Starting phenix.real_space_refine on Thu Mar 21 16:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9l_9950/03_2024/6k9l_9950.pdb" } resolution = 4.27 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= 0.000 sd= 0.002 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 98 5.16 5 C 18765 2.51 5 N 5801 2.21 5 O 5937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A ARG 2191": "NH1" <-> "NH2" Residue "A PHE 2265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2339": "NH1" <-> "NH2" Residue "A TYR 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2419": "NH1" <-> "NH2" Residue "A ARG 2443": "NH1" <-> "NH2" Residue "A ARG 2459": "NH1" <-> "NH2" Residue "A PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2612": "NH1" <-> "NH2" Residue "A ARG 2618": "NH1" <-> "NH2" Residue "A ARG 2741": "NH1" <-> "NH2" Residue "A ARG 2790": "NH1" <-> "NH2" Residue "A PHE 2796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2832": "NH1" <-> "NH2" Residue "A ARG 2849": "NH1" <-> "NH2" Residue "A ARG 2871": "NH1" <-> "NH2" Residue "A PHE 2908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2909": "NH1" <-> "NH2" Residue "A PHE 2927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2929": "NH1" <-> "NH2" Residue "B ARG 2151": "NH1" <-> "NH2" Residue "B ARG 2191": "NH1" <-> "NH2" Residue "B PHE 2265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2339": "NH1" <-> "NH2" Residue "B TYR 2360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2419": "NH1" <-> "NH2" Residue "B ARG 2443": "NH1" <-> "NH2" Residue "B ARG 2459": "NH1" <-> "NH2" Residue "B PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2612": "NH1" <-> "NH2" Residue "B ARG 2618": "NH1" <-> "NH2" Residue "B ARG 2741": "NH1" <-> "NH2" Residue "B ARG 2790": "NH1" <-> "NH2" Residue "B PHE 2796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2832": "NH1" <-> "NH2" Residue "B ARG 2849": "NH1" <-> "NH2" Residue "B ARG 2871": "NH1" <-> "NH2" Residue "B PHE 2908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2909": "NH1" <-> "NH2" Residue "B PHE 2927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2929": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30601 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 15303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2552, 15303 Classifications: {'peptide': 2552} Incomplete info: {'truncation_to_alanine': 1561} Link IDs: {'PTRANS': 76, 'TRANS': 2475} Chain breaks: 37 Unresolved chain link angles: 51 Unresolved non-hydrogen bonds: 5568 Unresolved non-hydrogen angles: 7116 Unresolved non-hydrogen dihedrals: 4639 Unresolved non-hydrogen chiralities: 534 Planarities with less than four sites: {'GLN:plan1': 84, 'ASP:plan': 88, 'TYR:plan': 59, 'ASN:plan1': 71, 'TRP:plan': 21, 'HIS:plan': 48, 'PHE:plan': 74, 'GLU:plan': 124, 'ARG:plan': 70} Unresolved non-hydrogen planarities: 2945 Chain: "B" Number of atoms: 15298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2551, 15298 Classifications: {'peptide': 2551} Incomplete info: {'truncation_to_alanine': 1560} Link IDs: {'PTRANS': 76, 'TRANS': 2474} Chain breaks: 37 Unresolved chain link angles: 51 Unresolved non-hydrogen bonds: 5565 Unresolved non-hydrogen angles: 7112 Unresolved non-hydrogen dihedrals: 4637 Unresolved non-hydrogen chiralities: 534 Planarities with less than four sites: {'GLN:plan1': 84, 'ASP:plan': 87, 'TYR:plan': 59, 'ASN:plan1': 71, 'TRP:plan': 21, 'HIS:plan': 48, 'PHE:plan': 74, 'GLU:plan': 124, 'ARG:plan': 70} Unresolved non-hydrogen planarities: 2942 Time building chain proxies: 18.26, per 1000 atoms: 0.60 Number of scatterers: 30601 At special positions: 0 Unit cell: (102.06, 221.94, 210.6, 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 98 16.00 O 5937 8.00 N 5801 7.00 C 18765 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: 11.52 Conformation dependent library (CDL) restraints added in 7.1 seconds 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9826 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 4 sheets defined 66.5% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 24 through 36 Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.869A pdb=" N ASP A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.569A pdb=" N LYS A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.524A pdb=" N SER A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.684A pdb=" N LEU A 121 " --> pdb=" O CYS A 117 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.540A pdb=" N VAL A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 237 removed outlier: 4.528A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.758A pdb=" N ASP A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 288 removed outlier: 3.669A pdb=" N THR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 339 through 357 