Starting phenix.real_space_refine on Tue Sep 15 14:53:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.map" model { file = "/net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sct_0126/09_2026/6sct_0126.cif" } resolution = 4.69 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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 186 5.16 5 C 25857 2.51 5 N 7008 2.21 5 O 7629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40680 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3168 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 9, 'TRANS': 369} Chain: "B" Number of atoms: 5405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5405 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 643} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3598 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 423} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 875 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 514 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 514 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "O" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 514 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "F" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3168 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 9, 'TRANS': 369} Chain: "K" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3168 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 9, 'TRANS': 369} Chain: "G" Number of atoms: 5405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5405 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 643} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 5405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5405 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 643} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3598 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 423} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3598 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 423} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 875 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 875 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.94, per 1000 atoms: 0.20 Number of scatterers: 40680 At special positions: 0 Unit cell: (264.275, 289.85, 110.825, 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 186 16.00 O 7629 8.00 N 7008 7.00 C 25857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 357 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 1249 through 1263 removed outlier: 3.513A pdb=" N TRP A1253 " --> pdb=" O SER A1249 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A1258 " --> pdb=" O LYS A1254 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1278 removed outlier: 3.580A pdb=" N MET A1271 " --> pdb=" O ARG A1267 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N HIS A1275 " --> pdb=" O MET A1271 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A1276 " --> pdb=" O CYS A1272 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1282 Processing helix chain 'A' and resid 1283 through 1294 removed outlier: 3.702A pdb=" N ASP A1292 " --> pdb=" O ASN A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1307 removed outlier: 4.263A pdb=" N THR A1301 " --> pdb=" O GLU A1297 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET A1302 " --> pdb=" O GLU A1298 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1327 removed outlier: 3.826A pdb=" N PHE A1317 " --> pdb=" O HIS A1313 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A1326 " --> pdb=" O ILE A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1340 removed outlier: 3.640A pdb=" N MET A1332 " --> pdb=" O LYS A1328 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A1333 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU A1334 " --> pdb=" O GLN A1330 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A1338 " --> pdb=" O GLU A1334 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A1339 " --> pdb=" O HIS A1335 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A1340 " --> pdb=" O LEU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1353 removed outlier: 3.776A pdb=" N VAL A1348 " --> pdb=" O ASN A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1368 Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 3.617A pdb=" N ALA A1374 " --> pdb=" O GLU A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1394 removed outlier: 4.052A pdb=" N ASP A1393 " --> pdb=" O GLY A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1398 Processing helix chain 'A' and resid 1401 through 1415 removed outlier: 3.717A pdb=" N TYR A1405 " --> pdb=" O VAL A1401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A1409 " --> pdb=" O TYR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1427 removed outlier: 4.274A pdb=" N LEU A1422 " --> pdb=" O LEU A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1443 removed outlier: 3.798A pdb=" N LYS A1441 " --> pdb=" O ASN A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 Processing helix chain 'A' and resid 1457 through 1459 No H-bonds generated for 'chain 'A' and resid 1457 through 1459' Processing helix chain 'A' and resid 1460 through 1475 Processing helix chain 'A' and resid 1477 through 1487 Processing helix chain 'A' and resid 1491 through 1500 removed outlier: 4.158A pdb=" N LEU A1495 " --> pdb=" O ASP A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1514 Processing helix chain 'A' and resid 1515 through 1519 Processing helix chain 'A' and resid 1523 through 1528 Processing helix chain 'A' and resid 1535 through 1545 removed outlier: 3.627A pdb=" N TYR A1540 " --> pdb=" O ASP A1536 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER A1542 " --> pdb=" O MET A1538 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1543 " --> pdb=" O GLN A1539 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A1545 " --> pdb=" O ALA A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 Processing helix chain 'A' and resid 1562 through 1564 No H-bonds generated for 'chain 'A' and resid 1562 through 1564' Processing helix chain 'A' and resid 1565 through 1572 removed outlier: 3.580A pdb=" N LEU A1570 " --> pdb=" O PHE A1566 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A1571 " --> pdb=" O GLY A1567 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A1572 " --> pdb=" O ALA A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1589 Processing helix chain 'A' and resid 1595 through 1626 removed outlier: 4.293A pdb=" N PHE A1599 " --> pdb=" O ALA A1595 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A1607 " --> pdb=" O MET A1603 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A1625 " --> pdb=" O LYS A1621 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.908A pdb=" N LEU B 834 " --> pdb=" O LYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 853 removed outlier: 3.638A pdb=" N LYS B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 857 Processing helix chain 'B' and resid 858 through 869 Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.076A pdb=" N ALA B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 880 " --> pdb=" O HIS B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 896 Processing helix chain 'B' and resid 901 through 913 removed outlier: 3.821A pdb=" N VAL B 905 " --> pdb=" O ASP B 901 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS B 911 " --> pdb=" O LYS B 907 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 925 removed outlier: 4.167A pdb=" N VAL B 919 " --> pdb=" O HIS B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 934 Processing helix chain 'B' and resid 939 through 950 removed outlier: 4.153A pdb=" N LEU B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 3.506A pdb=" N TRP B 956 " --> pdb=" O ASP B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 978 removed outlier: 4.038A pdb=" N LEU B 970 " --> pdb=" O TYR B 966 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN B 976 " --> pdb=" O ASP B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 981 No H-bonds generated for 'chain 'B' and resid 979 through 981' Processing helix chain 'B' and resid 985 through 999 removed outlier: 3.670A pdb=" N THR B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1014 removed outlier: 3.741A pdb=" N ASP B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1036 removed outlier: 4.184A pdb=" N THR B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1046 removed outlier: 3.507A pdb=" N GLU B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 4.008A pdb=" N ILE B1055 " --> pdb=" O ASP B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1075 Processing helix chain 'B' and resid 1078 through 1089 removed outlier: 3.664A pdb=" N VAL B1082 " --> pdb=" O ASN B1078 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B1083 " --> pdb=" O THR B1079 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B1084 " --> pdb=" O SER B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 removed outlier: 4.316A pdb=" N GLU B1097 " --> pdb=" O ASP B1093 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B1098 " --> pdb=" O ARG B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1119 removed outlier: 3.675A pdb=" N GLN B1117 " --> pdb=" O LYS B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1130 removed outlier: 4.360A pdb=" N ASP B1126 " --> pdb=" O LYS B1122 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B1127 " --> pdb=" O GLU B1123 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B1128 " --> pdb=" O ALA B1124 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B1130 " --> pdb=" O ASP B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1145 Processing helix chain 'B' and resid 1151 through 1161 removed outlier: 3.998A pdb=" N LYS B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1180 Processing helix chain 'B' and resid 1182 through 1192 removed outlier: 4.218A pdb=" N GLU B1188 " --> pdb=" O ALA B1184 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B1190 " --> pdb=" O LEU B1186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B1191 " --> pdb=" O GLU B1187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1208 removed outlier: 3.713A pdb=" N ARG B1204 " --> pdb=" O GLN B1200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B1206 " --> pdb=" O GLY B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1218 Processing helix chain 'B' and resid 1226 through 1235 removed outlier: 3.766A pdb=" N THR B1230 " --> pdb=" O ARG B1226 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N HIS B1233 " --> pdb=" O SER B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1248 removed outlier: 3.526A pdb=" N ASP B1242 " --> pdb=" O GLN B1238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B1246 " --> pdb=" O ASP B1242 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1263 Processing helix chain 'B' and resid 1266 through 1278 removed outlier: 3.671A pdb=" N GLN B1270 " --> pdb=" O PHE B1266 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET B1271 " --> pdb=" O ARG B1267 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS B1275 " --> pdb=" O MET B1271 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE B1276 " --> pdb=" O CYS B1272 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B1277 " --> pdb=" O GLY B1273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B1278 " --> pdb=" O LEU B1274 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1292 removed outlier: 4.310A pdb=" N GLU B1284 " --> pdb=" O ALA B1280 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B1285 " --> pdb=" O ASP B1281 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B1292 " --> pdb=" O ASN B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1295 through 1305 removed outlier: 3.677A pdb=" N ALA B1305 " --> pdb=" O THR B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1313 through 1327 removed outlier: 3.990A pdb=" N PHE B1317 " --> pdb=" O HIS B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1340 removed outlier: 3.596A pdb=" N HIS B1335 " --> pdb=" O LYS B1331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B1338 " --> pdb=" O GLU B1334 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B1339 " --> pdb=" O HIS B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1356 removed outlier: 3.948A pdb=" N ALA B1351 " --> pdb=" O LYS B1347 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1368 removed outlier: 3.518A pdb=" N LEU B1361 " --> pdb=" O LEU B1357 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B1362 " --> pdb=" O TRP B1358 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B1363 " --> pdb=" O ALA B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 removed outlier: 3.696A pdb=" N ILE B1376 " --> pdb=" O ASP B1372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B1377 " --> pdb=" O ASN B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1386 removed outlier: 3.749A pdb=" N ALA B1385 " --> pdb=" O HIS B1381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B1386 " --> pdb=" O PRO B1382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1381 through 1386' Processing helix chain 'B' and resid 1387 through 1395 Processing helix chain 'B' and resid 1396 through 1398 No H-bonds generated for 'chain 'B' and resid 1396 through 1398' Processing helix chain 'B' and resid 1402 through 1415 removed outlier: 3.686A pdb=" N ARG B1406 " --> pdb=" O GLU B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1427 removed outlier: 4.288A pdb=" N ASN B1420 " --> pdb=" O PRO B1416 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B1421 " --> pdb=" O LEU B1417 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B1425 " --> pdb=" O ASP B1421 " (cutoff:3.500A) Processing helix chain 'B' and resid 1432 through 1442 removed outlier: 3.639A pdb=" N VAL B1436 " --> pdb=" O HIS B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1445 through 1447 No H-bonds generated for 'chain 'B' and resid 1445 through 1447' Processing helix chain 'B' and resid 1448 through 1453 removed outlier: 4.067A pdb=" N ARG B1453 " --> pdb=" O LYS B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1460 through 1473 removed outlier: 3.678A pdb=" N LEU B1467 " --> pdb=" O VAL B1463 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B1468 " --> pdb=" O ASN B1464 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 4.082A pdb=" N HIS C 642 " --> pdb=" O ARG C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 657 removed outlier: 3.721A pdb=" N LEU C 651 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 680 through 685 Processing helix chain 'C' and resid 685 through 690 removed outlier: 4.183A pdb=" N TYR C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS C 690 " --> pdb=" O ALA C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 685 through 690' Processing helix chain 'C' and resid 695 through 704 Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 724 through 736 removed outlier: 3.839A pdb=" N HIS C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 Processing helix chain 'C' and resid 744 through 751 removed outlier: 3.822A pdb=" N ARG C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 766 removed outlier: 3.613A pdb=" N VAL C 759 " --> pdb=" O ASP C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 782 removed outlier: 4.515A pdb=" N ASP C 779 " --> pdb=" O ILE C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 795 removed outlier: 4.019A pdb=" N LEU C 787 " --> pdb=" O PHE C 783 