT: A 1864 GLU cc_start: 0.8003 (tp30) cc_final: 0.7630 (tp30) REVERT: A 1865 ASP cc_start: 0.8057 (t0) cc_final: 0.7771 (t0) REVERT: A 1868 ASN cc_start: 0.8678 (m110) cc_final: 0.8355 (m-40) REVERT: A 1870 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 1878 LYS cc_start: 0.9064 (tppt) cc_final: 0.8767 (mmmm) REVERT: A 1882 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8928 (ttmm) REVERT: A 1884 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8849 (ttpp) REVERT: A 1889 GLN cc_start: 0.7705 (pp30) cc_final: 0.7477 (pp30) REVERT: A 1892 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 1909 GLN cc_start: 0.8659 (tp40) cc_final: 0.8179 (tm-30) REVERT: A 1910 GLU cc_start: 0.8526 (tt0) cc_final: 0.7962 (tt0) REVERT: A 1915 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.1490 time to fit residues: 140.7805 Evaluate side-chains 615 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.0170 chunk 67 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 HIS A1192 GLN A1199 ASN A1900 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.100373 restraints weight = 47463.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.102971 restraints weight = 28502.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.104837 restraints weight = 19061.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.106102 restraints weight = 13450.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.107054 restraints weight = 10032.324| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 1.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17454 Z= 0.133 Angle : 0.651 9.543 23282 Z= 0.350 Chirality : 0.041 0.184 2582 Planarity : 0.003 0.041 3158 Dihedral : 4.300 19.123 2318 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.18), residues: 2150 helix: 2.01 (0.11), residues: 2108 sheet: None (None), residues: 0 loop : 2.01 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1540 TYR 0.011 0.002 TYR A1383 PHE 0.039 0.002 PHE A 945 TRP 0.043 0.004 TRP B1379 HIS 0.013 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00263 (17454) covalent geometry : angle 0.65062 (23282) hydrogen bonds : bond 0.04007 ( 1625) hydrogen bonds : angle 3.63283 ( 4872) ********************** 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 657 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1047 GLU cc_start: 0.8418 (mp0) cc_final: 0.8144 (pm20) REVERT: B 1181 LYS cc_start: 0.8880 (tppt) cc_final: 0.8258 (tppt) REVERT: B 1182 LEU cc_start: 0.8386 (mp) cc_final: 0.8067 (mp) REVERT: B 1222 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8560 (ttpt) REVERT: B 1224 LYS cc_start: 0.8020 (tppp) cc_final: 0.7776 (tppp) REVERT: B 1246 MET cc_start: 0.8241 (ppp) cc_final: 0.7616 (ppp) REVERT: B 1248 ARG cc_start: 0.8341 (mmt180) cc_final: 0.7955 (mmt180) REVERT: B 1249 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 1250 LYS cc_start: 0.8891 (ptmt) cc_final: 0.8429 (ptmm) REVERT: B 1254 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 1261 GLN cc_start: 0.8939 (tt0) cc_final: 0.8432 (tp40) REVERT: B 1265 ASN cc_start: 0.8369 (m110) cc_final: 0.7984 (m-40) REVERT: B 1266 GLU cc_start: 0.7962 (pp20) cc_final: 0.7700 (pp20) REVERT: B 1282 ASP cc_start: 0.8346 (m-30) cc_final: 0.7804 (t70) REVERT: B 1285 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8835 (ttmm) REVERT: B 1291 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 1297 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7804 (mtp-110) REVERT: B 1303 GLU cc_start: 0.8176 (pt0) cc_final: 0.7314 (pp20) REVERT: B 1321 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 