Starting phenix.real_space_refine on Sun Mar 24 08:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_0126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_0126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_0126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_0126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sct_0126/03_2024/6sct_0126.pdb" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 Residue "A PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "A TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "B GLU 863": "OE1" <-> "OE2" Residue "B ARG 865": "NH1" <-> "NH2" Residue "B ARG 903": "NH1" <-> "NH2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B GLU 954": "OE1" <-> "OE2" Residue "B ASP 999": "OD1" <-> "OD2" Residue "B GLU 1003": "OE1" <-> "OE2" Residue "B GLU 1067": "OE1" <-> "OE2" Residue "B ASP 1132": "OD1" <-> "OD2" Residue "B GLU 1208": "OE1" <-> "OE2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C ASP 724": "OD1" <-> "OD2" Residue "C ASP 770": "OD1" <-> "OD2" Residue "C ASP 786": "OD1" <-> "OD2" Residue "C ASP 827": "OD1" <-> "OD2" Residue "C ARG 865": "NH1" <-> "NH2" Residue "C ARG 903": "NH1" <-> "NH2" Residue "C GLU 954": "OE1" <-> "OE2" Residue "C ASP 999": "OD1" <-> "OD2" Residue "C ASP 1054": "OD1" <-> "OD2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ASP 135": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ASP 135": "OD1" <-> "OD2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O ASP 158": "OD1" <-> "OD2" Residue "F PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1434": "NH1" <-> "NH2" Residue "F TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1551": "OE1" <-> "OE2" Residue "K PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1434": "NH1" <-> "NH2" Residue "K TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1551": "OE1" <-> "OE2" Residue "G GLU 863": "OE1" <-> "OE2" Residue "G ARG 865": "NH1" <-> "NH2" Residue "G ARG 903": "NH1" <-> "NH2" Residue "G GLU 936": "OE1" <-> "OE2" Residue "G GLU 954": "OE1" <-> "OE2" Residue "G ASP 999": "OD1" <-> "OD2" Residue "G GLU 1003": "OE1" <-> "OE2" Residue "G GLU 1067": "OE1" <-> "OE2" Residue "G ASP 1132": "OD1" <-> "OD2" Residue "G GLU 1208": "OE1" <-> "OE2" Residue "L GLU 863": "OE1" <-> "OE2" Residue "L ARG 865": "NH1" <-> "NH2" Residue "L ARG 903": "NH1" <-> "NH2" Residue "L GLU 936": "OE1" <-> "OE2" Residue "L GLU 954": "OE1" <-> "OE2" Residue "L ASP 999": "OD1" <-> "OD2" Residue "L GLU 1003": "OE1" <-> "OE2" Residue "L GLU 1067": "OE1" <-> "OE2" Residue "L ASP 1132": "OD1" <-> "OD2" Residue "L GLU 1208": "OE1" <-> "OE2" Residue "H TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 709": "OE1" <-> "OE2" Residue "H ASP 724": "OD1" <-> "OD2" Residue "H ASP 770": "OD1" <-> "OD2" Residue "H ASP 786": "OD1" <-> "OD2" Residue "H ASP 827": "OD1" <-> "OD2" Residue "H ARG 865": "NH1" <-> "NH2" Residue "H ARG 903": "NH1" <-> "NH2" Residue "H GLU 954": "OE1" <-> "OE2" Residue "H ASP 999": "OD1" <-> "OD2" Residue "H ASP 1054": "OD1" <-> "OD2" Residue "M TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 709": "OE1" <-> "OE2" Residue "M ASP 724": "OD1" <-> "OD2" Residue "M ASP 770": "OD1" <-> "OD2" Residue "M ASP 786": "OD1" <-> "OD2" Residue "M ASP 827": "OD1" <-> "OD2" Residue "M ARG 865": "NH1" <-> "NH2" Residue "M ARG 903": "NH1" <-> "NH2" Residue "M GLU 954": "OE1" <-> "OE2" Residue "M ASP 999": "OD1" <-> "OD2" Residue "M ASP 1054": "OD1" <-> "OD2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ASP 211": "OD1" <-> "OD2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ASP 211": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 19.09, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.21 Conformation dependent library (CDL) restraints added in 6.7 seconds 9822 Ramachandran restraints generated. 4911 Oldfield, 0 Emsley, 4911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 357 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 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: 13.40 Time building geometry restraints manager: 16.42 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: 98.15 - 105.37: 601 105.37 - 112.59: 20526 112.59 - 119.81: 15740 119.81 - 127.02: 18769 127.02 - 134.24: 428 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 2.440 nonbonded pdb=" OH TYR A1574 " pdb=" OE1 GLN A1601 " model vdw 2.105 2.440 nonbonded pdb=" OH TYR F1574 " pdb=" OE1 GLN F1601 " model vdw 2.105 2.440 nonbonded pdb=" OG SER H 825 " pdb=" OD1 ASP H 827 " model vdw 2.107 2.440 nonbonded pdb=" OG SER C 825 " pdb=" OD1 ASP C 827 " model vdw 2.107 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 5.930 Check model and map are aligned: 0.570 Set scattering table: 0.310 Process input model: 93.510 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.910 ------------------------------------------------------------------------------- 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= 0.285 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 : 6.