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 433 through 450 removed outlier: 3.664A pdb=" N ILE A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 456 through 467 removed outlier: 4.160A pdb=" N VAL A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 493 Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 557 through 566 Processing helix chain 'A' and resid 576 through 587 removed outlier: 4.194A pdb=" N LEU A 580 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.867A pdb=" N VAL A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 4.329A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 685 through 697 removed outlier: 4.086A pdb=" N SER A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.753A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 730 through 741 removed outlier: 4.382A pdb=" N GLU A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 738 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 761 Processing helix chain 'A' and resid 830 through 838 removed outlier: 3.846A pdb=" N SER A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 861 Processing helix chain 'A' and resid 878 through 888 removed outlier: 3.794A pdb=" N ILE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 883 " --> pdb=" O ILE A 879 " (cutoff:3.500A) Proline residue: A 884 - end of helix Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.559A pdb=" N ASP A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 959 removed outlier: 3.772A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Proline residue: A 955 - end of helix Processing helix chain 'A' and resid 966 through 982 removed outlier: 3.979A pdb=" N LEU A 970 " --> pdb=" O VAL A 966 " (cutoff:3.500A) Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 989 through 1005 removed outlier: 3.712A pdb=" N GLY A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.794A pdb=" N GLN A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 3.715A pdb=" N ARG A1039 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1049 removed outlier: 3.678A pdb=" N LEU A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.678A pdb=" N LEU A1061 " --> pdb=" O TRP A1058 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A1063 " --> pdb=" O ILE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1089 removed outlier: 4.089A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1126 Proline residue: A1112 - end of helix removed outlier: 4.040A pdb=" N GLN A1116 " --> pdb=" O PRO A1112 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1118 " --> pdb=" O LYS A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1143 removed outlier: 3.981A pdb=" N HIS A1136 " --> pdb=" O ARG A1132 " (cutoff:3.500A) Proline residue: A1141 - end of helix Processing helix chain 'A' and resid 1149 through 1158 removed outlier: 3.842A pdb=" N VAL A1153 " --> pdb=" O ASN A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1170 Processing helix chain 'A' and resid 1170 through 1175 removed outlier: 3.944A pdb=" N ALA A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1197 through 1202 removed outlier: 4.086A pdb=" N PHE A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1218 removed outlier: 3.911A pdb=" N TYR A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1222 Processing helix chain 'A' and resid 1237 through 1244 Processing helix chain 'A' and resid 1254 through 1271 removed outlier: 4.365A pdb=" N HIS A1258 " --> pdb=" O VAL A1254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'A' and resid 1294 through 1298 Processing helix chain 'A' and resid 1301 through 1307 Processing helix chain 'A' and resid 1341 through 1345 Processing helix chain 'A' and resid 1353 through 1358 removed outlier: 3.556A pdb=" N SER A1357 " --> pdb=" O PRO A1354 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1358 " --> pdb=" O ALA A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.707A pdb=" N ASP A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1381 removed outlier: 3.692A pdb=" N HIS A1380 " --> pdb=" O PRO A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1386 removed outlier: 3.798A pdb=" N VAL A1385 " --> pdb=" O PHE A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1417 through 1423 Processing helix chain 'A' and resid 1436 through 1449 removed outlier: 3.583A pdb=" N LEU A1449 " --> pdb=" O PHE A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1474 removed outlier: 3.767A pdb=" N ALA A1462 " --> pdb=" O GLY A1458 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A1463 " --> pdb=" O GLY A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1483 Processing helix chain 'A' and resid 1484 through 1499 Processing helix chain 'A' and resid 1500 through 1501 No H-bonds generated for 'chain 'A' and resid 1500 through 1501' Processing helix chain 