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 789 " --> pdb=" O HIS C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 808 through 810 No H-bonds generated for 'chain 'C' and resid 808 through 810' Processing helix chain 'C' and resid 811 through 822 Processing helix chain 'C' and resid 825 through 834 removed outlier: 3.847A pdb=" N LEU C 834 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 853 removed outlier: 3.581A pdb=" N VAL C 846 " --> pdb=" O THR C 842 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 857 removed outlier: 3.667A pdb=" N LEU C 857 " --> pdb=" O ARG C 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 854 through 857' Processing helix chain 'C' and resid 858 through 869 removed outlier: 3.718A pdb=" N GLU C 868 " --> pdb=" O ALA C 864 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 869 " --> pdb=" O ARG C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 886 removed outlier: 3.744A pdb=" N ALA C 878 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C 879 " --> pdb=" O THR C 875 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 897 Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.797A pdb=" N VAL C 905 " --> pdb=" O ASP C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 925 removed outlier: 3.704A pdb=" N VAL C 919 " --> pdb=" O HIS C 915 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 935 Processing helix chain 'C' and resid 940 through 948 removed outlier: 3.863A pdb=" N VAL C 948 " --> pdb=" O SER C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 960 removed outlier: 3.597A pdb=" N TRP C 956 " --> pdb=" O ASP C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 982 removed outlier: 4.038A pdb=" N LEU C 970 " --> pdb=" O TYR C 966 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 971 " --> pdb=" O ARG C 967 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 980 " --> pdb=" O GLN C 976 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 981 " --> pdb=" O THR C 977 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 982 " --> pdb=" O ALA C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 998 removed outlier: 3.890A pdb=" N VAL C 988 " --> pdb=" O ASP C 984 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1014 Processing helix chain 'C' and resid 1024 through 1034 removed outlier: 4.580A pdb=" N THR C1031 " --> pdb=" O LEU C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1047 removed outlier: 3.630A pdb=" N GLU C1042 " --> pdb=" O THR C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1062 removed outlier: 4.177A pdb=" N ILE C1055 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1075 Processing helix chain 'D' and resid 101 through 161 removed outlier: 4.145A pdb=" N LYS D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 108 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.576A pdb=" N CYS D 209 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'E' and resid 102 through 156 removed outlier: 3.785A pdb=" N GLN E 110 " --> pdb=" O TRP E 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG E 142 " --> pdb=" O GLU E 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 156 removed outlier: 3.787A pdb=" N GLN J 110 " --> pdb=" O TRP J 106 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA J 119 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN J 141 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG J 142 " --> pdb=" O GLU J 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 156 removed outlier: 3.786A pdb=" N GLN O 110 " --> pdb=" O TRP O 106 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA O 119 " --> pdb=" O GLN O 115 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU O 136 " --> pdb=" O ALA O 132 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN O 141 " --> pdb=" O GLU O 137 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG O 142 " --> pdb=" O GLU O 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 1249 through 1263 removed outlier: 3.512A pdb=" N TRP F1253 " --> pdb=" O SER F1249 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE F1258 " --> pdb=" O LYS F1254 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA F1259 " --> pdb=" O GLU F1255 " (cutoff:3.500A) Processing helix chain 'F' and resid 1265 through 1278 removed outlier: 3.580A pdb=" N MET F1271 " --> pdb=" O ARG F1267 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N HIS F1275 " --> pdb=" O MET F1271 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE F1276 " --> pdb=" O CYS F1272 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F1278 " --> pdb=" O LEU F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1279 through 1282 Processing helix chain 'F' and resid 1283 through 1294 removed outlier: 3.703A pdb=" N ASP F1292 " --> pdb=" O ASN F1288 " (cutoff:3.500A) Processing helix chain 'F' and resid 1295 through 1307 removed outlier: 4.263A pdb=" N THR F1301 " --> pdb=" O GLU F1297 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET F1302 " --> pdb=" O GLU F1298 " (cutoff:3.500A) Processing helix chain 'F' and resid 1313 through 1327 removed outlier: 3.826A pdb=" N PHE F1317 " --> pdb=" O HIS F1313 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS F1326 " --> pdb=" O ILE F1322 " (cutoff:3.500A) Processing helix chain 'F' and resid 1328 through 1340 removed outlier: 3.640A pdb=" N MET F1332 " --> pdb=" O LYS F1328 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG F1333 " --> pdb=" O PRO F1329 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU F1334 " --> pdb=" O GLN F1330 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU F1338 " --> pdb=" O GLU F1334 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE F1339 " --> pdb=" O HIS F1335 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP F1340 " --> pdb=" O LEU F1336 " (cutoff:3.500A) Processing helix chain 'F' and resid 1344 through 1353 removed outlier: 3.776A pdb=" N VAL F1348 " --> pdb=" O ASN F1344 " (cutoff:3.500A) Processing helix chain 'F' and resid 1357 through 1368 Processing helix chain 'F' and resid 1370 through 1381 removed outlier: 3.618A pdb=" N ALA F1374 " --> pdb=" O GLU F1370 " (cutoff:3.500A) Processing helix chain 'F' and resid 1389 through 1394 removed outlier: 4.052A pdb=" N ASP F1393 " --> pdb=" O GLY F1389 " (cutoff:3.500A) Processing helix chain 'F' and resid 1395 through 1398 Processing helix chain 'F' and resid 1401 through 1415 removed outlier: 3.717A pdb=" N TYR F1405 " --> pdb=" O VAL F1401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F1409 " --> pdb=" O TYR F1405 " (cutoff:3.500A) Processing helix chain 'F' and resid 1418 through 1427 removed outlier: 4.274A pdb=" N LEU F1422 " --> pdb=" O LEU F1418 " (cutoff:3.500A) Processing helix chain 'F' and resid 1431 through 1443 removed outlier: 3.799A pdb=" N LYS F1441 " --> pdb=" O ASN F1437 " (cutoff:3.500A) Processing helix chain 'F' and resid 1448 through 1456 Processing helix chain 'F' and resid 1457 through 1459 No H-bonds generated for 'chain 'F' and resid 1457 through 1459' Processing helix chain 'F' and resid 1460 through 1475 Processing helix chain 'F' and resid 1477 through 1487 Processing helix chain 'F' and resid 1491 through 1500 removed outlier: 4.159A pdb=" N LEU F1495 " --> pdb=" O ASP F1491 " (cutoff:3.500A) Processing helix chain 'F' and resid 1504 through 1514 Processing helix chain 'F' and resid 1515 through 1519 Processing helix chain 'F' and resid 1523 through 1528 Processing helix chain 'F' and resid 1535 through 1545 removed outlier: 3.627A pdb=" N TYR F1540 " --> pdb=" O ASP F1536 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA F1541 " --> pdb=" O ALA F1537 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER F1542 " --> pdb=" O MET F1538 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F1543 " --> pdb=" O GLN F1539 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F1545 " --> pdb=" O ALA F1541 " (cutoff:3.500A) Processing helix chain 'F' and resid 1549 through 1560 Processing helix chain 'F' and resid 1562 through 1564 No H-bonds generated for 'chain 'F' and resid 1562 through 1564' Processing helix chain 'F' and resid 1565 through 1572 removed outlier: 3.580A pdb=" N LEU F1570 " --> pdb=" O PHE F1566 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F1571 " --> pdb=" O GLY F1567 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F1572 " --> pdb=" O ALA F1568 " (cutoff:3.500A) Processing helix chain 'F' and resid 1578 through 1589 Processing helix chain 'F' and resid 1595 through 1626 removed outlier: 4.293A pdb=" N PHE F1599 " --> pdb=" O ALA F1595 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU F1607 " --> pdb=" O MET F1603 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F1625 " --> pdb=" O LYS F1621 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F1626 " --> pdb=" O GLU F1622 " (cutoff:3.500A) Processing helix chain 'K' and resid 1249 through 1263 removed outlier: 3.514A pdb=" N TRP K1253 " --> pdb=" O SER K1249 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE K1258 " --> pdb=" O LYS K1254 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA K1259 " --> pdb=" O GLU K1255 " (cutoff:3.500A) Processing helix chain 'K' and resid 1265 through 1278 removed outlier: 3.579A pdb=" N MET K1271 " --> pdb=" O ARG K1267 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N HIS K1275 " --> pdb=" O MET K1271 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE K1276 " --> pdb=" O CYS K1272 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL K1278 " --> pdb=" O LEU K1274 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1282 Processing helix chain 'K' and resid 1283 through 1294 removed outlier: 3.702A pdb=" N ASP K1292 " --> pdb=" O ASN K1288 " (cutoff:3.500A) Processing helix chain 'K' and resid 1295 through 1307 removed outlier: 4.263A pdb=" N THR K1301 " --> pdb=" O GLU K1297 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET K1302 " --> pdb=" O GLU K1298 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU K1307 " --> pdb=" O LEU K1303 " (cutoff:3.500A) Processing helix chain 'K' and resid 1313 through 1327 removed outlier: 3.826A pdb=" N PHE K1317 " --> pdb=" O HIS K1313 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS K1326 " --> pdb=" O ILE K1322 " (cutoff:3.500A) Processing helix chain 'K' and resid 1328 through 1340 removed outlier: 3.639A pdb=" N MET K1332 " --> pdb=" O LYS K1328 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG K1333 " --> pdb=" O PRO K1329 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU K1334 " --> pdb=" O GLN K1330 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU K1338 " --> pdb=" O GLU K1334 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE K1339 " --> pdb=" O HIS K1335 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP K1340 " --> pdb=" O LEU K1336 " (cutoff:3.500A) Processing helix chain 'K' and resid 1344 through 1353 removed outlier: 3.776A pdb=" N VAL K1348 " --> pdb=" O ASN K1344 " (cutoff:3.500A) Processing helix chain 'K' and resid 1357 through 1368 Processing helix chain 'K' and resid 1370 through 1381 removed outlier: 3.618A pdb=" N ALA K1374 " --> pdb=" O GLU K1370 " (cutoff:3.500A) Processing helix chain 'K' and resid 1389 through 1394 removed outlier: 4.052A pdb=" N ASP K1393 " --> pdb=" O GLY K1389 " (cutoff:3.500A) Processing helix chain 'K' and resid 1395 through 1398 Processing helix chain 'K' and resid 1401 through 1415 removed outlier: 3.717A pdb=" N TYR K1405 " --> pdb=" O VAL K1401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN K1409 " --> pdb=" O TYR K1405 " (cutoff:3.500A) Processing helix chain 'K' and resid 1418 through 1427 removed outlier: 4.274A pdb=" N LEU K1422 " --> pdb=" O LEU K1418 " (cutoff:3.500A) Processing helix chain 'K' and resid 1431 through 1443 removed outlier: 3.799A pdb=" N LYS K1441 " --> pdb=" O ASN K1437 " (cutoff:3.500A) Processing helix chain 'K' and resid 1448 through 1456 Processing helix chain 'K' and resid 1457 through 1459 No H-bonds generated for 'chain 'K' and resid 1457 through 1459' Processing helix chain 'K' and resid 1460 through 1475 Processing helix chain 'K' and resid 1477 through 1487 Processing helix chain 'K' and resid 1491 through 1500 removed outlier: 4.159A pdb=" N LEU K1495 " --> pdb=" O ASP K1491 " (cutoff:3.500A) Processing helix chain 'K' and resid 1504 through 1514 Processing helix chain 'K' and resid 1515 through 1519 Processing helix chain 'K' and resid 1523 through 1528 Processing helix chain 'K' and resid 1535 through 1545 removed outlier: 3.627A pdb=" N TYR K1540 " --> pdb=" O ASP K1536 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA K1541 " --> pdb=" O ALA K1537 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER K1542 " --> pdb=" O MET K1538 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU K1543 " --> pdb=" O GLN K1539 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K1545 " --> pdb=" O ALA K1541 " (cutoff:3.500A) Processing helix chain 'K' and resid 1549 through 1560 Processing helix chain 'K' and resid 1562 through 1564 No H-bonds generated for 'chain 'K' and resid 1562 through 1564' Processing helix chain 'K' and resid 1565 through 1572 removed outlier: 3.580A pdb=" N LEU K1570 " --> pdb=" O PHE K1566 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE K1571 " --> pdb=" O GLY K1567 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K1572 " --> pdb=" O ALA K1568 " (cutoff:3.500A) Processing helix chain 'K' and resid 1578 through 1589 Processing helix chain 'K' and resid 1595 through 1626 removed outlier: 4.293A pdb=" N PHE K1599 " --> pdb=" O ALA K1595 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU K1607 " --> pdb=" O MET K1603 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN K1625 " --> pdb=" O LYS K1621 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA K1626 " --> pdb=" O GLU K1622 " (cutoff:3.500A) Processing helix chain 'G' and resid 811 through 823 Processing helix chain 'G' and resid 826 through 834 removed outlier: 3.908A pdb=" N LEU G 834 " --> pdb=" O LYS G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 844 through 853 removed outlier: 3.638A pdb=" N LYS G 851 " --> pdb=" O ALA G 847 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 852 " --> pdb=" O GLU G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 854 through 857 Processing helix chain 'G' and resid 858 through 869 Processing helix chain 'G' and resid 872 through 886 removed outlier: 4.076A pdb=" N ALA G 878 " --> pdb=" O ALA G 874 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 880 " --> pdb=" O HIS G 876 " (cutoff:3.500A) Processing helix chain 'G' and resid 890 through 896 Processing helix chain 'G' and resid 901 through 913 removed outlier: 3.822A pdb=" N VAL G 905 " --> pdb=" O ASP G 901 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS G 911 " --> pdb=" O LYS G 907 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG G 912 " --> pdb=" O TYR G 908 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 925 removed outlier: 4.167A pdb=" N VAL G 919 " --> pdb=" O HIS G 915 " (cutoff:3.500A) Processing helix chain 'G' and resid 926 through 934 Processing helix chain 'G' and resid 939 through 950 removed outlier: 4.153A pdb=" N LEU G 943 " --> pdb=" O LEU G 939 " (cutoff:3.500A) Processing helix chain 'G' and resid 952 through 960 removed outlier: 3.506A pdb=" N TRP G 956 " --> pdb=" O ASP G 952 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 978 removed outlier: 4.038A