Starting phenix.real_space_refine on Tue Aug 26 20:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sct_0126/08_2025/6sct_0126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sct_0126/08_2025/6sct_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_0126/08_2025/6sct_0126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sct_0126/08_2025/6sct_0126.map" model { file = "/net/cci-nas-00/data/ceres_data/6sct_0126/08_2025/6sct_0126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sct_0126/08_2025/6sct_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 8.84, per 1000 atoms: 0.22 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: 2.67 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.28 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: 8.35 Time building geometry restraints manager: 3.66 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: 0.010 Normalize map: mean=0, sd=1: 1.260 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 aren 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 covalent geometry : bond 0.00441 (41481) covalent geometry : angle 0.74828 (56064) hydrogen bonds : bond 0.17222 ( 2134) hydrogen bonds : angle 7.14057 ( 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 : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1163 time to fit residues: 4.0703 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 : 0.127 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 : 0.221 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: 0.1027 time to fit residues: 6.1747 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 : 0.218 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 : 0.144 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: 0.1107 time to fit residues: 4.8432 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 : 0.183 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 : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 130 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8200 (mp0) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.2465 time to fit residues: 3.8138 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 : 0.040 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 : 0.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.2699 time to fit residues: 2.4884 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 : 0.026 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** F1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 ASN F1456 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1248 ASN L1468 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 684 GLN H 690 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027294 restraints weight = 29471.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028217 restraints weight = 18445.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.028882 restraints weight = 12842.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.029363 restraints weight = 9614.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029707 restraints weight = 7607.930| |-----------------------------------------------------------------------------| r_work (final): 0.2696 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.033507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.027329 restraints weight = 62969.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.028120 restraints weight = 43321.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028719 restraints weight = 32382.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.029171 restraints weight = 25522.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029531 restraints weight = 20993.264| |-----------------------------------------------------------------------------| r_work (final): 0.2804 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031950 restraints weight = 32901.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032959 restraints weight = 24757.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033754 restraints weight = 19668.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034368 restraints weight = 16233.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034891 restraints weight = 13838.049| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-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 = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038008 restraints weight = 11366.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038623 restraints weight = 8943.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039078 restraints weight = 7484.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.039472 restraints weight = 6488.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.039763 restraints weight = 5703.647| |-----------------------------------------------------------------------------| 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 = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.025949 restraints weight = 8825.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.026294 restraints weight = 7011.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.026583 restraints weight = 5885.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.026779 restraints weight = 5097.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.026916 restraints weight = 4582.502| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2169 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 : 6.73 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 aren 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 H 995 TRP 0.027 0.001 TRP A1587 HIS 0.004 0.001 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00298 (41481) covalent geometry : angle 0.62665 (56064) hydrogen bonds : bond 0.04113 ( 2134) hydrogen bonds : angle 5.22507 ( 6339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8938 Ramachandran restraints generated. 