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP L1253 HIS 0.006 0.001 HIS C 690 PHE 0.019 0.002 PHE F1594 TYR 0.016 0.002 TYR K1411 ARG 0.005 0.000 ARG G 949 *********************** 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 fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2423 time to fit residues: 8.6217 Evaluate side-chains 21 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.406 Evaluate side-chains 48 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.500 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: 0.2077 time to fit residues: 12.5458 Evaluate side-chains 23 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.571 Evaluate side-chains 37 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.389 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: 0.2369 time to fit residues: 10.4835 Evaluate side-chains 19 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.453 Evaluate side-chains 15 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.118 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: 0.4760 time to fit residues: 7.4411 Evaluate side-chains 8 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.118 Evaluate side-chains 9 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.5174 time to fit residues: 4.8132 Evaluate side-chains 4 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 0.9980 chunk 368 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 380 optimal weight: 0.0170 chunk 147 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 283 optimal weight: 0.0670 chunk 441 optimal weight: 0.7980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1288 ASN F1291 GLN ** F1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 ASN F1456 GLN 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: L 853 ASN L1288 ASN L1468 ASN 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: H 653 ASN H 684 GLN ** H1049 ASN ** 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: ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41481 Z= 0.172 Angle : 0.595 10.390 56064 Z= 0.306 Chirality : 0.039 0.192 6156 Planarity : 0.004 0.046 7269 Dihedral : 4.768 21.623 5445 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4911 helix: -1.12 (0.08), residues: 3420 sheet: None (None), residues: 0 loop : -1.91 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1587 HIS 0.005 0.001 HIS F1313 PHE 0.034 0.001 PHE C 995 TYR 0.017 0.001 TYR K1574 ARG 0.014 0.000 ARG I 214 *********************** 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 32 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1379 MET cc_start: 0.8262 (mtp) cc_final: 0.7843 (ptm) REVERT: F 1603 MET cc_start: 0.7305 (mmm) cc_final: 0.6927 (mmm) outliers start: 2 outliers final: 0 residues processed: 31 average time/residue: 0.2065 time to fit residues: 7.7892 Evaluate side-chains 16 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.369 Evaluate side-chains 42 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: L 1155 LYS cc_start: 0.9301 (mttt) cc_final: 0.9039 (mtmm) REVERT: L 1270 GLN cc_start: 0.9207 (tt0) cc_final: 0.8762 (pp30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1898 time to fit residues: 10.8141 Evaluate side-chains 25 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.653 Evaluate side-chains 37 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 651 LEU cc_start: 0.8801 (tt) cc_final: 0.8526 (tt) REVERT: H 775 ILE cc_start: 0.9131 (pt) cc_final: 0.8731 (mp) REVERT: H 899 TYR cc_start: 0.7710 (m-80) cc_final: 0.7444 (m-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1910 time to fit residues: 8.8137 Evaluate side-chains 15 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.404 Evaluate side-chains 14 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.3546 time to fit residues: 5.2096 Evaluate side-chains 7 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.087 Evaluate side-chains 6 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.5156 time to fit residues: 3.2263 Evaluate side-chains 5 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 367 optimal weight: 0.0030 chunk 300 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 442 optimal weight: 3.9990 chunk 477 optimal weight: 0.8980 chunk 393 optimal weight: 0.0370 chunk 438 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 354 optimal weight: 20.0000 overall best weight: 0.5872 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1015 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 690 HIS ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 115 GLN N 126 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: ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 41481 Z= 0.377 Angle : 0.939 25.595 56064 Z= 0.489 Chirality : 0.049 0.519 6156 Planarity : 0.013 0.321 7269 Dihedral : 5.386 51.339 5445 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 0.47 % Allowed : 2.96 % Favored : 96.