'A' and resid 1512 through 1513 No H-bonds generated for 'chain 'A' and resid 1512 through 1513' Processing helix chain 'A' and resid 1514 through 1522 removed outlier: 3.587A pdb=" N HIS A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1534 through 1544 removed outlier: 3.698A pdb=" N TYR A1544 " --> pdb=" O ASP A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1556 Processing helix chain 'A' and resid 1557 through 1563 Processing helix chain 'A' and resid 1569 through 1576 Processing helix chain 'A' and resid 1577 through 1584 removed outlier: 3.625A pdb=" N LYS A1580 " --> pdb=" O THR A1577 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A1581 " --> pdb=" O GLN A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1603 Processing helix chain 'A' and resid 1611 through 1619 removed outlier: 4.128A pdb=" N LEU A1617 " --> pdb=" O GLY A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1634 Processing helix chain 'A' and resid 1635 through 1639 removed outlier: 3.940A pdb=" N ASN A1638 " --> pdb=" O SER A1635 " (cutoff:3.500A) Proline residue: A1639 - end of helix No H-bonds generated for 'chain 'A' and resid 1635 through 1639' Processing helix chain 'A' and resid 1640 through 1651 Processing helix chain 'A' and resid 1657 through 1673 removed outlier: 4.136A pdb=" N HIS A1661 " --> pdb=" O MET A1657 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A1672 " --> pdb=" O LEU A1668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1673 " --> pdb=" O GLU A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1684 Processing helix chain 'A' and resid 1702 through 1708 Processing helix chain 'A' and resid 1714 through 1727 removed outlier: 3.836A pdb=" N VAL A1727 " --> pdb=" O VAL A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1738 through 1744 removed outlier: 3.892A pdb=" N ALA A1742 " --> pdb=" O LYS A1738 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1750 No H-bonds generated for 'chain 'A' and resid 1748 through 1750' Processing helix chain 'A' and resid 1751 through 1756 Processing helix chain 'A' and resid 1760 through 1762 No H-bonds generated for 'chain 'A' and resid 1760 through 1762' Processing helix chain 'A' and resid 1763 through 1769 removed outlier: 3.580A pdb=" N PHE A1767 " --> pdb=" O TYR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1825 Processing helix chain 'A' and resid 1826 through 1836 removed outlier: 3.611A pdb=" N ASP A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1841 through 1847 Processing helix chain 'A' and resid 1855 through 1875 removed outlier: 3.650A pdb=" N HIS A1865 " --> pdb=" O LEU A1861 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A1868 " --> pdb=" O THR A1864 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A1875 " --> pdb=" O THR A1871 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1892 removed outlier: 3.725A pdb=" N THR A1885 " --> pdb=" O SER A1881 " (cutoff:3.500A) Proline residue: A1886 - end of helix Processing helix chain 'A' and resid 1904 through 1913 removed outlier: 3.828A pdb=" N THR A1908 " --> pdb=" O LYS A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1934 removed outlier: 5.616A pdb=" N ALA A1931 " --> pdb=" O PHE A1928 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A1932 " --> pdb=" O ASN A1929 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A1934 " --> pdb=" O ALA A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1937 through 1949 Processing helix chain 'A' and resid 1951 through 1969 removed outlier: 3.635A pdb=" N LEU A1955 " --> pdb=" O HIS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2013 removed outlier: 4.358A pdb=" N ASP A2003 " --> pdb=" O ILE A1999 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2022 Processing helix chain 'A' and resid 2042 through 2048 removed outlier: 3.662A pdb=" N LEU A2046 " --> pdb=" O TRP A2042 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A2047 " --> pdb=" O GLY A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2058 Processing helix chain 'A' and resid 2059 through 2072 removed outlier: 3.837A pdb=" N GLN A2066 " --> pdb=" O ALA A2062 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A2067 " --> pdb=" O GLY A2063 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A2071 " --> pdb=" O ALA A2067 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A2072 " --> pdb=" O LEU A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2084 removed outlier: 4.331A pdb=" N VAL A2079 " --> pdb=" O HIS A2075 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A2080 " --> pdb=" O ILE A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2100 removed outlier: 3.632A pdb=" N HIS A2099 " --> pdb=" O LEU A2095 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A2100 " --> pdb=" O GLU A2096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2095 