4469 Oldfield, 0 Emsley, 4469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 1332 MET cc_start: 0.8642 (ttp) cc_final: 0.8434 (tpt) REVERT: F 1502 HIS cc_start: 0.8391 (t-90) cc_final: 0.8097 (t70) outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.0856 time to fit residues: 3.2255 Evaluate side-chains 17 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.094 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 : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1155 LYS cc_start: 0.9692 (mttt) cc_final: 0.9362 (mtmm) REVERT: L 1159 MET cc_start: 0.9181 (ptt) cc_final: 0.8832 (tmm) REVERT: L 1197 HIS cc_start: 0.8677 (m90) cc_final: 0.8293 (m-70) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0697 time to fit residues: 4.0877 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 : 0.211 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 : 0.143 Fit side-chains revert: symmetry clash REVERT: H 651 LEU cc_start: 0.9485 (tt) cc_final: 0.9260 (tt) REVERT: H 655 PHE cc_start: 0.8807 (m-80) cc_final: 0.8325 (m-80) REVERT: H 775 ILE cc_start: 0.9336 (pt) cc_final: 0.9017 (mp) REVERT: H 799 TYR cc_start: 0.8586 (m-10) cc_final: 0.8000 (m-80) REVERT: H 885 ASP cc_start: 0.7949 (m-30) cc_final: 0.7467 (m-30) REVERT: H 899 TYR cc_start: 0.8987 (m-80) cc_final: 0.8619 (m-80) REVERT: H 986 GLU cc_start: 0.9560 (mp0) cc_final: 0.9329 (mp0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0629 time to fit residues: 2.7135 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 : 0.164 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 : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 130 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8895 (mp0) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.2054 time to fit residues: 2.9886 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 : 0.040 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: 0.2720 time to fit residues: 1.9567 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 : 0.025 ------------------------------------------------------------------------------- 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: 0.0060 chunk 364 optimal weight: 0.0870 chunk 331 optimal weight: 30.0000 chunk 407 optimal weight: 0.0770 chunk 286 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 481 optimal weight: 9.9990 chunk 294 optimal weight: 0.0770 chunk 110 optimal weight: 0.0070 chunk 204 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 overall best weight: 0.0508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1275 HIS K1288 ASN K1291 GLN ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 839 GLN B 935 ASN B1191 ASN B1288 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 HIS C 808 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029083 restraints weight = 28384.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030056 restraints weight = 17849.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.030779 restraints weight = 12523.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.031278 restraints weight = 9459.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031654 restraints weight = 7560.000| |-----------------------------------------------------------------------------| r_work (final): 0.2773 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.035176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.028484 restraints weight = 61983.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029345 restraints weight = 42787.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029974 restraints weight = 32069.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.030462 restraints weight = 25417.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.030844 restraints weight = 20938.806| |-----------------------------------------------------------------------------| r_work (final): 0.2820 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030368 restraints weight = 34562.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.031188 restraints weight = 26665.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.031902 restraints weight = 21898.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.032467 restraints weight = 18370.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032918 restraints weight = 15830.846| |-----------------------------------------------------------------------------| r_work (final): 0.2817 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.040659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035208 restraints weight = 11757.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035729 restraints weight = 9096.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036257 restraints weight = 7545.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036621 restraints weight = 6333.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.036898 restraints weight = 5493.351| |-----------------------------------------------------------------------------| r_work (final): 0.2958 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.034091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.028117 restraints weight = 7872.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.028733 restraints weight = 5552.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.029159 restraints weight = 4232.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.029472 restraints weight = 3437.