1325 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.8003 (mtm110) REVERT: B 1357 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 1358 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 1367 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7925 (tpp80) REVERT: B 1393 GLU cc_start: 0.7712 (pp20) cc_final: 0.7290 (pp20) REVERT: B 1395 GLU cc_start: 0.7883 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 1396 GLU cc_start: 0.7645 (pp20) cc_final: 0.7264 (pp20) REVERT: B 1400 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8531 (mtmm) REVERT: B 1402 GLN cc_start: 0.8685 (mt0) cc_final: 0.8476 (mt0) REVERT: B 1431 THR cc_start: 0.8598 (m) cc_final: 0.8297 (t) REVERT: B 1455 LYS cc_start: 0.8330 (mptt) cc_final: 0.8112 (mptt) REVERT: B 1457 ILE cc_start: 0.8932 (pt) cc_final: 0.8652 (mm) REVERT: B 1478 SER cc_start: 0.8751 (m) cc_final: 0.8397 (p) REVERT: B 1481 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7727 (mp0) REVERT: B 1492 LEU cc_start: 0.8578 (mp) cc_final: 0.8377 (mm) REVERT: B 1497 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 1498 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 1504 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 1509 GLU cc_start: 0.8304 (tt0) cc_final: 0.8088 (tt0) REVERT: B 1529 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7902 (ttt-90) REVERT: B 1542 GLU cc_start: 0.7932 (tp30) cc_final: 0.7487 (tp30) REVERT: B 1544 GLU cc_start: 0.8430 (pt0) cc_final: 0.8115 (pt0) REVERT: B 1549 GLN cc_start: 0.8285 (pp30) cc_final: 0.8043 (tm-30) REVERT: B 1556 GLU cc_start: 0.7712 (mp0) cc_final: 0.7327 (mp0) REVERT: B 1560 GLU cc_start: 0.8894 (tt0) cc_final: 0.8599 (mm-30) REVERT: B 1565 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8281 (tttt) REVERT: B 1571 LEU cc_start: 0.8579 (mt) cc_final: 0.8182 (mt) REVERT: B 1577 ARG cc_start: 0.7943 (ptp-170) cc_final: 0.7385 (ptp-170) REVERT: B 1582 ARG cc_start: 0.8437 (ptt90) cc_final: 0.8105 (ttp-170) REVERT: B 1585 GLN cc_start: 0.7722 (pp30) cc_final: 0.6834 (tm-30) REVERT: B 1588 GLU cc_start: 0.8218 (pm20) cc_final: 0.7703 (pm20) REVERT: B 1590 GLU cc_start: 0.8495 (mp0) cc_final: 0.8229 (mp0) REVERT: B 1593 ASN cc_start: 0.8214 (t0) cc_final: 0.7870 (t0) REVERT: B 1598 HIS cc_start: 0.8569 (p90) cc_final: 0.8325 (p90) REVERT: B 1602 LEU cc_start: 0.8824 (tp) cc_final: 0.8564 (tt) REVERT: B 1614 LYS cc_start: 0.8608 (mtpp) cc_final: 0.7999 (mtpp) REVERT: B 1627 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 1634 GLU cc_start: 0.8157 (tp30) cc_final: 0.7435 (tp30) REVERT: B 1638 ASP cc_start: 0.8063 (t0) cc_final: 0.7593 (t0) REVERT: B 1651 ILE cc_start: 0.9043 (mt) cc_final: 0.8836 (mt) REVERT: B 1653 LYS cc_start: 0.9134 (tttt) cc_final: 0.8696 (ttmm) REVERT: B 1657 GLN cc_start: 0.7746 (tp40) cc_final: 0.7470 (tp40) REVERT: B 1659 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8015 (ttmm) REVERT: B 1667 GLU cc_start: 0.8042 (tp30) cc_final: 0.7584 (tp30) REVERT: B 1677 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 1678 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8113 (mp10) REVERT: B 1683 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 1691 ASN cc_start: 0.7367 (p0) cc_final: 0.7043 (p0) REVERT: B 1720 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8133 (tp40) REVERT: B 1737 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9121 (tptp) REVERT: B 1741 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 1760 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 1764 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8499 (mmmm) REVERT: B 1772 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8309 (ttm-80) REVERT: B 1775 ASP cc_start: 0.8139 (t0) cc_final: 0.7924 (t0) REVERT: B 1786 THR cc_start: 0.8886 (p) cc_final: 0.8515 (t) REVERT: B 1789 LYS cc_start: 0.8900 (tppp) cc_final: 0.8572 (tppp) REVERT: B 1818 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8491 (mmmm) REVERT: B 1820 ILE cc_start: 0.8375 (mt) cc_final: 0.8107 (tp) REVERT: B 1824 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 1833 GLU cc_start: 0.8142 (tp30) cc_final: 0.7242 (tp30) REVERT: B 1837 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 1838 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8689 (mm-40) REVERT: B 1840 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.7824 (ttm-80) REVERT: B 1852 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7892 (tp30) REVERT: B 1853 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8266 (tpp80) REVERT: B 1865 ASP cc_start: 0.8003 (m-30) cc_final: 0.7691 (m-30) REVERT: B 1866 ARG cc_start: 0.8574 (ttp-170) cc_final: 0.7756 (tmm-80) REVERT: B 1867 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8463 (mmmm) REVERT: B 1870 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6198 (mt-10) REVERT: B 1871 ARG cc_start: 0.8212 (ptt90) cc_final: 0.7669 (ptt90) REVERT: B 1873 GLN cc_start: 0.8728 (tp40) cc_final: 0.8366 (tm-30) REVERT: B 1878 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7890 (mmmt) REVERT: B 1881 GLN cc_start: 0.8422 (pm20) cc_final: 0.8186 (pm20) REVERT: B 1882 LYS cc_start: 0.9205 (tttp) cc_final: 0.8671 (tmtt) REVERT: B 1884 LYS cc_start: 0.8827 (tppp) cc_final: 0.8424 (tppp) REVERT: B 1888 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8311 (mmm-85) REVERT: B 1889 GLN cc_start: 0.8745 (mt0) cc_final: 0.8279 (tp40) REVERT: B 1903 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8636 (mmtt) REVERT: B 1906 LYS cc_start: 0.8996 (tppt) cc_final: 0.8786 (tppt) REVERT: B 1908 GLN cc_start: 0.8563 (tp40) cc_final: 0.8188 (tp-100) REVERT: B 1911 LEU cc_start: 0.8481 (tt) cc_final: 0.7925 (tt) REVERT: B 1915 GLU cc_start: 0.8319 (pt0) cc_final: 0.7995 (pt0) REVERT: B 1917 ARG cc_start: 0.8990 (mtp-110) cc_final: 0.8596 (ttp-110) REVERT: B 1927 LYS cc_start: 0.8715 (tptp) cc_final: 0.8446 (tptp) REVERT: A 949 LYS cc_start: 0.7678 (mptt) cc_final: 0.7386 (tptt) REVERT: A 952 GLU cc_start: 0.8544 (pt0) cc_final: 0.7785 (mt-10) REVERT: A 1040 ASP cc_start: 0.7498 (m-30) cc_final: 0.7228 (m-30) REVERT: A 1179 MET cc_start: 0.6708 (ppp) cc_final: 0.6430 (ppp) REVERT: A 1202 LYS cc_start: 0.9164 (pptt) cc_final: 0.8827 (pptt) REVERT: A 1243 LEU cc_start: 0.7505 (mt) cc_final: 0.7166 (tt) REVERT: A 1250 LYS cc_start: 0.8972 (pptt) cc_final: 0.8637 (pptt) REVERT: A 1261 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8589 (tp40) REVERT: A 1265 ASN cc_start: 0.8736 (m-40) cc_final: 0.8432 (t0) REVERT: A 1267 ILE cc_start: 0.8757 (pt) cc_final: 0.7870 (mm) REVERT: A 1270 LYS cc_start: 0.8588 (mmtp) cc_final: 0.8215 (mtmm) REVERT: A 1273 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 1275 ASN cc_start: 0.9013 (m110) cc_final: 0.8749 (m110) REVERT: A 1276 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7404 (ttm-80) REVERT: A 1291 GLU cc_start: 0.7928 (pt0) cc_final: 0.7544 (pt0) REVERT: A 1297 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8607 (ttm-80) REVERT: A 1299 LEU cc_start: 0.8425 (mm) cc_final: 0.7630 (tt) REVERT: A 1300 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8029 (tp30) REVERT: A 1325 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8265 (ttp80) REVERT: A 1329 GLU cc_start: 0.8173 (tp30) cc_final: 0.7941 (tp30) REVERT: A 1330 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7794 (mm-30) REVERT: A 1338 LEU cc_start: 0.8945 (mt) cc_final: 0.8738 (mm) REVERT: A 1345 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 1350 ASN cc_start: 0.7729 (t0) cc_final: 0.7432 (t0) REVERT: A 1353 GLU cc_start: 0.8339 (mp0) cc_final: 0.7610 (mp0) REVERT: A 1356 GLU cc_start: 0.8295 (tp30) cc_final: 0.7806 (tp30) REVERT: A 1357 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 1358 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 1360 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 1362 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8473 (ttmm) REVERT: A 1379 TRP cc_start: 0.7224 (m100) cc_final: 0.6656 (m100) REVERT: A 1392 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 1407 GLU cc_start: 0.7824 (pp20) cc_final: 0.7622 (pp20) REVERT: A 1409 GLU cc_start: 0.7424 (tm-30) cc_final: 0.5985 (tm-30) REVERT: A 1413 GLU cc_start: 0.7454 (pm20) cc_final: 0.6736 (pm20) REVERT: A 1417 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8034 (mm-40) REVERT: A 1423 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 1424 LYS cc_start: 0.8818 (tptm) cc_final: 0.8351 (tppt) REVERT: A 1429 LEU cc_start: 0.8997 (tt) cc_final: 0.8752 (tt) REVERT: A 1432 GLU cc_start: 0.7752 (mp0) cc_final: 0.7174 (mp0) REVERT: A 1434 GLU cc_start: 0.8191 (mp0) cc_final: 0.7815 (mp0) REVERT: A 1451 GLU cc_start: 0.7837 (pt0) cc_final: 0.7502 (pt0) REVERT: A 1452 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8788 (tppt) REVERT: A 1458 ASP cc_start: 0.7960 (p0) cc_final: 0.7467 (p0) REVERT: A 1463 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 1467 LYS cc_start: 0.8253 (ttmm) cc_final: 0.8020 (ttmm) REVERT: A 1481 GLU cc_start: 0.7991 (tp30) cc_final: 0.7671 (tp30) REVERT: A 1488 GLU cc_start: 0.7488 (tp30) cc_final: 0.6790 (tp30) REVERT: A 1492 LEU cc_start: 0.8663 (mt) cc_final: 0.8234 (mm) REVERT: A 1501 GLU cc_start: 0.8557 (pt0) cc_final: 0.8228 (pt0) REVERT: A 1504 GLU cc_start: 0.7830 (mp0) cc_final: 0.7351 (mp0) REVERT: A 1511 LYS cc_start: 0.8836 (mptt) cc_final: 0.8503 (mmmm) REVERT: A 1516 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7142 (mm-30) REVERT: A 1540 ARG cc_start: 0.8127 (tmt-80) cc_final: 0.7839 (tmt-80) REVERT: A 1559 LEU cc_start: 0.8551 (tp) cc_final: 0.7828 (tp) REVERT: A 1560 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 1561 GLN cc_start: 0.7876 (pp30) cc_final: 0.7512 (pp30) REVERT: A 1563 GLU cc_start: 0.8416 (tp30) cc_final: 0.7987 (tp30) REVERT: A 1572 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 1597 ASN cc_start: 0.8830 (m-40) cc_final: 0.8608 (t0) REVERT: A 1599 GLN cc_start: 0.8416 (tt0) cc_final: 0.8165 (tp40) REVERT: A 1618 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 1622 MET cc_start: 0.7572 (tpp) cc_final: 0.6777 (tpp) REVERT: A 1623 LYS cc_start: 0.8634 (tppt) cc_final: 0.7956 (tppt) REVERT: A 1627 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 1642 LYS cc_start: 0.8521 (ttpp) cc_final: 0.7981 (ttmm) REVERT: A 1646 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 1649 LYS cc_start: 0.9182 (tttp) cc_final: 0.8675 (ttmm) REVERT: A 1662 GLN cc_start: 0.8649 (tt0) cc_final: 0.8111 (tp40) REVERT: A 1692 GLU cc_start: 0.8138 (tp30) cc_final: 0.7655 (tp30) REVERT: A 1712 GLN cc_start: 0.8774 (mm110) cc_final: 0.8486 (mm-40) REVERT: A 1735 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8878 (tptp) REVERT: A 1737 LYS cc_start: 0.8986 (tttp) cc_final: 0.8754 (tttm) REVERT: A 1754 ASN