through 2100' Processing helix chain 'A' and resid 2124 through 2135 Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2161 removed outlier: 3.750A pdb=" N ARG A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2169 through 2191 removed outlier: 3.772A pdb=" N LEU A2182 " --> pdb=" O ALA A2178 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A2183 " --> pdb=" O ILE A2179 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A2191 " --> pdb=" O GLU A2187 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2211 removed outlier: 4.126A pdb=" N LEU A2211 " --> pdb=" O LYS A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2215 Processing helix chain 'A' and resid 2220 through 2233 Processing helix chain 'A' and resid 2234 through 2236 No H-bonds generated for 'chain 'A' and resid 2234 through 2236' Processing helix chain 'A' and resid 2240 through 2242 No H-bonds generated for 'chain 'A' and resid 2240 through 2242' Processing helix chain 'A' and resid 2243 through 2264 removed outlier: 3.667A pdb=" N ILE A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A2264 " --> pdb=" O ILE A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2281 removed outlier: 3.871A pdb=" N ALA A2274 " --> pdb=" O LEU A2270 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A2275 " --> pdb=" O PRO A2271 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A2276 " --> pdb=" O GLU A2272 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN A2277 " --> pdb=" O ARG A2273 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A2278 " --> pdb=" O ALA A2274 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2302 removed outlier: 4.380A pdb=" N GLU A2295 " --> pdb=" O TRP A2291 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA A2296 " --> pdb=" O GLN A2292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A2302 " --> pdb=" O VAL A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2322 removed outlier: 3.860A pdb=" N LEU A2312 " --> pdb=" O ALA A2308 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A2313 " --> pdb=" O LEU A2309 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A2317 " --> pdb=" O LYS A2313 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A2318 " --> pdb=" O GLN A2314 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2349 removed outlier: 4.164A pdb=" N THR A2335 " --> pdb=" O LYS A2331 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A2336 " --> pdb=" O LEU A2332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS A2341 " --> pdb=" O CYS A2337 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A2346 " --> pdb=" O GLY A2342 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A2347 " --> pdb=" O ASN A2343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A2348 " --> pdb=" O TRP A2344 " (cutoff:3.500A) Processing helix chain 'A' and resid 2377 through 2420 removed outlier: 3.938A pdb=" N GLU A2409 " --> pdb=" O MET A2405 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A2410 " --> pdb=" O LYS A2406 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A2414 " --> pdb=" O PHE A2410 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A2415 " --> pdb=" O GLU A2411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A2418 " --> pdb=" O GLN A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2474 removed outlier: 3.567A pdb=" N VAL A2441 " --> pdb=" O TYR A2437 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A2454 " --> pdb=" O LEU A2450 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU A2455 " --> pdb=" O ALA A2451 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A2456 " --> pdb=" O LEU A2452 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A2460 " --> pdb=" O LYS A2456 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A2461 " --> pdb=" O GLU A2457 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A2466 " --> pdb=" O PHE A2462 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A2474 " --> pdb=" O TYR A2470 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2484 removed outlier: 3.607A pdb=" N TRP A2483 " --> pdb=" O HIS A2480 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A2484 " --> pdb=" O ASP A2481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2480 through 2484' Processing helix chain 'A' and resid 2485 through 2490 Processing helix chain 'A' and resid 2499 through 2502 Processing helix chain 'A' and resid 2503 through 2508 Processing helix chain 'A' and resid 2516 through 2518 No H-bonds generated for 'chain 'A' and resid 2516 through 2518' Processing helix chain 'A' and resid 2519 through 2528 removed outlier: 3.658A pdb=" N ALA A2524 " --> pdb=" O MET A2520 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA A2525 " --> pdb=" O TYR A2521 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2552 