pdb=" N LEU G 970 " --> pdb=" O TYR G 966 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN G 976 " --> pdb=" O ASP G 972 " (cutoff:3.500A) Processing helix chain 'G' and resid 979 through 981 No H-bonds generated for 'chain 'G' and resid 979 through 981' Processing helix chain 'G' and resid 985 through 999 removed outlier: 3.669A pdb=" N THR G 991 " --> pdb=" O GLU G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1005 through 1014 removed outlier: 3.741A pdb=" N ASP G1014 " --> pdb=" O LYS G1010 " (cutoff:3.500A) Processing helix chain 'G' and resid 1025 through 1036 removed outlier: 4.184A pdb=" N THR G1031 " --> pdb=" O LEU G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1038 through 1046 removed outlier: 3.508A pdb=" N GLU G1042 " --> pdb=" O THR G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1051 through 1062 removed outlier: 4.008A pdb=" N ILE G1055 " --> pdb=" O ASP G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1075 Processing helix chain 'G' and resid 1078 through 1089 removed outlier: 3.664A pdb=" N VAL G1082 " --> pdb=" O ASN G1078 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN G1083 " --> pdb=" O THR G1079 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL G1084 " --> pdb=" O SER G1080 " (cutoff:3.500A) Processing helix chain 'G' and resid 1091 through 1102 removed outlier: 4.316A pdb=" N GLU G1097 " --> pdb=" O ASP G1093 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE G1098 " --> pdb=" O ARG G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1104 through 1119 removed outlier: 3.675A pdb=" N GLN G1117 " --> pdb=" O LYS G1113 " (cutoff:3.500A) Processing helix chain 'G' and resid 1122 through 1130 removed outlier: 4.359A pdb=" N ASP G1126 " --> pdb=" O LYS G1122 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER G1127 " --> pdb=" O GLU G1123 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR G1128 " --> pdb=" O ALA G1124 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G1130 " --> pdb=" O ASP G1126 " (cutoff:3.500A) Processing helix chain 'G' and resid 1136 through 1145 Processing helix chain 'G' and resid 1151 through 1161 removed outlier: 3.998A pdb=" N LYS G1155 " --> pdb=" O GLU G1151 " (cutoff:3.500A) Processing helix chain 'G' and resid 1167 through 1180 Processing helix chain 'G' and resid 1182 through 1192 removed outlier: 4.218A pdb=" N GLU G1188 " --> pdb=" O ALA G1184 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G1190 " --> pdb=" O LEU G1186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN G1191 " --> pdb=" O GLU G1187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G1192 " --> pdb=" O GLU G1188 " (cutoff:3.500A) Processing helix chain 'G' and resid 1200 through 1208 removed outlier: 3.713A pdb=" N ARG G1204 " --> pdb=" O GLN G1200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR G1206 " --> pdb=" O GLY G1202 " (cutoff:3.500A) Processing helix chain 'G' and resid 1213 through 1218 Processing helix chain 'G' and resid 1226 through 1235 removed outlier: 3.766A pdb=" N THR G1230 " --> pdb=" O ARG G1226 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N HIS G1233 " --> pdb=" O SER G1229 " (cutoff:3.500A) Processing helix chain 'G' and resid 1237 through 1248 removed outlier: 3.526A pdb=" N ASP G1242 " --> pdb=" O GLN G1238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS G1246 " --> pdb=" O ASP G1242 " (cutoff:3.500A) Processing helix chain 'G' and resid 1249 through 1263 Processing helix chain 'G' and resid 1266 through 1278 removed outlier: 3.671A pdb=" N GLN G1270 " --> pdb=" O PHE G1266 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET G1271 " --> pdb=" O ARG G1267 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS G1275 " --> pdb=" O MET G1271 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE G1276 " --> pdb=" O CYS G1272 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G1277 " --> pdb=" O GLY G1273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G1278 " --> pdb=" O LEU G1274 " (cutoff:3.500A) Processing helix chain 'G' and resid 1280 through 1292 removed outlier: 4.310A pdb=" N GLU G1284 " --> pdb=" O ALA G1280 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G1285 " --> pdb=" O ASP G1281 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP G1292 " --> pdb=" O ASN G1288 " (cutoff:3.500A) Processing helix chain 'G' and resid 1295 through 1305 removed outlier: 3.677A pdb=" N ALA G1305 " --> pdb=" O THR G1301 " (cutoff:3.500A) Processing helix chain 'G' and resid 1313 through 1327 removed outlier: 3.989A pdb=" N PHE G1317 " --> pdb=" O HIS G1313 " (cutoff:3.500A) Processing helix chain 'G' and resid 1331 through 1340 removed outlier: 3.595A pdb=" N HIS G1335 " --> pdb=" O LYS G1331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G1338 " --> pdb=" O GLU G1334 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE G1339 " --> pdb=" O HIS G1335 " (cutoff:3.500A) Processing helix chain 'G' and resid 1345 through 1356 removed outlier: 3.948A pdb=" N ALA G1351 " --> pdb=" O LYS G1347 " (cutoff:3.500A) Processing helix chain 'G' and resid 1357 through 1368 removed outlier: 3.518A pdb=" N LEU G1361 " --> pdb=" O LEU G1357 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL G1362 " --> pdb=" O TRP G1358 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE G1363 " --> pdb=" O ALA G1359 " (cutoff:3.500A) Processing helix chain 'G' and resid 1370 through 1381 removed outlier: 3.697A pdb=" N ILE G1376 " --> pdb=" O ASP G1372 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR G1377 " --> pdb=" O ASN G1373 " (cutoff:3.500A) Processing helix chain 'G' and resid 1381 through 1386 removed outlier: 3.749A pdb=" N ALA G1385 " --> pdb=" O HIS G1381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP G1386 " --> pdb=" O PRO G1382 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1381 through 1386' Processing helix chain 'G' and resid 1387 through 1395 Processing helix chain 'G' and resid 1396 through 1398 No H-bonds generated for 'chain 'G' and resid 1396 through 1398' Processing helix chain 'G' and resid 1402 through 1415 removed outlier: 3.685A pdb=" N ARG G1406 " --> pdb=" O GLU G1402 " (cutoff:3.500A) Processing helix chain 'G' and resid 1416 through 1427 removed outlier: 4.288A pdb=" N ASN G1420 " --> pdb=" O PRO G1416 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP G1421 " --> pdb=" O LEU G1417 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL G1425 " --> pdb=" O ASP G1421 " (cutoff:3.500A) Processing helix chain 'G' and resid 1432 through 1442 removed outlier: 3.640A pdb=" N VAL G1436 " --> pdb=" O HIS G1432 " (cutoff:3.500A) Processing helix chain 'G' and resid 1445 through 1447 No H-bonds generated for 'chain 'G' and resid 1445 through 1447' Processing helix chain 'G' and resid 1448 through 1453 removed outlier: 4.068A pdb=" N ARG G1453 " --> pdb=" O LYS G1449 " (cutoff:3.500A) Processing helix chain 'G' and resid 1460 through 1473 removed outlier: 3.678A pdb=" N LEU G1467 " --> pdb=" O VAL G1463 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN G1468 " --> pdb=" O ASN G1464 " (cutoff:3.500A) Processing helix chain 'L' and resid 811 through 823 Processing helix chain 'L' and resid 826 through 834 removed outlier: 3.908A pdb=" N LEU L 834 " --> pdb=" O LYS L 830 " (cutoff:3.500A) Processing helix chain 'L' and resid 844 through 853 removed outlier: 3.637A pdb=" N LYS L 851 " --> pdb=" O ALA L 847 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG L 852 " --> pdb=" O GLU L 848 " (cutoff:3.500A) Processing helix chain 'L' and resid 854 through 857 Processing helix chain 'L' and resid 858 through 869 Processing helix chain 'L' and resid 872 through 886 removed outlier: 4.076A pdb=" N ALA L 878 " --> pdb=" O ALA L 874 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA L 880 " --> pdb=" O HIS L 876 " (cutoff:3.500A) Processing helix chain 'L' and resid 890 through 896 Processing helix chain 'L' and resid 901 through 913 removed outlier: 3.821A pdb=" N VAL L 905 " --> pdb=" O ASP L 901 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS L 911 " --> pdb=" O LYS L 907 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG L 912 " --> pdb=" O TYR L 908 " (cutoff:3.500A) Processing helix chain 'L' and resid 913 through 925 removed outlier: 4.167A pdb=" N VAL L 919 " --> pdb=" O HIS L 915 " (cutoff:3.500A) Processing helix chain 'L' and resid 926 through 934 Processing helix chain 'L' and resid 939 through 950 removed outlier: 4.153A pdb=" N LEU L 943 " --> pdb=" O LEU L 939 " (cutoff:3.500A) Processing helix chain 'L' and resid 952 through 960 removed outlier: 3.507A pdb=" N TRP L 956 " --> pdb=" O ASP L 952 " (cutoff:3.500A) Processing helix chain 'L' and resid 966 through 978 removed outlier: 4.037A pdb=" N LEU L 970 " --> pdb=" O TYR L 966 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLN L 976 " --> pdb=" O ASP L 972 " (cutoff:3.500A) Processing helix chain 'L' and resid 979 through 981 No H-bonds generated for 'chain 'L' and resid 979 through 981' Processing helix chain 'L' and resid 985 through 999 removed outlier: 3.670A pdb=" N THR L 991 " --> pdb=" O GLU L 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 1005 through 1014 removed outlier: 3.741A pdb=" N ASP L1014 " --> pdb=" O LYS L1010 " (cutoff:3.500A) Processing helix chain 'L' and resid 1025 through 1036 removed outlier: 4.185A pdb=" N THR L1031 " --> pdb=" O LEU L1027 " (cutoff:3.500A) Processing helix chain 'L' and resid 1038 through 1046 removed outlier: 3.508A pdb=" N GLU L1042 " --> pdb=" O THR L1038 " (cutoff:3.500A) Processing helix chain 'L' and resid 1051 through 1062 removed outlier: 4.008A pdb=" N ILE L1055 " --> pdb=" O ASP L1051 " (cutoff:3.500A) Processing helix chain 'L' and resid 1065 through 1075 Processing helix chain 'L' and resid 1078 through 1089 removed outlier: 3.664A pdb=" N VAL L1082 " --> pdb=" O ASN L1078 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN L1083 " --> pdb=" O THR L1079 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL L1084 " --> pdb=" O SER L1080 " (cutoff:3.500A) Processing helix chain 'L' and resid 1091 through 1102 removed outlier: 4.316A pdb=" N GLU L1097 " --> pdb=" O ASP L1093 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE L1098 " --> pdb=" O ARG L1094 " (cutoff:3.500A) Processing helix chain 'L' and resid 1104 through 1119 removed outlier: 3.675A pdb=" N GLN L1117 " --> pdb=" O LYS L1113 " (cutoff:3.500A) Processing helix chain 'L' and resid 1122 through 1130 removed outlier: 4.359A pdb=" N ASP L1126 " --> pdb=" O LYS L1122 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER L1127 " --> pdb=" O GLU L1123 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR L1128 " --> pdb=" O ALA L1124 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS L1130 " --> pdb=" O ASP L1126 " (cutoff:3.500A) Processing helix chain 'L' and resid 1136 through 1145 Processing helix chain 'L' and resid 1151 through 1161 removed outlier: 3.998A pdb=" N LYS L1155 " --> pdb=" O GLU L1151 " (cutoff:3.500A) Processing helix chain 'L' and resid 1167 through 1180 Processing helix chain 'L' and resid 1182 through 1192 removed outlier: 4.219A pdb=" N GLU L1188 " --> pdb=" O ALA L1184 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L1190 " --> pdb=" O LEU L1186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN L1191 " --> pdb=" O GLU L1187 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L1192 " --> pdb=" O GLU L1188 " (cutoff:3.500A) Processing helix chain 'L' and resid 1200 through 1208 removed outlier: 3.714A pdb=" N ARG L1204 " --> pdb=" O GLN L1200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR L1206 " --> pdb=" O GLY L1202 " (cutoff:3.500A) Processing helix chain 'L' and resid 1213 through 1218 Processing helix chain 'L' and resid 1226 through 1235 removed outlier: 3.767A pdb=" N THR L1230 " --> pdb=" O ARG L1226 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS L1233 " --> pdb=" O SER L1229 " (cutoff:3.500A) Processing helix chain 'L' and resid 1237 through 1248 removed outlier: 3.526A pdb=" N ASP L1242 " --> pdb=" O GLN L1238 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS L1246 " --> pdb=" O ASP L1242 " (cutoff:3.500A) Processing helix chain 'L' and resid 1249 through 1263 Processing helix chain 'L' and resid 1266 through 1278 removed outlier: 3.670A pdb=" N GLN L1270 " --> pdb=" O PHE L1266 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET L1271 " --> pdb=" O ARG L1267 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS L1275 " --> pdb=" O MET L1271 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE L1276 " --> pdb=" O CYS L1272 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL L1277 " --> pdb=" O GLY L1273 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL L1278 " --> pdb=" O LEU L1274 " (cutoff:3.500A) Processing helix chain 'L' and resid 1280 through 1292 removed outlier: 4.309A pdb=" N GLU L1284 " --> pdb=" O ALA L1280 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU L1285 " --> pdb=" O ASP L1281 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP L1292 " --> pdb=" O ASN L1288 " (cutoff:3.500A) Processing helix chain 'L' and resid 1295 through 1305 removed outlier: 3.677A pdb=" N ALA L1305 " --> pdb=" O THR L1301 " (cutoff:3.500A) Processing helix chain 'L' and resid 1313 through 1327 removed outlier: 3.990A pdb=" N PHE L1317 " --> pdb=" O HIS L1313 " (cutoff:3.500A) Processing helix chain 'L' and resid 1331 through 1340 removed outlier: 3.596A pdb=" N HIS L1335 " --> pdb=" O LYS L1331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L1338 " --> pdb=" O GLU L1334 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE L1339 " --> pdb=" O HIS L1335 " (cutoff:3.500A) Processing helix chain 'L' and resid 1345 through 1356 removed outlier: 3.948A pdb=" N ALA L1351 " --> pdb=" O LYS L1347 " (cutoff:3.500A) Processing helix chain 'L' and resid 1357 through 1368 removed outlier: 3.518A pdb=" N LEU L1361 " --> pdb=" O LEU L1357 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL L1362 " --> pdb=" O TRP L1358 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE L1363 " --> pdb=" O ALA L1359 " (cutoff:3.500A) Processing helix chain 'L' and resid 1370 through 1381 removed outlier: 3.696A pdb=" N ILE L1376 " --> pdb=" O ASP L1372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR L1377 " --> pdb=" O ASN L1373 " (cutoff:3.500A) Processing helix chain 'L' and resid 1381 through 1386 removed outlier: 3.749A pdb=" N ALA L1385 " --> pdb=" O HIS L1381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP L1386 " --> pdb=" O PRO L1382 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1381 through 1386' Processing helix chain 'L' and resid 1387 through 1395 Processing helix chain 'L' and resid 1396 through 1398 No H-bonds generated for 'chain 'L' and resid 1396 through 1398' Processing helix chain 'L' and resid 1402 through 1415 removed outlier: 3.685A pdb=" N ARG L1406 " --> pdb=" O GLU L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1416 through 1427 removed outlier: 4.289A pdb=" N ASN L1420 " --> pdb=" O PRO L1416 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP L1421 " --> pdb=" O LEU L1417 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL L1425 " --> pdb=" O ASP L1421 " (cutoff:3.500A) Processing helix chain 'L' and resid 1432 through 1442 removed outlier: 3.639A pdb=" N VAL L1436 " --> pdb=" O HIS L1432 " (cutoff:3.500A) Processing helix chain 'L' and resid 