cc_start: 0.8443 (t0) cc_final: 0.8186 (t0) REVERT: A 1757 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8576 (ttpt) REVERT: A 1762 LYS cc_start: 0.9320 (ttmt) cc_final: 0.9060 (ttmt) REVERT: A 1778 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7971 (mtt-85) REVERT: A 1783 HIS cc_start: 0.9060 (t-90) cc_final: 0.8757 (t-170) REVERT: A 1785 GLN cc_start: 0.8529 (tp40) cc_final: 0.8153 (tm-30) REVERT: A 1792 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8922 (tppp) REVERT: A 1795 GLU cc_start: 0.7946 (tp30) cc_final: 0.7704 (tp30) REVERT: A 1802 GLN cc_start: 0.8858 (tp40) cc_final: 0.8520 (tm-30) REVERT: A 1822 LYS cc_start: 0.8530 (tttm) cc_final: 0.8244 (ttpp) REVERT: A 1824 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 1840 ARG cc_start: 0.8037 (mpp80) cc_final: 0.7733 (mtm110) REVERT: A 1846 LYS cc_start: 0.9189 (tttm) cc_final: 0.8909 (ttmm) REVERT: A 1853 ARG cc_start: 0.8331 (mtp-110) cc_final: 0.7696 (ttm110) REVERT: A 1860 PHE cc_start: 0.9086 (t80) cc_final: 0.8880 (t80) REVERT: A 1864 GLU cc_start: 0.8024 (tp30) cc_final: 0.7441 (tp30) REVERT: A 1865 ASP cc_start: 0.8079 (t0) cc_final: 0.7708 (t0) REVERT: A 1868 ASN cc_start: 0.8666 (m110) cc_final: 0.8135 (m-40) REVERT: A 1870 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 1871 ARG cc_start: 0.8640 (tpt90) cc_final: 0.8418 (tpt90) REVERT: A 1878 LYS cc_start: 0.9055 (tppt) cc_final: 0.8753 (mmmm) REVERT: A 1882 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8921 (ttmm) REVERT: A 1884 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8819 (ttpp) REVERT: A 1889 GLN cc_start: 0.7735 (pp30) cc_final: 0.7454 (pp30) REVERT: A 1892 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 1909 GLN cc_start: 0.8650 (tp40) cc_final: 0.8196 (tm-30) REVERT: A 1910 GLU cc_start: 0.8511 (tt0) cc_final: 0.7962 (tt0) REVERT: A 1915 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.1499 time to fit residues: 141.6855 Evaluate side-chains 617 residues out of total 1846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 96 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1720 GLN B1783 HIS A 917 GLN A1537 GLN A1900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.119845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.097053 restraints weight = 47044.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.099686 restraints weight = 28165.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.101454 restraints weight = 18760.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.102698 restraints weight = 13438.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.103522 restraints weight = 10199.684| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 1.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17454 Z= 0.152 Angle : 0.682 8.845 23282 Z= 0.370 Chirality : 0.043 0.164 2582 Planarity : 0.003 0.042 3158 Dihedral : 4.294 21.497 2318 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.18), residues: 2150 helix: 1.97 (0.11), residues: 2105 sheet: None (None), residues: 0 loop : 1.30 (0.95), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1540 TYR 0.035 0.003 TYR B1654 PHE 0.036 0.002 PHE A 945 TRP 0.043 0.005 TRP B1379 HIS 0.012 0.001 HIS B1598 Details of bonding type rmsd covalent geometry : bond 0.00304 (17454) covalent geometry : angle 0.68179 (23282) hydrogen bonds : bond 0.04072 ( 1625) hydrogen bonds : angle 3.77361 ( 4872) =============================================================================== Job complete usr+sys time: 5040.37 seconds wall clock time: 86 minutes 57.11 seconds (5217.11 seconds total)