removed outlier: 4.059A pdb=" N ARG A2547 " --> pdb=" O ASN A2543 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A2548 " --> pdb=" O LEU A2544 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A2549 " --> pdb=" O ILE A2545 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2565 removed outlier: 3.605A pdb=" N THR A2556 " --> pdb=" O HIS A2552 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A2561 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A2562 " --> pdb=" O PHE A2558 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A2563 " --> pdb=" O ILE A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2613 removed outlier: 4.366A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2634 removed outlier: 3.849A pdb=" N VAL A2620 " --> pdb=" O MET A2616 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A2621 " --> pdb=" O VAL A2617 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A2634 " --> pdb=" O LEU A2630 " (cutoff:3.500A) Processing helix chain 'A' and resid 2635 through 2640 removed outlier: 3.853A pdb=" N LYS A2639 " --> pdb=" O ALA A2635 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A2640 " --> pdb=" O THR A2636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2635 through 2640' Processing helix chain 'A' and resid 2653 through 2659 Processing helix chain 'A' and resid 2723 through 2728 Processing helix chain 'A' and resid 2729 through 2742 removed outlier: 3.928A pdb=" N GLN A2733 " --> pdb=" O GLN A2729 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A2742 " --> pdb=" O LEU A2738 " (cutoff:3.500A) Processing helix chain 'A' and resid 2743 through 2747 removed outlier: 3.775A pdb=" N LYS A2747 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2780 Processing helix chain 'A' and resid 2786 through 2791 removed outlier: 3.733A pdb=" N TYR A2791 " --> pdb=" O ALA A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2809 removed outlier: 3.740A pdb=" N GLN A2802 " --> pdb=" O ALA A2798 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A2804 " --> pdb=" O GLN A2800 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A2809 " --> pdb=" O MET A2805 " (cutoff:3.500A) Processing helix chain 'A' and resid 2815 through 2826 removed outlier: 3.947A pdb=" N ASN A2826 " --> pdb=" O ASP A2822 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2835 removed outlier: 3.509A pdb=" N TYR A2833 " --> pdb=" O VAL A2830 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) Processing helix chain 'A' and resid 2841 through 2867 removed outlier: 3.606A pdb=" N ILE A2861 " --> pdb=" O ALA A2857 " (cutoff:3.500A) Processing helix chain 'A' and resid 2911 through 2918 Processing helix chain 'A' and resid 2926 through 2936 removed outlier: 4.022A pdb=" N GLU A2936 " --> pdb=" O GLU A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2941 through 2953 removed outlier: 3.678A pdb=" N LEU A2945 " --> pdb=" O SER A2941 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A2946 " --> pdb=" O GLN A2942 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR A2947 " --> pdb=" O GLU A2943 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A2948 " --> pdb=" O THR A2944 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A2949 " --> pdb=" O LEU A2945 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A2950 " --> pdb=" O LEU A2946 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A2951 " --> pdb=" O THR A2947 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2979 removed outlier: 3.597A pdb=" N GLU A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) Processing helix chain 'A' and resid 3000 through 3017 removed outlier: 3.953A pdb=" N LEU A3017 " --> pdb=" O LEU A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3027 through 3038 removed outlier: 4.041A pdb=" N VAL A3032 " --> pdb=" O VAL A3028 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASN A3033 " --> pdb=" O GLY A3029 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3046 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 39 through 44 removed outlier: 3.919A pdb=" N ASP B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.626A pdb=" N LYS B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.721A pdb=" N LEU B 121 " --> pdb=" O CYS B 117 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.099A pdb=" N ARG B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.740A pdb=" N ASP B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.778A pdb=" N THR B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 433 through 449 Proline residue: B 444 - end of helix Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 475 through 492 Processing helix chain 'B' and resid 497 through 515 removed outlier: 3.701A pdb=" N GLN B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 557 through 566 Processing helix