1445 through 1447 No H-bonds generated for 'chain 'L' and resid 1445 through 1447' Processing helix chain 'L' and resid 1448 through 1453 removed outlier: 4.067A pdb=" N ARG L1453 " --> pdb=" O LYS L1449 " (cutoff:3.500A) Processing helix chain 'L' and resid 1460 through 1473 removed outlier: 3.679A pdb=" N LEU L1467 " --> pdb=" O VAL L1463 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN L1468 " --> pdb=" O ASN L1464 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 643 removed outlier: 4.082A pdb=" N HIS H 642 " --> pdb=" O ARG H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 647 through 657 removed outlier: 3.721A pdb=" N LEU H 651 " --> pdb=" O ASN H 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 653 " --> pdb=" O GLU H 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 673 Processing helix chain 'H' and resid 680 through 685 Processing helix chain 'H' and resid 685 through 690 removed outlier: 4.183A pdb=" N TYR H 689 " --> pdb=" O VAL H 685 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS H 690 " --> pdb=" O ALA H 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 685 through 690' Processing helix chain 'H' and resid 695 through 704 Processing helix chain 'H' and resid 709 through 715 Processing helix chain 'H' and resid 716 through 718 No H-bonds generated for 'chain 'H' and resid 716 through 718' Processing helix chain 'H' and resid 724 through 736 removed outlier: 3.840A pdb=" N HIS H 728 " --> pdb=" O ASP H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 740 through 743 Processing helix chain 'H' and resid 744 through 751 removed outlier: 3.823A pdb=" N ARG H 749 " --> pdb=" O GLU H 745 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 766 removed outlier: 3.613A pdb=" N VAL H 759 " --> pdb=" O ASP H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 773 through 782 removed outlier: 4.515A pdb=" N ASP H 779 " --> pdb=" O ILE H 775 " (cutoff:3.500A) Processing helix chain 'H' and resid 783 through 795 removed outlier: 4.019A pdb=" N LEU H 787 " --> pdb=" O PHE H 783 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU H 789 " --> pdb=" O HIS H 785 " (cutoff:3.500A) Processing helix chain 'H' and resid 798 through 807 Processing helix chain 'H' and resid 808 through 810 No H-bonds generated for 'chain 'H' and resid 808 through 810' Processing helix chain 'H' and resid 811 through 822 Processing helix chain 'H' and resid 825 through 834 removed outlier: 3.847A pdb=" N LEU H 834 " --> pdb=" O LYS H 830 " (cutoff:3.500A) Processing helix chain 'H' and resid 842 through 853 removed outlier: 3.581A pdb=" N VAL H 846 " --> pdb=" O THR H 842 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 847 " --> pdb=" O ASP H 843 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS H 851 " --> pdb=" O ALA H 847 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 857 removed outlier: 3.667A pdb=" N LEU H 857 " --> pdb=" O ARG H 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 854 through 857' Processing helix chain 'H' and resid 858 through 869 removed outlier: 3.718A pdb=" N GLU H 868 " --> pdb=" O ALA H 864 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 869 " --> pdb=" O ARG H 865 " (cutoff:3.500A) Processing helix chain 'H' and resid 873 through 886 removed outlier: 3.744A pdb=" N ALA H 878 " --> pdb=" O ALA H 874 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU H 879 " --> pdb=" O THR H 875 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS H 881 " --> pdb=" O ASN H 877 " (cutoff:3.500A) Processing helix chain 'H' and resid 891 through 897 Processing helix chain 'H' and resid 901 through 909 removed outlier: 3.797A pdb=" N VAL H 905 " --> pdb=" O ASP H 901 " (cutoff:3.500A) Processing helix chain 'H' and resid 913 through 925 removed outlier: 3.703A pdb=" N VAL H 919 " --> pdb=" O HIS H 915 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG H 923 " --> pdb=" O VAL H 919 " (cutoff:3.500A) Processing helix chain 'H' and resid 926 through 935 Processing helix chain 'H' and resid 940 through 948 removed outlier: 3.863A pdb=" N VAL H 948 " --> pdb=" O SER H 944 " (cutoff:3.500A) Processing helix chain 'H' and resid 952 through 960 removed outlier: 3.598A pdb=" N TRP H 956 " --> pdb=" O ASP H 952 " (cutoff:3.500A) Processing helix chain 'H' and resid 966 through 982 removed outlier: 4.038A pdb=" N LEU H 970 " --> pdb=" O TYR H 966 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE H 971 " --> pdb=" O ARG H 967 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN H 976 " --> pdb=" O ASP H 972 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU H 979 " --> pdb=" O VAL H 975 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER H 980 " --> pdb=" O GLN H 976 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU H 981 " --> pdb=" O THR H 977 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR H 982 " --> pdb=" O ALA H 978 " (cutoff:3.500A) Processing helix chain 'H' and resid 984 through 998 removed outlier: 3.890A pdb=" N VAL H 988 " --> pdb=" O ASP H 984 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR H 991 " --> pdb=" O GLU H 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 1005 through 1014 Processing helix chain 'H' and resid 1024 through 1034 removed outlier: 4.580A pdb=" N THR H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) Processing helix chain 'H' and resid 1038 through 1047 removed outlier: 3.630A pdb=" N GLU H1042 " --> pdb=" O THR H1038 " (cutoff:3.500A) Processing helix chain 'H' and resid 1051 through 1062 removed outlier: 4.177A pdb=" N ILE H1055 " --> pdb=" O ASP H1051 " (cutoff:3.500A) Processing helix chain 'H' and resid 1065 through 1075 Processing helix chain 'M' and resid 638 through 643 removed outlier: 4.082A pdb=" N HIS M 642 " --> pdb=" O ARG M 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 647 through 657 removed outlier: 3.722A pdb=" N LEU M 651 " --> pdb=" O ASN M 647 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN M 653 " --> pdb=" O GLU M 649 " (cutoff:3.500A) Processing helix chain 'M' and resid 662 through 673 Processing helix chain 'M' and resid 680 through 685 Processing helix chain 'M' and resid 685 through 690 removed outlier: 4.183A pdb=" N TYR M 689 " --> pdb=" O VAL M 685 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS M 690 " --> pdb=" O ALA M 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 685 through 690' Processing helix chain 'M' and resid 695 through 704 Processing helix chain 'M' and resid 709 through 715 Processing helix chain 'M' and resid 716 through 718 No H-bonds generated for 'chain 'M' and resid 716 through 718' Processing helix chain 'M' and resid 724 through 736 removed outlier: 3.839A pdb=" N HIS M 728 " --> pdb=" O ASP M 724 " (cutoff:3.500A) Processing helix chain 'M' and resid 740 through 743 Processing helix chain 'M' and resid 744 through 751 removed outlier: 3.822A pdb=" N ARG M 749 " --> pdb=" O GLU M 745 " (cutoff:3.500A) Processing helix chain 'M' and resid 755 through 766 removed outlier: 3.613A pdb=" N VAL M 759 " --> pdb=" O ASP M 755 " (cutoff:3.500A) Processing helix chain 'M' and resid 773 through 782 removed outlier: 4.515A pdb=" N ASP M 779 " --> pdb=" O ILE M 775 " (cutoff:3.500A) Processing helix chain 'M' and resid 783 through 795 removed outlier: 4.018A pdb=" N LEU M 787 " --> pdb=" O PHE M 783 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU M 789 " --> pdb=" O HIS M 785 " (cutoff:3.500A) Processing helix chain 'M' and resid 798 through 807 Processing helix chain 'M' and resid 808 through 810 No H-bonds generated for 'chain 'M' and resid 808 through 810' Processing helix chain 'M' and resid 811 through 822 Processing helix chain 'M' and resid 825 through 834 removed outlier: 3.847A pdb=" N LEU M 834 " --> pdb=" O LYS M 830 " (cutoff:3.500A) Processing helix chain 'M' and resid 842 through 853 removed outlier: 3.580A pdb=" N VAL M 846 " --> pdb=" O THR M 842 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA M 847 " --> pdb=" O ASP M 843 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS M 851 " --> pdb=" O ALA M 847 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 857 removed outlier: 3.667A pdb=" N LEU M 857 " --> pdb=" O ARG M 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 854 through 857' Processing helix chain 'M' and resid 858 through 869 removed outlier: 3.718A pdb=" N GLU M 868 " --> pdb=" O ALA M 864 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY M 869 " --> pdb=" O ARG M 865 " (cutoff:3.500A) Processing helix chain 'M' and resid 873 through 886 removed outlier: 3.744A pdb=" N ALA M 878 " --> pdb=" O ALA M 874 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU M 879 " --> pdb=" O THR M 875 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS M 881 " --> pdb=" O ASN M 877 " (cutoff:3.500A) Processing helix chain 'M' and resid 891 through 897 Processing helix chain 'M' and resid 901 through 909 removed outlier: 3.797A pdb=" N VAL M 905 " --> pdb=" O ASP M 901 " (cutoff:3.500A) Processing helix chain 'M' and resid 913 through 925 removed outlier: 3.704A pdb=" N VAL M 919 " --> pdb=" O HIS M 915 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG M 923 " --> pdb=" O VAL M 919 " (cutoff:3.500A) Processing helix chain 'M' and resid 926 through 935 Processing helix chain 'M' and resid 940 through 948 removed outlier: 3.863A pdb=" N VAL M 948 " --> pdb=" O SER M 944 " (cutoff:3.500A) Processing helix chain 'M' and resid 952 through 960 removed outlier: 3.597A pdb=" N TRP M 956 " --> pdb=" O ASP M 952 " (cutoff:3.500A) Processing helix chain 'M' and resid 966 through 982 removed outlier: 4.037A pdb=" N LEU M 970 " --> pdb=" O TYR M 966 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 971 " --> pdb=" O ARG M 967 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN M 976 " --> pdb=" O ASP M 972 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU M 979 " --> pdb=" O VAL M 975 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER M 980 " --> pdb=" O GLN M 976 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU M 981 " --> pdb=" O THR M 977 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR M 982 " --> pdb=" O ALA M 978 " (cutoff:3.500A) Processing helix chain 'M' and resid 984 through 998 removed outlier: 3.890A pdb=" N VAL M 988 " --> pdb=" O ASP M 984 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR M 991 " --> pdb=" O GLU M 987 " (cutoff:3.500A) Processing helix chain 'M' and resid 1005 through 1014 Processing helix chain 'M' and resid 1024 through 1034 removed outlier: 4.580A pdb=" N THR M1031 " --> pdb=" O LEU M1027 " (cutoff:3.500A) Processing helix chain 'M' and resid 1038 through 1047 removed outlier: 3.631A pdb=" N GLU M1042 " --> pdb=" O THR M1038 " (cutoff:3.500A) Processing helix chain 'M' and resid 1051 through 1062 removed outlier: 4.176A pdb=" N ILE M1055 " --> pdb=" O ASP M1051 " (cutoff:3.500A) Processing helix chain 'M' and resid 1065 through 1075 Processing helix chain 'I' and resid 101 through 161 removed outlier: 4.145A pdb=" N LYS I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG I 142 " --> pdb=" O GLU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 205 through 209 removed outlier: 3.576A pdb=" N CYS I 209 " --> pdb=" O SER I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 219 Processing helix chain 'N' and resid 101 through 161 removed outlier: 4.145A pdb=" N LYS N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA N 119 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG N 142 " --> pdb=" O GLU N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 199 Processing helix chain 'N' and resid 205 through 209 removed outlier: 3.576A pdb=" N CYS N 209 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 219 2134 hydrogen bonds defined for protein. 6339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.66 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13447 1.34 - 1.46: 6006 1.46 - 1.57: 21752 1.57 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 41481 Sorted by residual: bond pdb=" N THR C 769 " pdb=" CA THR C 769 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.35e+00 bond pdb=" N THR M 769 " pdb=" CA THR M 769 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.31e+00 bond pdb=" N THR H 769 " pdb=" CA THR H 769 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.24e+00 bond pdb=" N LEU C 768 " pdb=" CA LEU C 768 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.22e+00 bond pdb=" N LEU M 768 " pdb=" CA LEU M 768 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.21e+00 ... (remaining 41476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 54914 2.11 - 4.22: 1014 4.22 - 6.33: 127 6.33 - 8.44: 6 8.44 - 10.54: 3 Bond angle restraints: 56064 Sorted by residual: angle pdb=" C THR H 769 " pdb=" CA THR H 769 " pdb=" CB THR H 769 " ideal model delta sigma weight residual 110.42 120.96 -10.54 1.99e+00 2.53e-01 2.81e+01 angle pdb=" C THR C 769 " pdb=" CA THR C 769 " pdb=" CB THR C 769 " ideal model delta sigma weight residual 110.42 120.95 -10.53 1.99e+00 2.53e-01 2.80e+01 angle pdb=" C THR M 769 " pdb=" CA THR M 769 " pdb=" CB THR M 769 " ideal model delta sigma weight residual 110.42 120.91 -10.49 1.99e+00 2.53e-01 2.78e+01 angle pdb=" C LEU M 772 " pdb=" N PRO M 773 " pdb=" CA PRO M 773 " ideal model delta sigma weight residual 119.84 125.79 -5.95 1.25e+00 6.40e-01 2.27e+01 angle pdb=" C LEU H 772 " pdb=" N PRO H 773 " pdb=" CA PRO H 773 " ideal model delta sigma weight residual 119.84 125.78 -5.94 1.25e+00 6.40e-01 2.26e+01 ... (remaining 56059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22682 17.97 - 35.94: 2152 35.94 - 53.91: 450 53.91 - 71.88: 75 71.88 - 89.85: 45 Dihedral angle restraints: 25404 sinusoidal: 10620 harmonic: 14784 Sorted by residual: dihedral pdb=" C THR H 769 " pdb=" N THR H 769 " pdb=" CA THR H 769 " pdb=" CB THR H 769 " ideal model delta harmonic sigma weight residual -122.00 -136.64 14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C THR C 769 " pdb=" N THR C 769 " pdb=" CA THR C 769 " pdb=" CB THR C 769 " ideal model delta harmonic sigma weight residual -122.00 -136.63 14.63 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C THR M 769 " pdb=" N THR M 769 " pdb=" CA THR M 769 " pdb=" CB THR M 769 " ideal model delta harmonic sigma weight residual -122.00 -136.55 14.55 0 2.50e+00 1.60e-01 3.39e+01 ... (remaining 25401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5882 0.082 - 0.165: 268 0.165 - 0.247: 3 0.247 - 0.330: 0 0.330 - 0.412: 3 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA THR H 769 " pdb=" N THR H 769 " pdb=" C THR H 769 " pdb=" CB THR H 769 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA THR C 769 " pdb=" N THR C 769 " pdb=" C THR C 769 " pdb=" CB THR C 769 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA THR M 769 " pdb=" N THR M 769 " pdb=" C THR M 769 " pdb=" CB THR M 769 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 6153 not shown) Planarity restraints: 7269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 766 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C ALA M 766 " 0.083 2.00e-02 2.50e+03 pdb=" O ALA M 766 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS M 767 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 766 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C ALA C 766 " 0.083 2.00e-02 2.50e+03 pdb=" O ALA C 766 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS C 767 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 766 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C ALA H 766 " -0.083 2.00e-02 2.50e+03 pdb=" O ALA H 766 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS H 767 " 0.027 2.00e-02 2.50e+03 ... (remaining 7266 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 930 2.66 - 3.22: 44462 3.22 - 3.78: 64002 3.78 - 4.34: 88854 4.34 - 4.90: 134509 Nonbonded interactions: 332757 Sorted by model distance: nonbonded pdb=" OH TYR K1574 " pdb=" OE1 GLN K1601 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR A1574 " pdb=" OE1 GLN A1601 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR F1574 " pdb=" OE1 GLN F1601 " model vdw 2.105 3.040 nonbonded pdb=" OG SER H 825 " pdb=" OD1 ASP H 827 " model vdw 2.107 3.040 nonbonded pdb=" OG SER C 825 " pdb=" OD1 ASP C 827 " model vdw 2.107 3.040 ... (remaining 332752 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. 