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.029631 restraints weight = 2925.741| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 41481 Z= 0.190 Angle : 0.853 23.510 56064 Z= 0.437 Chirality : 0.048 0.482 6156 Planarity : 0.009 0.133 7269 Dihedral : 5.200 20.744 5445 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.71 % Rotamer: Outliers : 0.47 % Allowed : 2.63 % Favored : 96.90 % 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 aren not related in a simple way. whole: -2.58 (0.11), residues: 4911 helix: -1.43 (0.08), residues: 3426 sheet: None (None), residues: 0 loop : -2.00 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG B 945 TYR 0.076 0.005 TYR K1574 PHE 0.044 0.003 PHE A1339 TRP 0.080 0.004 TRP F1358 HIS 0.014 0.002 HIS K1432 Details of bonding type rmsd covalent geometry : bond 0.00414 (41481) covalent geometry : angle 0.85329 (56064) hydrogen bonds : bond 0.04337 ( 2134) hydrogen bonds : angle 5.46040 ( 6339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5666 Ramachandran restraints generated. 2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5666 Ramachandran restraints generated. 2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: K 1314 MET cc_start: 0.9318 (tmm) cc_final: 0.9039 (tmm) REVERT: K 1332 MET cc_start: 0.8834 (ttp) cc_final: 0.8482 (tpt) REVERT: K 1502 HIS cc_start: 0.8143 (t-90) cc_final: 0.7688 (t-90) REVERT: K 1538 MET cc_start: 0.8569 (ttp) cc_final: 0.7629 (tmm) outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 0.1015 time to fit residues: 3.6074 Evaluate side-chains 17 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.125 Evaluate side-chains 39 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 1155 LYS cc_start: 0.9582 (mttt) cc_final: 0.9285 (mtmm) REVERT: B 1159 MET cc_start: 0.8952 (ptt) cc_final: 0.8729 (tmm) REVERT: B 1302 MET cc_start: 0.9225 (ptp) cc_final: 0.8694 (ptm) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0707 time to fit residues: 3.9458 Evaluate side-chains 24 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.216 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 : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 670 MET cc_start: 0.8594 (mtm) cc_final: 0.8303 (ptp) REVERT: C 765 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6952 (mm-30) REVERT: C 986 GLU cc_start: 0.9521 (mp0) cc_final: 0.9235 (mp0) REVERT: C 995 PHE cc_start: 0.8886 (m-10) cc_final: 0.8508 (m-10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0703 time to fit residues: 2.6093 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 : 0.090 Evaluate side-chains 13 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9212 (mmp80) cc_final: 0.8956 (mmm160) REVERT: N 130 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8645 (mp0) REVERT: N 207 LYS cc_start: 0.6405 (mptt) cc_final: 0.6028 (mptt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1679 time to fit residues: 2.2760 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 : 0.045 Evaluate side-chains 5 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2305 time to fit residues: 1.2025 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 253 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 393 optimal weight: 40.0000 chunk 174 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 12 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1270 GLN K1288 ASN ** K1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027718 restraints weight = 30591.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.028711 restraints weight = 19408.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029430 restraints weight = 13681.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029913 restraints weight = 10374.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030306 restraints weight = 8378.394| |-----------------------------------------------------------------------------| r_work (final): 0.2715 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.034063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027885 restraints weight = 61518.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.028732 restraints weight = 41490.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029361 restraints weight = 30534.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029849 restraints weight = 23913.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.030221 restraints weight = 19386.856| |-----------------------------------------------------------------------------| r_work (final): 0.2809 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029361 restraints weight = 35459.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030197 restraints weight = 27488.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.030855 restraints weight = 22343.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.031368 restraints weight = 18817.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.031786 restraints weight = 16284.563| |-----------------------------------------------------------------------------| r_work (final): 0.2781 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.039835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034164 restraints weight = 12254.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034761 restraints weight = 9505.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035229 restraints weight = 7797.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035596 restraints weight = 6635.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035795 restraints weight = 5818.599| |-----------------------------------------------------------------------------| r_work (final): 0.2929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.032799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.027651 restraints weight = 7613.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.028010 restraints weight = 5610.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.028281 restraints weight = 4516.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.028441 restraints weight = 3823.