chain 'B' and resid 576 through 587 removed outlier: 4.240A pdb=" N LEU B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.853A pdb=" N VAL B 607 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 4.350A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 638 Proline residue: B 631 - end of helix Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 685 through 697 removed outlier: 4.091A pdb=" N SER B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 removed outlier: 3.793A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 702 " --> pdb=" O SER B 698 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.639A pdb=" N LEU B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 747 through 761 removed outlier: 3.662A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 removed outlier: 3.569A pdb=" N VAL B 835 " --> pdb=" O ASP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 860 Processing helix chain 'B' and resid 878 through 888 removed outlier: 3.783A pdb=" N ILE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 883 " --> pdb=" O ILE B 879 " (cutoff:3.500A) Proline residue: B 884 - end of helix Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.552A pdb=" N ASP B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 959 removed outlier: 3.750A pdb=" N LEU B 951 " --> pdb=" O TYR B 947 " (cutoff:3.500A) Proline residue: B 955 - end of helix Processing helix chain 'B' and resid 966 through 982 removed outlier: 3.966A pdb=" N LEU B 970 " --> pdb=" O VAL B 966 " (cutoff:3.500A) Proline residue: B 972 - end of helix Processing helix chain 'B' and resid 989 through 1005 removed outlier: 3.710A pdb=" N GLY B1002 " --> pdb=" O VAL B 998 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1020 removed outlier: 3.787A pdb=" N GLN B1017 " --> pdb=" O ASP B1013 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B1018 " --> pdb=" O ALA B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.764A pdb=" N ARG B1039 " --> pdb=" O PHE B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.683A pdb=" N LEU B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1066 removed outlier: 3.666A pdb=" N LEU B1061 " --> pdb=" O TRP B1058 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B1063 " --> pdb=" O ILE B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1089 removed outlier: 4.085A pdb=" N THR B1075 " --> pdb=" O ASN B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1115 Proline residue: B1112 - end of helix Processing helix chain 'B' and resid 1115 through 1126 Processing helix chain 'B' and resid 1132 through 1143 removed outlier: 3.966A pdb=" N HIS B1136 " --> pdb=" O ARG B1132 " (cutoff:3.500A) Proline residue: B1141 - end of helix Processing helix chain 'B' and resid 1149 through 1158 removed outlier: 3.832A pdb=" N VAL B1153 " --> pdb=" O ASN B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1170 Processing helix chain 'B' and resid 1170 through 1175 removed outlier: 3.966A pdb=" N ALA B1175 " --> pdb=" O GLN B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1202 removed outlier: 3.542A pdb=" N GLY B1202 " --> pdb=" O SER B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1212 through 1218 removed outlier: 3.916A pdb=" N TYR B1216 " --> pdb=" O SER B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1222 Processing helix chain 'B' and resid 1237 through 1244 Processing helix chain 'B' and resid 1254 through 1271 removed outlier: 4.371A pdb=" N HIS B1258 " --> pdb=" O VAL B1254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B1271 " --> pdb=" O GLU B1267 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1282 Processing helix chain 'B' and resid 1283 through 1285 No H-bonds generated for 'chain 'B' and resid 1283 through 1285' Processing helix chain 'B' and resid 1294 through 1298 Processing helix chain 'B' and resid 1301 through 1307 Processing helix chain 'B' and resid 1353 through 1358 removed outlier: 3.582A pdb=" N SER B1357 " --> pdb=" O PRO B1354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B1358 " --> pdb=" O ALA B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1365 through 1373 removed outlier: 3.712A pdb=" N ASP B1371 " --> pdb=" O ASP B1367 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1386 removed outlier: 3.824A pdb=" N VAL B1385 " --> pdb=" O PHE B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1400 removed outlier: 3.950A pdb=" N THR B1399 " --> pdb=" O CYS B1396 " (cutoff:3.500A) Processing helix chain 'B' and resid 1417 through 1423 Processing helix chain 'B' and resid 1436 through 1449 removed outlier: 3.588A pdb=" N LEU B1449 " --> pdb=" O PHE B1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 1457 through 1474 removed outlier: 3.799A pdb=" N ALA B1462 " --> pdb=" O GLY B1458 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B1463 " --> pdb=" O GLY B1459 " (cutoff:3.500A) Processing helix chain 'B' and resid 1477 through 1483 Processing helix chain 'B' and resid 1484 through 1501 removed outlier: 3.592A pdb=" N ASP B1496 " --> pdb=" O SER B1492 " (cutoff:3.500A) Processing helix chain 'B' and resid 1514 through 1522 removed outlier: 3.585A pdb=" N HIS B1518 " --> pdb=" O GLU B1514 " (cutoff:3.500A) Processing helix chain 'B' and resid 1531 through 1533 No H-bonds generated for 'chain 'B' and resid 1531 through 1533' Processing helix chain 'B' and resid 1534 through 1544 removed outlier: 3.711A pdb=" N TYR B1544 " --> pdb=" O ASP B1540 " (cutoff:3.500A) Processing helix chain 'B' and resid 1549 through 1556 Processing helix chain 'B' and resid 1557 through 1563 Processing helix chain 'B' and resid 1569 through 1576 Processing helix chain 'B' and resid 1577 through 1584 removed outlier: 3.680A pdb=" N LYS B1580 " --> pdb=" O THR B1577 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B1581 " --> pdb=" O GLN B1578 " (cutoff:3.500A) Processing helix chain 'B' and resid 1592 through 1603 Processing helix chain 'B' and resid 1611 through 1619 removed outlier: 4.061A pdb=" N LEU B1617 " --> pdb=" O GLY B1613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1634 Processing helix chain 'B' and resid 1635 through 1639 removed outlier: 3.942A pdb=" N ASN B1638 " --> pdb=" O SER B1635 " (cutoff:3.500A) Proline residue: B1639 - end of helix No H-bonds generated for 'chain 'B' and resid 1635 through 1639' Processing helix chain 'B' and resid 1640 through 1651 removed outlier: 3.507A pdb=" N LEU B1651 " --> pdb=" O LEU B1647 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1673 removed outlier: 4.129A pdb=" N HIS B1661 " --> pdb=" O MET B1657 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B1672 " --> pdb=" O LEU B1668 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B1673 " --> pdb=" O GLU B1669 " (cutoff:3.500A) Processing helix chain 'B' and resid 1677 through 1684 Processing helix chain 'B' and resid 1705 through 1710 removed outlier: 3.719A pdb=" N GLN B1709 " --> pdb=" O LYS B1706 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP B1710 " --> pdb=" O GLU B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1713 through 1726 removed outlier: 4.440A pdb=" N TYR B1717 " --> pdb=" O ILE B1713 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1737 removed outlier: 3.505A pdb=" N CYS B1736 " --> pdb=" O ALA B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1738 through 1744 removed outlier: 3.866A pdb=" N ALA B1742 " --> pdb=" O LYS B1738 " (cutoff:3.500A) Processing helix chain 'B' and resid 1748 through 1750 No H-bonds generated for 'chain 'B' and resid 1748 through 1750' Processing helix chain 'B' and resid 1751 through 1756 Processing helix chain 'B' and resid 1760 through 1762 No H-bonds generated for 'chain 'B' and resid 1760 through 1762' Processing helix chain 'B' and resid 1763 through 1769 Processing helix chain 'B' and resid 1822 through 1825 Processing helix chain 'B' and resid 1826 through 1836 removed outlier: 3.620A pdb=" N ASP B1836 " --> pdb=" O GLU B1832 " (cutoff:3.500A) Processing helix chain 'B' and resid 1841 through 1847 Processing helix chain 'B' and resid 1855 through 1875 removed outlier: 3.654A pdb=" N HIS B1865 " --> pdb=" O LEU B1861 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B1868 " --> pdb=" O THR B1864 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B1875 " --> pdb=" O THR B1871 " (cutoff:3.500A) Processing helix chain 'B' and resid 1878 through 1892 removed outlier: 3.730A pdb=" N THR B1885 " --> pdb=" O SER B1881 " (cutoff:3.500A) Proline residue: B1886 - end of helix Processing helix chain 'B' and resid 1904 through 1913 removed outlier: 3.806A pdb=" N THR B1908 " --> pdb=" O LYS B1904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1934 removed outlier: 5.660A pdb=" N ALA B1931 " --> pdb=" O PHE B1928 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B1932 " --> pdb=" O ASN B1929 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B1934 " --> pdb=" O ALA B1931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1937 through 1949 removed outlier: 3.719A pdb=" N SER B1947 " --> pdb=" O LYS B1943 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B1948 " --> pdb=" O VAL B1944 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1969 removed outlier: 3.801A pdb=" N LEU B1955 " --> pdb=" O HIS B1951 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2013 removed outlier: 4.196A pdb=" N ASP B2003 " --> pdb=" O ILE B1999 " (cutoff:3.500A) Processing helix chain 'B' and resid 2014 through 2022 Processing helix chain 'B' and resid 2057 through 2072 removed outlier: 3.894A pdb=" N GLY B2072 " --> pdb=" O LEU B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2075 