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: 1.180 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.047 41481 Z= 0.215 Angle : 0.748 10.545 56064 Z= 0.427 Chirality : 0.038 0.412 6156 Planarity : 0.004 0.062 7269 Dihedral : 15.129 89.847 15756 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.47 % Favored : 92.40 % Rotamer: Outliers : 0.27 % Allowed : 1.80 % Favored : 97.93 % Cbeta Deviations : 0.06 % 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: -3.74 (0.11), residues: 4911 helix: -2.40 (0.07), residues: 3240 sheet: None (None), residues: 0 loop : -2.28 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 949 TYR 0.016 0.002 TYR K1411 PHE 0.019 0.002 PHE F1594 TRP 0.011 0.002 TRP L1253 HIS 0.006 0.001 HIS C 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (41481) covalent geometry : angle 0.74828 / 0.43 (56064) hydrogen bonds : bond 0.17222 / 11.56 ( 2134) hydrogen bonds : angle 7.14057 / 5.00 ( 6339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1024 time to fit residues: 3.6272 Evaluate side-chains 21 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.120 Evaluate side-chains 48 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1155 LYS cc_start: 0.9439 (mttt) cc_final: 0.8981 (mtmm) REVERT: B 1391 PHE cc_start: 0.8354 (t80) cc_final: 0.7840 (t80) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.0911 time to fit residues: 5.5184 Evaluate side-chains 23 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.188 Evaluate side-chains 37 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 700 GLU cc_start: 0.8364 (tt0) cc_final: 0.7997 (tt0) REVERT: C 765 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6877 (mm-30) REVERT: C 792 TYR cc_start: 0.7493 (t80) cc_final: 0.7259 (t80) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.0940 time to fit residues: 4.1418 Evaluate side-chains 19 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.116 Evaluate side-chains 15 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8200 (mp0) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2100 time to fit residues: 3.2605 Evaluate side-chains 8 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.037 Evaluate side-chains 9 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2315 time to fit residues: 2.1389 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 0.0070 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 3.9990 overall best weight: 1.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1288 ASN A1291 GLN ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN A1456 GLN B1468 ASN C 684 GLN C 973 GLN E 146 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.027363 restraints weight = 28944.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028420 restraints weight = 17978.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029187 restraints weight = 12553.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029745 restraints weight = 9430.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030148 restraints weight = 7489.505| |-----------------------------------------------------------------------------| r_work (final): 0.2708 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.033508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.027335 restraints weight = 62985.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.028131 restraints weight = 43286.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.028727 restraints weight = 32325.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.029181 restraints weight = 25495.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.029516 restraints weight = 20967.346| |-----------------------------------------------------------------------------| r_work (final): 0.2804 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031956 restraints weight = 32879.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032959 restraints weight = 24642.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033747 restraints weight = 19618.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034359 restraints weight = 16212.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034873 restraints weight = 13832.825| |-----------------------------------------------------------------------------| r_work (final): 0.2855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038008 restraints weight = 11366.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038648 restraints weight = 8944.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039035 restraints weight = 7420.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.039478 restraints weight = 6493.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.039707 restraints weight = 5709.355| |-----------------------------------------------------------------------------| r_work (final): 0.3051 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.033600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.025950 restraints weight = 8825.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.026305 restraints weight = 7013.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.026588 restraints weight = 5862.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.026780 restraints weight = 5084.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.026917 restraints weight = 4575.884| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 41481 Z= 0.142 Angle : 0.627 11.897 56064 Z= 0.326 Chirality : 0.040 0.158 6156 Planarity : 0.006 0.165 7269 Dihedral : 4.881 21.910 5445 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.89 % 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: -2.28 (0.11), residues: 4911 helix: -1.19 (0.08), residues: 3450 sheet: None (None), residues: 0 loop : -1.94 (0.18), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 214 TYR 0.015 0.001 TYR K1574 PHE 0.034 0.001 PHE C 995 TRP 0.027 0.001 TRP A1587 HIS 0.004 0.001 HIS L 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (41481) covalent geometry : angle 0.62665 / 0.33 (56064) hydrogen bonds : bond 0.04113 / 2.74 ( 2134) hydrogen bonds : angle 5.22507 / 3.69 ( 6339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: K 1332 MET cc_start: 0.8648 (ttp) cc_final: 0.8259 (tpt) REVERT: K 1424 MET cc_start: 0.9211 (mmm) cc_final: 0.8862 (mmm) REVERT: K 1502 HIS cc_start: 0.8303 (t-90) cc_final: 0.7847 (t70) REVERT: K 1538 MET cc_start: 0.8518 (ttp) cc_final: 0.7856 (tmm) outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.0936 time to fit residues: 3.3321 Evaluate side-chains 19 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.115 Evaluate side-chains 42 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1155 LYS cc_start: 0.9692 (mttt) cc_final: 0.9363 (mtmm) REVERT: L 1159 MET cc_start: 0.9182 (ptt) cc_final: 0.8833 (tmm) REVERT: L 1197 HIS cc_start: 0.8675 (m90) cc_final: 0.8292 (m-70) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0714 time to fit residues: 4.1616 Evaluate side-chains 25 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.200 Evaluate side-chains 33 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: H 651 LEU cc_start: 0.9492 (tt) cc_final: 0.9279 (tt) REVERT: H 655 PHE cc_start: 0.8825 (m-80) cc_final: 0.8344 (m-80) REVERT: H 775 ILE cc_start: 0.9332 (pt) cc_final: 0.9020 (mp) REVERT: H 799 TYR cc_start: 0.8621 (m-10) cc_final: 0.8026 (m-80) REVERT: H 885 ASP cc_start: 0.7934 (m-30) cc_final: 0.7457 (m-30) REVERT: H 899 TYR cc_start: 0.9015 (m-80) cc_final: 0.8656 (m-80) REVERT: H 986 GLU cc_start: 0.9569 (mp0) cc_final: 0.9344 (mp0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0669 time to fit residues: 2.8544 Evaluate side-chains 19 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.143 Evaluate side-chains 14 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 130 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8889 (mp0) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.2027 time to fit residues: 2.9475 Evaluate side-chains 9 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.037 Evaluate side-chains 7 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2257 time to fit residues: 1.6232 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 38 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 481 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1279 HIS ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1456 GLN L1117 GLN L1248 ASN L1468 ASN H 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.034694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.027624 restraints weight = 29278.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.028559 restraints weight = 18397.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029238 restraints weight = 12908.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029729 restraints weight = 9727.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030039 restraints weight = 7756.156| |-----------------------------------------------------------------------------| r_work (final): 0.2687 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.027558 restraints weight = 63558.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.028375 restraints weight = 43728.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.028981 restraints weight = 32730.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029443 restraints weight = 25879.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029811 restraints weight = 21326.628| |-----------------------------------------------------------------------------| r_work (final): 0.2779 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.037867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029432 restraints weight = 35242.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030291 restraints weight = 27010.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030968 restraints weight = 21892.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.031511 restraints weight = 18350.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.031924 restraints weight = 15795.379| |-----------------------------------------------------------------------------| r_work (final): 0.2786 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034333 restraints weight = 11428.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034931 restraints weight = 8968.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035315 restraints weight = 7374.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.035726 restraints weight = 6389.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.035997 restraints weight = 5580.831| |-----------------------------------------------------------------------------| r_work (final): 0.2941 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.032900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.027920 restraints weight = 7513.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.028340 restraints weight = 5596.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.028622 restraints weight = 4459.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.028797 restraints weight = 3760.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.028883 restraints weight = 3355.171| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41481 Z= 0.136 Angle : 0.587 7.544 56064 Z= 0.308 Chirality : 0.040 0.162 6156 Planarity : 0.004 0.048 7269 Dihedral : 4.677 20.127 5445 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -1.72 (0.12), residues: 4911 helix: -0.68 (0.09), residues: 3498 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L1311 TYR 0.025 0.001 TYR K1411 PHE 0.016 0.001 PHE F1594 TRP 0.037 0.001 TRP K1587 HIS 0.004 0.001 HIS L 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (41481) covalent geometry : angle 0.58719 / 0.31 (56064) hydrogen bonds : bond 0.03385 / 2.24 ( 2134) hydrogen bonds : angle 4.92736 / 3.49 ( 6339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1332 MET cc_start: 0.8543 (ttp) cc_final: 0.8186 (tpt) REVERT: K 1378 MET cc_start: 0.8651 (ttp) cc_final: 0.8368 (ttt) REVERT: K 1502 HIS cc_start: 0.8261 (t-90) cc_final: 0.7870 (t70) REVERT: K 1538 MET cc_start: 0.8478 (ttp) cc_final: 0.7892 (tmm) REVERT: K 1609 LYS cc_start: 0.9014 (pttt) cc_final: 0.8744 (ptpp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1031 time to fit residues: 2.9393 Evaluate side-chains 19 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.126 Evaluate side-chains 34 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: B 1015 ASN cc_start: 0.8899 (t0) cc_final: 0.8667 (p0) REVERT: B 1155 LYS cc_start: 0.9629 (mttt) cc_final: 0.9099 (mtmm) REVERT: B 1270 GLN cc_start: 0.9034 (pp30) cc_final: 0.8719 (pm20) REVERT: B 1302 MET cc_start: 0.9175 (ptp) cc_final: 0.8220 (ptp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0691 time to fit residues: 3.3958 Evaluate side-chains 26 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.210 Evaluate side-chains 30 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.143 Fit side-chains REVERT: C 668 ARG cc_start: 0.9217 (ttm110) cc_final: 0.8906 (mtm110) REVERT: C 670 MET cc_start: 0.8524 (mtm) cc_final: 0.8267 (ptp) REVERT: C 700 GLU cc_start: 0.9241 (pp20) cc_final: 0.9008 (pp20) REVERT: C 709 GLU cc_start: 0.4877 (mm-30) cc_final: 0.4307 (mm-30) REVERT: C 775 ILE cc_start: 0.9391 (pt) cc_final: 0.9056 (mp) REVERT: C 899 TYR cc_start: 0.9004 (m-80) cc_final: 0.8625 (m-80) REVERT: C 995 PHE cc_start: 0.8903 (m-10) cc_final: 0.8518 (m-10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0705 time to fit residues: 2.7518 Evaluate side-chains 16 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.135 Evaluate side-chains 12 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9280 (mmp80) cc_final: 0.9019 (mmm160) REVERT: N 130 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9003 (mp0) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1881 time to fit residues: 2.3508 Evaluate side-chains 10 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.035 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1836 time to fit residues: 0.7775 Evaluate side-chains 2 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 253 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 370 optimal weight: 0.3980 chunk 276 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 GLN B1288 ASN B1468 ASN C 684 GLN C 973 GLN ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.027666 restraints weight = 28798.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028664 restraints weight = 18131.