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 4911 helix: -1.37 (0.08), residues: 3453 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.005 TRP F1358 HIS 0.016 0.002 HIS K1432 PHE 0.046 0.004 PHE K1339 TYR 0.060 0.005 TYR F1487 ARG 0.039 0.002 ARG B 945 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: F 1619 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8162 (mp) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.1807 time to fit residues: 6.5540 Evaluate side-chains 19 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.390 Evaluate side-chains 37 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: L 1155 LYS cc_start: 0.9191 (mttt) cc_final: 0.8975 (mtmm) REVERT: L 1302 MET cc_start: 0.8723 (ptp) cc_final: 0.8416 (ptm) REVERT: L 1379 MET cc_start: 0.7900 (mtp) cc_final: 0.7551 (mtp) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1867 time to fit residues: 9.5982 Evaluate side-chains 23 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.651 Evaluate side-chains 30 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 775 ILE cc_start: 0.9084 (pt) cc_final: 0.8685 (mp) REVERT: H 885 ASP cc_start: 0.6484 (m-30) cc_final: 0.6051 (m-30) REVERT: H 995 PHE cc_start: 0.8495 (m-10) cc_final: 0.8242 (m-80) outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 0.2096 time to fit residues: 7.8307 Evaluate side-chains 17 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.444 Evaluate side-chains 11 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: N 207 LYS cc_start: 0.5367 (mptt) cc_final: 0.5160 (mptt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.4294 time to fit residues: 4.9723 Evaluate side-chains 8 residues out of total 97 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.107 Evaluate side-chains 5 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.5184 time to fit residues: 2.7180 Evaluate side-chains 3 residues out of total 55 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5195 > 50: distance: 0 - 1: 16.208 distance: 1 - 2: 26.652 distance: 1 - 4: 18.740 distance: 2 - 3: 28.997 distance: 2 - 5: 28.885 distance: 5 - 6: 14.531 distance: 6 - 7: 20.978 distance: 6 - 9: 47.487 distance: 7 - 8: 44.912 distance: 7 - 13: 41.024 distance: 9 - 10: 38.922 distance: 10 - 11: 49.824 distance: 10 - 12: 57.765 distance: 13 - 14: 18.001 distance: 14 - 15: 45.728 distance: 14 - 17: 31.393 distance: 15 - 16: 13.005 distance: 15 - 22: 28.410 distance: 17 - 18: 15.763 distance: 18 - 19: 31.029 distance: 19 - 20: 35.762 distance: 19 - 21: 8.591 distance: 22 - 23: 24.276 distance: 23 - 24: 10.212 distance: 23 - 26: 8.457 distance: 24 - 25: 5.485 distance: 24 - 30: 20.818 distance: 25 - 56: 30.330 distance: 26 - 27: 51.445 distance: 27 - 28: 8.231 distance: 27 - 29: 52.272 distance: 30 - 31: 18.555 distance: 31 - 32: 17.741 distance: 31 - 34: 20.318 distance: 32 - 33: 29.244 distance: 32 - 39: 32.159 distance: 33 - 64: 46.872 distance: 34 - 35: 24.031 distance: 35 - 36: 46.632 distance: 36 - 37: 7.245 distance: 36 - 38: 24.105 distance: 39 - 40: 24.365 distance: 40 - 41: 15.869 distance: 40 - 43: 5.845 distance: 41 - 42: 10.596 distance: 41 - 48: 10.585 distance: 42 - 72: 32.024 distance: 43 - 44: 30.893 distance: 44 - 45: 60.539 distance: 45 - 46: 45.292 distance: 45 - 47: 22.492 distance: 48 - 49: 20.534 distance: 49 - 50: 43.175 distance: 49 - 52: 9.790 distance: 50 - 51: 3.721 distance: 50 - 56: 11.486 distance: 51 - 84: 21.998 distance: 52 - 53: 36.976 distance: 53 - 54: 18.214 distance: 53 - 55: 27.556 distance: 56 - 57: 13.735 distance: 57 - 58: 19.164 distance: 57 - 60: 14.664 distance: 58 - 59: 28.790 distance: 58 - 64: 31.933 distance: 60 - 61: 16.181 distance: 60 - 62: 21.629 distance: 61 - 63: 20.409 distance: 64 - 65: 5.649 distance: 65 - 66: 28.093 distance: 65 - 68: 8.353 distance: 66 - 67: 16.060 distance: 66 - 72: 34.499 distance: 68 - 69: 33.823 distance: 69 - 70: 16.437 distance: 69 - 71: 29.188 distance: 72 - 73: 34.673 distance: 73 - 74: 25.620 distance: 73 - 76: 45.065 distance: 74 - 75: 13.957 distance: 74 - 84: 27.457 distance: 76 - 77: 22.037 distance: 77 - 78: 8.040 distance: 77 - 79: 10.928 distance: 78 - 80: 4.715 distance: 79 - 81: 7.534 distance: 80 - 82: 11.820 distance: 81 - 82: 10.311 distance: 82 - 83: 5.831 distance: 84 - 85: 19.166