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.028621 restraints weight = 3427.663| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 41481 Z= 0.259 Angle : 0.960 45.756 56064 Z= 0.470 Chirality : 0.049 0.450 6156 Planarity : 0.009 0.165 7269 Dihedral : 5.313 24.693 5445 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.82 % Favored : 92.06 % Rotamer: Outliers : 0.27 % Allowed : 2.56 % Favored : 97.17 % 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 aren not related in a simple way. whole: -3.01 (0.11), residues: 4911 helix: -1.69 (0.08), residues: 3438 sheet: None (None), residues: 0 loop : -2.34 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.002 ARG L 945 TYR 0.063 0.004 TYR K1534 PHE 0.052 0.004 PHE F1599 TRP 0.102 0.005 TRP F1358 HIS 0.017 0.002 HIS K1432 Details of bonding type rmsd covalent geometry : bond 0.00561 (41481) covalent geometry : angle 0.95987 (56064) hydrogen bonds : bond 0.04358 ( 2134) hydrogen bonds : angle 5.53375 ( 6339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5666 Ramachandran restraints generated. 2833 Oldfield, 0 Emsley, 2833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5666 Ramachandran restraints generated. 2833 Oldfield, 0 Emsley, 2833 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: 2 poor density : 27 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: K 1314 MET cc_start: 0.9314 (tmm) cc_final: 0.9057 (tmm) REVERT: K 1332 MET cc_start: 0.8905 (ttp) cc_final: 0.8651 (tpt) REVERT: K 1502 HIS cc_start: 0.8250 (t-90) cc_final: 0.7819 (t70) REVERT: K 1538 MET cc_start: 0.8587 (ttp) cc_final: 0.8179 (tmm) REVERT: K 1592 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8884 (mmp) REVERT: K 1619 LEU cc_start: 0.9376 (mp) cc_final: 0.9140 (mp) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.0949 time to fit residues: 3.1639 Evaluate side-chains 17 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.162 Evaluate side-chains 37 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 983 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7808 (mm-40) REVERT: B 1041 MET cc_start: 0.9513 (mmp) cc_final: 0.9273 (mmm) REVERT: B 1138 MET cc_start: 0.9055 (mpp) cc_final: 0.8853 (mpp) REVERT: B 1155 LYS cc_start: 0.9631 (mttt) cc_final: 0.9343 (mtmm) REVERT: B 1302 MET cc_start: 0.9224 (ptp) cc_final: 0.8619 (ptm) REVERT: B 1314 MET cc_start: 0.8668 (ppp) cc_final: 0.8101 (ppp) REVERT: B 1332 MET cc_start: 0.8416 (mmm) cc_final: 0.8168 (tpt) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.0621 time to fit residues: 3.3319 Evaluate side-chains 26 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.225 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 : 0.110 Fit side-chains revert: symmetry clash REVERT: C 668 ARG cc_start: 0.9296 (ttm110) cc_final: 0.9017 (mtm110) REVERT: C 670 MET cc_start: 0.8549 (mtm) cc_final: 0.8332 (ptp) REVERT: C 765 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7019 (mm-30) REVERT: C 986 GLU cc_start: 0.9526 (mp0) cc_final: 0.9247 (mp0) REVERT: C 995 PHE cc_start: 0.8920 (m-10) cc_final: 0.8504 (m-10) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0793 time to fit residues: 2.4966 Evaluate side-chains 13 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.147 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 : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 111 ARG cc_start: 0.9235 (mmp80) cc_final: 0.8990 (mmm160) REVERT: N 130 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8570 (mt-10) REVERT: N 207 LYS cc_start: 0.6707 (mptt) cc_final: 0.6329 (mptt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.2054 time to fit residues: 2.1500 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 : 0.023 Evaluate side-chains 5 residues out of total 55 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2304 time to fit residues: 1.1914 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 : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.3743 > 50: distance: 0 - 1: 16.386 distance: 1 - 2: 15.820 distance: 1 - 4: 24.365 distance: 2 - 3: 17.621 distance: 2 - 5: 15.997 distance: 5 - 6: 21.035 distance: 6 - 7: 8.480 distance: 6 - 9: 9.177 distance: 7 - 8: 12.222 distance: 7 - 17: 11.019 distance: 9 - 10: 9.140 distance: 10 - 11: 11.207 distance: 10 - 12: 18.618 distance: 11 - 13: 19.938 distance: 12 - 14: 11.024 distance: 13 - 15: 31.711 distance: 14 - 15: 9.567 distance: 15 - 16: 10.247 distance: 17 - 18: 11.432 distance: 18 - 19: 13.350 distance: 18 - 21: 10.761 distance: 19 - 20: 12.019 distance: 19 - 25: 23.041 distance: 21 - 22: 15.927 distance: 22 - 23: 39.006 distance: 22 - 24: 10.572 distance: 25 - 26: 18.745 distance: 26 - 27: 6.031 distance: 26 - 29: 6.967 distance: 27 - 28: 13.992 distance: 27 - 36: 20.303 distance: 28 - 49: 44.969 distance: 29 - 30: 12.274 distance: 30 - 31: 30.199 distance: 30 - 32: 25.203 distance: 31 - 33: 9.720 distance: 32 - 34: 7.643 distance: 33 - 35: 27.031 distance: 34 - 35: 41.679 distance: 36 - 37: 11.878 distance: 37 - 38: 17.939 distance: 37 - 40: 14.573 distance: 38 - 39: 15.906 distance: 39 - 57: 31.462 distance: 40 - 41: 7.124 distance: 41 - 42: 14.526 distance: 42 - 43: 8.248 distance: 43 - 44: 3.081 distance: 45 - 46: 25.486 distance: 46 - 47: 25.856 distance: 47 - 48: 10.278 distance: 47 - 49: 14.197 distance: 49 - 50: 36.283 distance: 50 - 51: 37.972 distance: 50 - 53: 28.447 distance: 51 - 52: 3.927 distance: 51 - 57: 20.858 distance: 53 - 54: 12.012 distance: 54 - 55: 14.911 distance: 54 - 56: 25.399 distance: 57 - 58: 11.598 distance: 58 - 59: 19.588 distance: 58 - 61: 17.241 distance: 59 - 60: 20.741 distance: 59 - 65: 9.629 distance: 61 - 62: 18.955 distance: 62 - 63: 12.618 distance: 62 - 64: 16.160 distance: 65 - 66: 7.699 distance: 66 - 67: 13.962 distance: 66 - 69: 15.980 distance: 67 - 68: 24.150 distance: 67 - 76: 43.524 distance: 69 - 70: 13.996 distance: 70 - 71: 10.609 distance: 71 - 72: 8.782 distance: 72 - 73: 7.687 distance: 73 - 75: 12.313 distance: 76 - 77: 19.492 distance: 77 - 78: 12.093 distance: 77 - 80: 15.266 distance: 78 - 79: 12.573