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029387 restraints weight = 12828.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029930 restraints weight = 9745.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030332 restraints weight = 7757.179| |-----------------------------------------------------------------------------| r_work (final): 0.2701 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.035012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.028377 restraints weight = 62019.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.029234 restraints weight = 42815.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.029866 restraints weight = 32033.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.030356 restraints weight = 25369.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.030745 restraints weight = 20847.081| |-----------------------------------------------------------------------------| r_work (final): 0.2819 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.029543 restraints weight = 35137.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.030399 restraints weight = 26802.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.031070 restraints weight = 21602.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031619 restraints weight = 18025.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032031 restraints weight = 15512.065| |-----------------------------------------------------------------------------| r_work (final): 0.2794 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033993 restraints weight = 11321.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034680 restraints weight = 8508.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.035201 restraints weight = 6804.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.035530 restraints weight = 5661.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035874 restraints weight = 4935.828| |-----------------------------------------------------------------------------| r_work (final): 0.2954 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.029920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.024888 restraints weight = 8037.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.025335 restraints weight = 5720.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.025706 restraints weight = 4393.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.025969 restraints weight = 3559.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.026154 restraints weight = 3025.603| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 41481 Z= 0.110 Angle : 0.567 8.542 56064 Z= 0.291 Chirality : 0.039 0.160 6156 Planarity : 0.004 0.062 7269 Dihedral : 4.497 19.465 5445 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % 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: -1.25 (0.12), residues: 4911 helix: -0.34 (0.09), residues: 3501 sheet: None (None), residues: 0 loop : -1.81 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 214 TYR 0.020 0.001 TYR K1411 PHE 0.012 0.001 PHE F1391 TRP 0.017 0.001 TRP J 106 HIS 0.004 0.001 HIS F1589 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (41481) covalent geometry : angle 0.56680 / 0.29 (56064) hydrogen bonds : bond 0.03063 / 2.03 ( 2134) hydrogen bonds : angle 4.60522 / 3.28 ( 6339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 1332 MET cc_start: 0.8682 (ttp) cc_final: 0.8291 (tpt) REVERT: K 1378 MET cc_start: 0.8762 (ttp) cc_final: 0.8338 (ttp) REVERT: K 1379 MET cc_start: 0.8842 (mtp) cc_final: 0.8341 (ptm) REVERT: K 1502 HIS cc_start: 0.7984 (t-90) cc_final: 0.7694 (t70) REVERT: K 1538 MET cc_start: 0.8530 (ttp) cc_final: 0.7779 (tmm) REVERT: K 1596 MET cc_start: 0.8085 (ptt) cc_final: 0.7492 (ppp) REVERT: K 1623 GLU cc_start: 0.7191 (pp20) cc_final: 0.6982 (pp20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0870 time to fit residues: 3.0083 Evaluate side-chains 21 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.121 Evaluate side-chains 43 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 1009 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 1015 ASN cc_start: 0.8911 (t0) cc_final: 0.8674 (p0) REVERT: B 1064 LEU cc_start: 0.9109 (mp) cc_final: 0.8866 (mp) REVERT: B 1155 LYS cc_start: 0.9779 (mttt) cc_final: 0.9186 (mtmm) REVERT: B 1270 GLN cc_start: 0.8975 (pp30) cc_final: 0.8329 (pm20) REVERT: B 1302 MET cc_start: 0.9125 (ptp) cc_final: 0.8270 (ptm) REVERT: B 1430 LEU cc_start: 0.8949 (tp) cc_final: 0.8375 (mt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0839 time to fit residues: 4.8212 Evaluate side-chains 28 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.221 Evaluate side-chains 27 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: C 765 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7320 (mm-30) REVERT: C 775 ILE cc_start: 0.9389 (pt) cc_final: 0.9073 (mp) REVERT: C 899 TYR cc_start: 0.8971 (m-80) cc_final: 0.8657 (m-80) REVERT: C 995 PHE cc_start: 0.8773 (m-10) cc_final: 0.8523 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0622 time to fit residues: 2.2255 Evaluate side-chains 16 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.174 Evaluate side-chains 14 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: N 130 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9056 (mp0) REVERT: N 207 LYS cc_start: 0.6182 (mptt) cc_final: 0.5771 (mptt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1701 time to fit residues: 2.4913 Evaluate side-chains 9 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2370 time to fit residues: 0.7535 Evaluate side-chains 2 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 238 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 421 optimal weight: 20.0000 chunk 376 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 356 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 653 ASN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1275 HIS ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1354 GLN ** K1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN N 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.031479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.024590 restraints weight = 31437.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.025474 restraints weight = 19336.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026107 restraints weight = 13464.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026560 restraints weight = 10205.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.026889 restraints weight = 8209.182| |-----------------------------------------------------------------------------| r_work (final): 0.2604 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.025725 restraints weight = 65247.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026489 restraints weight = 44888.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.027059 restraints weight = 33524.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.027483 restraints weight = 26379.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027803 restraints weight = 21712.081| |-----------------------------------------------------------------------------| r_work (final): 0.2738 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.028998 restraints weight = 34892.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029988 restraints weight = 25284.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030746 restraints weight = 19718.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031347 restraints weight = 16136.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031822 restraints weight = 13635.673| |-----------------------------------------------------------------------------| r_work (final): 0.2790 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.032544 restraints weight = 12107.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033212 restraints weight = 9017.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.033707 restraints weight = 7214.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033960 restraints weight = 6017.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034285 restraints weight = 5360.375| |-----------------------------------------------------------------------------| r_work (final): 0.2890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.032210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.027201 restraints weight = 8485.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.027572 restraints weight = 5992.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.027808 restraints weight = 4727.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.027997 restraints weight = 4021.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.028108 restraints weight = 3569.777| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41481 Z= 0.190 Angle : 0.621 12.499 56064 Z= 0.325 Chirality : 0.041 0.218 6156 Planarity : 0.004 0.050 7269 Dihedral : 4.656 23.729 5445 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -0.99 (0.12), residues: 4911 helix: -0.16 (0.09), residues: 3477 sheet: None (None), residues: 0 loop : -1.67 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G1311 TYR 0.016 0.001 TYR K1411 PHE 0.013 0.001 PHE F1594 TRP 0.014 0.001 TRP E 106 HIS 0.006 0.001 HIS H 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (41481) covalent geometry : angle 0.62115 / 0.32 (56064) hydrogen bonds : bond 0.03263 / 2.16 ( 2134) hydrogen bonds : angle 4.75616 / 3.39 ( 6339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1502 HIS cc_start: 0.8341 (t-90) cc_final: 0.7887 (t70) REVERT: A 1592 MET cc_start: 0.9201 (mmp) cc_final: 0.8916 (mmp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0891 time to fit residues: 2.2719 Evaluate side-chains 16 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.126 Evaluate side-chains 37 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1120 MET cc_start: 0.9103 (mtp) cc_final: 0.8750 (mtp) REVERT: L 1151 GLU cc_start: 0.8913 (pm20) cc_final: 0.8562 (pm20) REVERT: L 1155 LYS cc_start: 0.9718 (mttt) cc_final: 0.9350 (mtmm) REVERT: L 1197 HIS cc_start: 0.8751 (m90) cc_final: 0.8481 (m-70) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0625 time to fit residues: 3.3136 Evaluate side-chains 25 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.203 Evaluate side-chains 25 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.130 Fit side-chains REVERT: H 655 PHE cc_start: 0.8963 (m-80) cc_final: 0.8553 (m-80) REVERT: H 775 ILE cc_start: 0.9340 (pt) cc_final: 0.9030 (mp) REVERT: H 799 TYR cc_start: 0.8700 (m-80) cc_final: 0.8152 (m-80) REVERT: H 995 PHE cc_start: 0.9178 (m-10) cc_final: 0.8852 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0419 time to fit residues: 1.5857 Evaluate side-chains 15 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.139 Evaluate side-chains 11 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.038 Fit side-chains REVERT: I 111 ARG cc_start: 0.9290 (mmp80) cc_final: 0.9082 (mmm160) REVERT: I 130 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8815 (mp0) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1239 time to fit residues: 1.4587 Evaluate side-chains 6 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.036 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1588 time to fit residues: 0.5181 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 181 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 460 optimal weight: 0.0270 chunk 238 optimal weight: 9.9990 chunk 461 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 255 optimal weight: 0.5980 chunk 361 optimal weight: 0.7980 chunk 264 optimal weight: 6.9990 chunk 419 optimal weight: 0.5980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 935 ASN L1248 ASN ** L1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 ASN I 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.027556 restraints weight = 28985.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028529 restraints weight = 18268.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.029233 restraints weight = 12855.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.029744 restraints weight = 9716.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030115 restraints weight = 7757.320| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027008 restraints weight = 63655.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027814 restraints weight = 44404.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028407 restraints weight = 33084.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.028863 restraints weight = 26062.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029210 restraints weight = 21375.146| |-----------------------------------------------------------------------------| r_work (final): 0.2791 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.037093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.028635 restraints weight = 34799.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029516 restraints weight = 26266.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.030225 restraints weight = 21037.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.030751 restraints weight = 17521.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.031199 restraints weight = 15098.682| |-----------------------------------------------------------------------------| r_work (final): 0.2788 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033391 restraints weight = 11919.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034038 restraints weight = 9007.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034539 restraints weight = 7218.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034938 restraints weight = 6058.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.035253 restraints weight = 5238.671| |-----------------------------------------------------------------------------| r_work (final): 0.2929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.030230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.025142 restraints weight = 8232.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.025593 restraints weight = 5829.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.025978 restraints weight = 4508.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.026230 restraints weight = 3666.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.026425 restraints weight = 3137.481| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 41481 Z= 0.112 Angle : 0.582 8.495 56064 Z= 0.297 Chirality : 0.040 0.215 6156 Planarity : 0.003 0.044 7269 Dihedral : 4.513 20.425 5445 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.85 (0.12), residues: 4911 helix: -0.06 (0.09), residues: 3498 sheet: None (None), residues: 0 loop : -1.61 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1311 TYR 0.025 0.001 TYR K1411 PHE 0.018 0.001 PHE K1391 TRP 0.019 0.001 TRP E 106 HIS 0.003 0.001 HIS L1381 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (41481) covalent geometry : angle 0.58240 / 0.30 (56064) hydrogen bonds : bond 0.02979 / 1.96 ( 2134) hydrogen bonds : angle 4.49989 / 3.20 ( 6339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: K 1302 MET cc_start: 0.8099 (mpp) cc_final: 0.7795 (mpp) REVERT: K 1502 HIS cc_start: 0.7867 (t-90) cc_final: 0.7654 (t70) REVERT: K 1538 MET cc_start: 0.8403 (ttp) cc_final: 0.7886 (tmm) REVERT: K 1623 GLU cc_start: 0.7232 (pp20) cc_final: 0.6971 (pp20) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0737 time to fit residues: 2.3318 Evaluate side-chains 19 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.119 Evaluate side-chains 36 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: L 889 ASN cc_start: 0.8074 (p0) cc_final: 0.7822 (p0) REVERT: L 1120 MET cc_start: 0.9189 (mtp) cc_final: 0.8908 (mtp) REVERT: L 1151 GLU cc_start: 0.9051 (pm20) cc_final: 0.8776 (pm20) REVERT: L 1155 LYS cc_start: 0.9715 (mttt) cc_final: 0.9262 (mtmm) REVERT: L 1197 HIS cc_start: 0.8680 (m90) cc_final: 0.8293 (m-70) REVERT: L 1271 MET cc_start: 0.8623 (ptp) cc_final: 0.8415 (ptm) REVERT: L 1430 LEU cc_start: 0.8900 (tp) cc_final: 0.8457 (mt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0787 time to fit residues: 3.8677 Evaluate side-chains 27 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.218 Evaluate side-chains 26 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 700 GLU cc_start: 0.9260 (pp20) cc_final: 0.8991 (pp20) REVERT: C 775 ILE cc_start: 0.9435 (pt) cc_final: 0.9042 (mp) REVERT: C 790 TYR cc_start: 0.9218 (t80) cc_final: 0.8771 (t80) REVERT: C 792 TYR cc_start: 0.9329 (t80) cc_final: 0.9122 (t80) REVERT: C 883 TYR cc_start: 0.9156 (m-10) cc_final: 0.8947 (t80) REVERT: C 995 PHE cc_start: 0.8811 (m-10) cc_final: 0.8527 (m-80) REVERT: C 1048 ASP cc_start: 0.9216 (p0) cc_final: 0.9009 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0557 time to fit residues: 2.0072 Evaluate side-chains 18 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.144 Evaluate side-chains 15 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9359 (mmp80) cc_final: 0.9050 (mmm160) REVERT: N 130 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8993 (mp0) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1537 time to fit residues: 2.4113 Evaluate side-chains 8 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.048 Evaluate side-chains 2 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2049 time to fit residues: 0.4489 Evaluate side-chains 2 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 223 optimal weight: 0.9990 chunk 391 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 376 optimal weight: 0.0980 chunk 313 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 340 optimal weight: 0.0370 overall best weight: 0.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 653 ASN C 808 ASN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.035303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.027911 restraints weight = 29294.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028871 restraints weight = 18694.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029582 restraints weight = 13303.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030105 restraints weight = 10094.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030503 restraints weight = 8075.777| |-----------------------------------------------------------------------------| r_work (final): 0.2701 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.033763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027589 restraints weight = 63444.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028396 restraints weight = 43727.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.029000 restraints weight = 32702.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.029472 restraints weight = 25782.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.029821 restraints weight = 21170.043| |-----------------------------------------------------------------------------| r_work (final): 0.2797 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.038096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029509 restraints weight = 35212.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030415 restraints weight = 26832.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031111 restraints weight = 21498.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.031665 restraints weight = 17998.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032059 restraints weight = 15461.702| |-----------------------------------------------------------------------------| r_work (final): 0.2805 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.038942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033503 restraints weight = 11551.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034089 restraints weight = 8822.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034561 restraints weight = 7164.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.034916 restraints weight = 6083.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035135 restraints weight = 5283.058| |-----------------------------------------------------------------------------| r_work (final): 0.2932 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.030252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.023845 restraints weight = 9661.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.024304 restraints weight = 6887.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.024692 restraints weight = 5339.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.024981 restraints weight = 4341.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.025157 restraints weight = 3704.698| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 41481 Z= 0.107 Angle : 0.574 7.942 56064 Z= 0.291 Chirality : 0.040 0.173 6156 Planarity : 0.003 0.046 7269 Dihedral : 4.398 17.746 5445 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -0.71 (0.12), residues: 4911 helix: 0.05 (0.09), residues: 3480 sheet: None (None), residues: 0 loop : -1.57 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 214 TYR 0.018 0.001 TYR F1411 PHE 0.014 0.001 PHE G1391 TRP 0.018 0.001 TRP O 106 HIS 0.003 0.001 HIS H 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (41481) covalent geometry : angle 0.57357 / 0.29 (56064) hydrogen bonds : bond 0.02866 / 1.89 ( 2134) hydrogen bonds : angle 4.40171 / 3.12 ( 6339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: K 1378 MET cc_start: 0.9182 (ttm) cc_final: 0.8801 (tpp) REVERT: K 1538 MET cc_start: 0.8347 (ttp) cc_final: 0.7683 (tmm) REVERT: K 1596 MET cc_start: 0.8319 (ppp) cc_final: 0.8034 (ppp) REVERT: K 1623 GLU cc_start: 0.7271 (pp20) cc_final: 0.7032 (pp20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0699 time to fit residues: 2.3472 Evaluate side-chains 19 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.100 Evaluate side-chains 36 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: L 1120 MET cc_start: 0.9161 (mtp) cc_final: 0.8895 (mtp) REVERT: L 1151 GLU cc_start: 0.9035 (pm20) cc_final: 0.8798 (pm20) REVERT: L 1155 LYS cc_start: 0.9710 (mttt) cc_final: 0.9254 (mtmm) REVERT: L 1197 HIS cc_start: 0.8637 (m90) cc_final: 0.8301 (m-70) REVERT: L 1271 MET cc_start: 0.8653 (ptp) cc_final: 0.8385 (ptm) REVERT: L 1302 MET cc_start: 0.9274 (ptm) cc_final: 0.9050 (ptp) REVERT: L 1332 MET cc_start: 0.8772 (mmm) cc_final: 0.8127 (mmm) REVERT: L 1430 LEU cc_start: 0.8854 (tp) cc_final: 0.8400 (mt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0579 time to fit residues: 3.0191 Evaluate side-chains 25 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.192 Evaluate side-chains 25 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.135 Fit side-chains REVERT: C 775 ILE cc_start: 0.9367 (pt) cc_final: 0.9019 (mp) REVERT: C 790 TYR cc_start: 0.9208 (t80) cc_final: 0.8825 (t80) REVERT: C 792 TYR cc_start: 0.9323 (t80) cc_final: 0.9109 (t80) REVERT: C 879 LEU cc_start: 0.9305 (tp) cc_final: 0.8900 (tp) REVERT: C 883 TYR cc_start: 0.9157 (m-10) cc_final: 0.8822 (t80) REVERT: C 995 PHE cc_start: 0.8763 (m-10) cc_final: 0.8528 (m-80) REVERT: C 1048 ASP cc_start: 0.9219 (p0) cc_final: 0.9003 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0549 time to fit residues: 1.8998 Evaluate side-chains 14 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.161 Evaluate side-chains 12 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9380 (mmp80) cc_final: 0.9111 (mmm160) REVERT: N 130 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8968 (mp0) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1465 time to fit residues: 1.8520 Evaluate side-chains 7 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.037 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1223 time to fit residues: 0.5310 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 300 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 234 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 251 optimal weight: 0.0370 chunk 195 optimal weight: 0.6980 chunk 422 optimal weight: 0.9980 chunk 318 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 347 optimal weight: 0.2980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 146 GLN ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.033638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.026555 restraints weight = 29684.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027431 restraints weight = 19077.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028070 restraints weight = 13650.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.028535 restraints weight = 10460.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028891 restraints weight = 8446.860| |-----------------------------------------------------------------------------| r_work (final): 0.2678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.034358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.028308 restraints weight = 61229.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029041 restraints weight = 43658.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.029597 restraints weight = 33343.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.030016 restraints weight = 26807.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.030360 restraints weight = 22413.814| |-----------------------------------------------------------------------------| r_work (final): 0.2832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.036570 restraints weight = 31020.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037622 restraints weight = 22958.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.038447 restraints weight = 18279.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.039099 restraints weight = 15191.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039606 restraints weight = 13017.527| |-----------------------------------------------------------------------------| r_work (final): 0.2847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.039525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034074 restraints weight = 11746.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034683 restraints weight = 8967.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035112 restraints weight = 7244.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035518 restraints weight = 6161.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035822 restraints weight = 5311.482| |-----------------------------------------------------------------------------| r_work (final): 0.2960 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.029928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.024621 restraints weight = 8366.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.025087 restraints weight = 5954.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.025401 restraints weight = 4651.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.025704 restraints weight = 3920.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.025915 restraints weight = 3355.417| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 41481 Z= 0.105 Angle : 0.571 8.205 56064 Z= 0.292 Chirality : 0.040 0.164 6156 Planarity : 0.003 0.045 7269 Dihedral : 4.305 17.105 5445 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -0.69 (0.12), residues: 4911 helix: 0.09 (0.09), residues: 3468 sheet: None (None), residues: 0 loop : -1.60 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1311 TYR 0.017 0.001 TYR F1411 PHE 0.012 0.001 PHE M 708 TRP 0.018 0.001 TRP G 956 HIS 0.003 0.001 HIS A1335 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (41481) covalent geometry : angle 0.57144 / 0.29 (56064) hydrogen bonds : bond 0.02792 / 1.84 ( 2134) hydrogen bonds : angle 4.29989 / 3.06 ( 6339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 1502 HIS cc_start: 0.8068 (t70) cc_final: 0.7606 (t-90) REVERT: A 1538 MET cc_start: 0.8908 (ttp) cc_final: 0.7892 (tmm) REVERT: A 1592 MET cc_start: 0.9000 (mmp) cc_final: 0.8734 (mmp) REVERT: A 1605 GLU cc_start: 0.8819 (tt0) cc_final: 0.8593 (pt0) REVERT: A 1623 GLU cc_start: 0.7530 (pp20) cc_final: 0.7277 (pp20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0609 time to fit residues: 2.0724 Evaluate side-chains 21 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.072 Evaluate side-chains 37 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: L 819 LEU cc_start: 0.8901 (tt) cc_final: 0.8691 (pp) REVERT: L 889 ASN cc_start: 0.8879 (p0) cc_final: 0.8616 (p0) REVERT: L 1041 MET cc_start: 0.9627 (mmp) cc_final: 0.9403 (mmp) REVERT: L 1120 MET cc_start: 0.9127 (mtp) cc_final: 0.8840 (mtp) REVERT: L 1151 GLU cc_start: 0.8937 (pm20) cc_final: 0.8735 (pm20) REVERT: L 1155 LYS cc_start: 0.9704 (mttt) cc_final: 0.9241 (mtmm) REVERT: L 1197 HIS cc_start: 0.8671 (m90) cc_final: 0.8380 (m-70) REVERT: L 1302 MET cc_start: 0.9246 (ptm) cc_final: 0.9016 (ptp) REVERT: L 1332 MET cc_start: 0.8832 (mmm) cc_final: 0.8551 (mmm) REVERT: L 1430 LEU cc_start: 0.8839 (tp) cc_final: 0.8374 (mt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0607 time to fit residues: 3.1880 Evaluate side-chains 30 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.209 Evaluate side-chains 29 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: H 700 GLU cc_start: 0.9261 (pp20) cc_final: 0.9051 (pp20) REVERT: H 790 TYR cc_start: 0.9303 (t80) cc_final: 0.9053 (t80) REVERT: H 799 TYR cc_start: 0.8793 (m-80) cc_final: 0.8400 (m-80) REVERT: H 883 TYR cc_start: 0.9217 (m-10) cc_final: 0.8951 (t80) REVERT: H 995 PHE cc_start: 0.9122 (m-10) cc_final: 0.8714 (m-10) REVERT: H 1048 ASP cc_start: 0.9094 (p0) cc_final: 0.8864 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0439 time to fit residues: 1.8424 Evaluate side-chains 17 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.134 Evaluate side-chains 11 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9412 (mmp80) cc_final: 0.9150 (mmm160) REVERT: N 130 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8988 (mp0) REVERT: N 207 LYS cc_start: 0.6273 (mptt) cc_final: 0.5817 (mptt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.2001 time to fit residues: 2.2944 Evaluate side-chains 8 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.035 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1270 time to fit residues: 0.5503 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 77 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 337 optimal weight: 0.6980 chunk 222 optimal weight: 0.0040 chunk 435 optimal weight: 0.3980 chunk 406 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.034278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.027161 restraints weight = 30476.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028039 restraints weight = 19650.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.028689 restraints weight = 14108.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.029168 restraints weight = 10841.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029514 restraints weight = 8766.893| |-----------------------------------------------------------------------------| r_work (final): 0.2720 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.035708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029147 restraints weight = 59060.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.029960 restraints weight = 41750.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.030595 restraints weight = 31957.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.031079 restraints weight = 25446.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031461 restraints weight = 21054.381| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.031926 restraints weight = 32397.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.032931 restraints weight = 23594.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033703 restraints weight = 18490.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034327 restraints weight = 15205.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034833 restraints weight = 12883.115| |-----------------------------------------------------------------------------| r_work (final): 0.2932 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.036820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031631 restraints weight = 11851.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032319 restraints weight = 8588.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.032836 restraints weight = 6638.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033245 restraints weight = 5408.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.033544 restraints weight = 4564.692| |-----------------------------------------------------------------------------| r_work (final): 0.2915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.030522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.025200 restraints weight = 7949.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.025617 restraints weight = 5672.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.025981 restraints weight = 4398.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.026255 restraints weight = 3619.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.026435 restraints weight = 3113.285| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 41481 Z= 0.110 Angle : 0.588 8.100 56064 Z= 0.300 Chirality : 0.040 0.208 6156 Planarity : 0.003 0.044 7269 Dihedral : 4.326 17.251 5445 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -0.69 (0.12), residues: 4911 helix: 0.10 (0.09), residues: 3468 sheet: None (None), residues: 0 loop : -1.63 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1406 TYR 0.028 0.001 TYR F1411 PHE 0.021 0.001 PHE G1391 TRP 0.016 0.001 TRP E 106 HIS 0.003 0.001 HIS K1589 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (41481) covalent geometry : angle 0.58785 / 0.30 (56064) hydrogen bonds : bond 0.02830 / 1.85 ( 2134) hydrogen bonds : angle 4.32615 / 3.05 ( 6339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 1502 HIS cc_start: 0.7983 (t70) cc_final: 0.7429 (t70) REVERT: A 1538 MET cc_start: 0.8859 (ttp) cc_final: 0.7888 (tmm) REVERT: A 1592 MET cc_start: 0.8696 (mmp) cc_final: 0.8308 (mmp) REVERT: A 1596 MET cc_start: 0.7682 (ptt) cc_final: 0.7246 (ppp) REVERT: A 1605 GLU cc_start: 0.8714 (tt0) cc_final: 0.8477 (pt0) REVERT: A 1623 GLU cc_start: 0.7531 (pp20) cc_final: 0.7261 (pp20) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0763 time to fit residues: 2.4108 Evaluate side-chains 18 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.123 Evaluate side-chains 39 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1064 LEU cc_start: 0.9006 (mt) cc_final: 0.8727 (mp) REVERT: B 1155 LYS cc_start: 0.9681 (mttt) cc_final: 0.9150 (mtmm) REVERT: B 1302 MET cc_start: 0.9174 (ptm) cc_final: 0.8673 (ptp) REVERT: B 1332 MET cc_start: 0.8515 (mmm) cc_final: 0.7869 (mmm) REVERT: B 1430 LEU cc_start: 0.8658 (tp) cc_final: 0.8118 (mt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0740 time to fit residues: 3.9577 Evaluate side-chains 27 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.173 Evaluate side-chains 27 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: H 649 GLU cc_start: 0.9583 (tp30) cc_final: 0.9376 (mm-30) REVERT: H 700 GLU cc_start: 0.9230 (pp20) cc_final: 0.8951 (pp20) REVERT: H 790 TYR cc_start: 0.9244 (t80) cc_final: 0.9000 (t80) REVERT: H 799 TYR cc_start: 0.8764 (m-80) cc_final: 0.7371 (m-80) REVERT: H 995 PHE cc_start: 0.9048 (m-10) cc_final: 0.8648 (m-10) REVERT: H 1048 ASP cc_start: 0.9096 (p0) cc_final: 0.8867 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0610 time to fit residues: 2.2219 Evaluate side-chains 18 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.143 Evaluate side-chains 12 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: D 130 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8944 (mp0) REVERT: D 204 LYS cc_start: 0.8410 (mttm) cc_final: 0.8041 (mmtm) REVERT: D 211 ASP cc_start: 0.8602 (t0) cc_final: 0.7600 (m-30) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1914 time to fit residues: 2.3890 Evaluate side-chains 8 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.024 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.1748 time to fit residues: 0.5698 Evaluate side-chains 3 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 281 optimal weight: 0.3980 chunk 238 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 194 optimal weight: 3.9990 chunk 406 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 129 optimal weight: 0.0980 chunk 237 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 GLN B1279 HIS ** B1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 795 ASN H1049 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027256 restraints weight = 30124.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028114 restraints weight = 19767.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.028759 restraints weight = 14338.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029234 restraints weight = 11103.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.029586 restraints weight = 9019.488| |-----------------------------------------------------------------------------| r_work (final): 0.2724 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.035887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029265 restraints weight = 59721.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.030068 restraints weight = 42412.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.030705 restraints weight = 32668.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031184 restraints weight = 26125.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031573 restraints weight = 21751.165| |-----------------------------------------------------------------------------| r_work (final): 0.2852 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.040863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031745 restraints weight = 32557.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032769 restraints weight = 23899.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033573 restraints weight = 18698.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034201 restraints weight = 15289.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.034706 restraints weight = 12922.098| |-----------------------------------------------------------------------------| r_work (final): 0.2934 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.039185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.033723 restraints weight = 12220.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034328 restraints weight = 9198.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.034783 restraints weight = 7450.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.035134 restraints weight = 6275.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.035423 restraints weight = 5515.869| |-----------------------------------------------------------------------------| r_work (final): 0.2947 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.030441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.025156 restraints weight = 7603.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.025565 restraints weight = 5439.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.025916 restraints weight = 4260.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.026198 restraints weight = 3541.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.026289 restraints weight = 3043.995| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 41481 Z= 0.107 Angle : 0.584 7.804 56064 Z= 0.298 Chirality : 0.040 0.209 6156 Planarity : 0.003 0.052 7269 Dihedral : 4.267 18.704 5445 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.65 (0.12), residues: 4911 helix: 0.13 (0.09), residues: 3459 sheet: None (None), residues: 0 loop : -1.63 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G1406 TYR 0.030 0.001 TYR F1411 PHE 0.013 0.001 PHE G1391 TRP 0.015 0.001 TRP E 106 HIS 0.003 0.001 HIS F1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (41481) covalent geometry : angle 0.58407 / 0.30 (56064) hydrogen bonds : bond 0.02740 / 1.80 ( 2134) hydrogen bonds : angle 4.29751 / 3.04 ( 6339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 1332 MET cc_start: 0.8760 (mmm) cc_final: 0.8471 (mmm) REVERT: A 1538 MET cc_start: 0.8828 (ttp) cc_final: 0.7868 (tmm) REVERT: A 1592 MET cc_start: 0.8716 (mmp) cc_final: 0.8284 (mmp) REVERT: A 1605 GLU cc_start: 0.8731 (tt0) cc_final: 0.8467 (pt0) REVERT: A 1623 GLU cc_start: 0.7538 (pp20) cc_final: 0.7264 (pp20) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0730 time to fit residues: 2.0850 Evaluate side-chains 18 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.079 Evaluate side-chains 34 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1155 LYS cc_start: 0.9800 (mttt) cc_final: 0.9328 (mtmm) REVERT: B 1430 LEU cc_start: 0.8667 (tp) cc_final: 0.8319 (mt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0791 time to fit residues: 3.6669 Evaluate side-chains 25 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.151 Evaluate side-chains 27 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: H 649 GLU cc_start: 0.9581 (tp30) cc_final: 0.9377 (mm-30) REVERT: H 700 GLU cc_start: 0.9194 (pp20) cc_final: 0.8712 (pp20) REVERT: H 790 TYR cc_start: 0.9270 (t80) cc_final: 0.9023 (t80) REVERT: H 799 TYR cc_start: 0.7928 (m-80) cc_final: 0.7438 (m-80) REVERT: H 995 PHE cc_start: 0.9062 (m-10) cc_final: 0.8619 (m-10) REVERT: H 1048 ASP cc_start: 0.9210 (p0) cc_final: 0.9007 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0594 time to fit residues: 2.1694 Evaluate side-chains 19 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.139 Evaluate side-chains 10 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9296 (mmp80) cc_final: 0.9072 (mmm160) REVERT: N 130 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9062 (mp0) REVERT: N 207 LYS cc_start: 0.5705 (mppt) cc_final: 0.5322 (mptt) REVERT: N 211 ASP cc_start: 0.8892 (t0) cc_final: 0.8351 (m-30) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1728 time to fit residues: 1.8191 Evaluate side-chains 9 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.036 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1185 time to fit residues: 0.5079 Evaluate side-chains 4 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 13 optimal weight: 0.0170 chunk 465 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 281 optimal weight: 0.1980 chunk 17 optimal weight: 0.0370 chunk 86 optimal weight: 0.0170 chunk 47 optimal weight: 0.3980 chunk 173 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.0632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027725 restraints weight = 30114.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.028585 restraints weight = 19983.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029220 restraints weight = 14520.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.029667 restraints weight = 11269.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.030036 restraints weight = 9239.251| |-----------------------------------------------------------------------------| r_work (final): 0.2715 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029060 restraints weight = 60717.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.029798 restraints weight = 43613.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030351 restraints weight = 33543.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030773 restraints weight = 27057.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031121 restraints weight = 22780.722| |-----------------------------------------------------------------------------| r_work (final): 0.2861 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.032886 restraints weight = 33035.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033890 restraints weight = 24579.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034663 restraints weight = 19602.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.035310 restraints weight = 16260.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035813 restraints weight = 13776.515| |-----------------------------------------------------------------------------| r_work (final): 0.2959 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.039820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034356 restraints weight = 12252.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034912 restraints weight = 9430.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035382 restraints weight = 7725.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.035663 restraints weight = 6565.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035983 restraints weight = 5839.412| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.030301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.024826 restraints weight = 7942.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.025243 restraints weight = 5771.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.025580 restraints weight = 4534.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.025853 restraints weight = 3800.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.026060 restraints weight = 3285.167| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41481 Z= 0.110 Angle : 0.587 9.937 56064 Z= 0.297 Chirality : 0.040 0.198 6156 Planarity : 0.003 0.046 7269 Dihedral : 4.194 18.436 5445 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.50 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.12), residues: 4911 helix: 0.23 (0.09), residues: 3450 sheet: None (None), residues: 0 loop : -1.58 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.027 0.001 TYR K1411 PHE 0.010 0.001 PHE C 708 TRP 0.015 0.001 TRP G 956 HIS 0.003 0.001 HIS K1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (41481) covalent geometry : angle 0.58682 / 0.30 (56064) hydrogen bonds : bond 0.02874 / 1.90 ( 2134) hydrogen bonds : angle 4.23371 / 2.99 ( 6339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.63 seconds wall clock time: 56 minutes 32.10 seconds (3392.10 seconds total)