through 2084 removed outlier: 4.312A pdb=" N VAL B2079 " --> pdb=" O HIS B2075 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B2080 " --> pdb=" O ILE B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2100 removed outlier: 3.650A pdb=" N HIS B2099 " --> pdb=" O LEU B2095 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B2100 " --> pdb=" O GLU B2096 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2095 through 2100' Processing helix chain 'B' and resid 2124 through 2135 Processing helix chain 'B' and resid 2140 through 2160 removed outlier: 3.519A pdb=" N LYS B2153 " --> pdb=" O TYR B2149 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B2154 " --> pdb=" O ALA B2150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B2155 " --> pdb=" O ARG B2151 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU B2156 " --> pdb=" O VAL B2152 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU B2157 " --> pdb=" O LYS B2153 " (cutoff:3.500A) Processing helix chain 'B' and resid 2169 through 2190 removed outlier: 3.754A pdb=" N LEU B2182 " --> pdb=" O ALA B2178 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B2187 " --> pdb=" O GLU B2183 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B2188 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2211 removed outlier: 4.137A pdb=" N LEU B2211 " --> pdb=" O LYS B2207 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2215 Processing helix chain 'B' and resid 2220 through 2233 Processing helix chain 'B' and resid 2234 through 2236 No H-bonds generated for 'chain 'B' and resid 2234 through 2236' Processing helix chain 'B' and resid 2240 through 2242 No H-bonds generated for 'chain 'B' and resid 2240 through 2242' Processing helix chain 'B' and resid 2243 through 2264 removed outlier: 3.649A pdb=" N ILE B2247 " --> pdb=" O GLN B2243 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B2264 " --> pdb=" O ILE B2260 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2274 removed outlier: 3.678A pdb=" N ALA B2274 " --> pdb=" O LEU B2270 " (cutoff:3.500A) Processing helix chain 'B' and resid 2274 through 2281 removed outlier: 3.799A pdb=" N ILE B2278 " --> pdb=" O ALA B2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2302 removed outlier: 4.481A pdb=" N GLU B2295 " --> pdb=" O TRP B2291 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B2296 " --> pdb=" O GLN B2292 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B2302 " --> pdb=" O VAL B2298 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2322 removed outlier: 3.840A pdb=" N LEU B2312 " --> pdb=" O ALA B2308 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B2313 " --> pdb=" O LEU B2309 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B2317 " --> pdb=" O LYS B2313 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B2318 " --> pdb=" O GLN B2314 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B2321 " --> pdb=" O LYS B2317 " (cutoff:3.500A) Processing helix chain 'B' and resid 2329 through 2349 removed outlier: 4.207A pdb=" N THR B2335 " --> pdb=" O LYS B2331 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B2336 " --> pdb=" O LEU B2332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B2338 " --> pdb=" O TYR B2334 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B2341 " --> pdb=" O CYS B2337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B2347 " --> pdb=" O ASN B2343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B2348 " --> pdb=" O TRP B2344 " (cutoff:3.500A) Processing helix chain 'B' and resid 2377 through 2420 removed outlier: 3.950A pdb=" N GLU B2409 " --> pdb=" O MET B2405 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B2410 " --> pdb=" O LYS B2406 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B2414 " --> pdb=" O PHE B2410 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B2415 " --> pdb=" O GLU B2411 " (cutoff:3.500A) Processing helix chain 'B' and resid 2437 through 2474 removed outlier: 3.573A pdb=" N VAL B2441 " --> pdb=" O TYR B2437 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA B2454 " --> pdb=" O LEU B2450 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B2455 " --> pdb=" O ALA B2451 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B2456 " --> pdb=" O LEU B2452 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS B2460 " --> pdb=" O LYS B2456 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B2461 " --> pdb=" O GLU B2457 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B2466 " --> pdb=" O PHE B2462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B2474 " --> pdb=" O TYR B2470 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2484 removed outlier: 3.598A pdb=" N TRP B2483 " --> pdb=" O HIS B2480 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B2484 " --> pdb=" O ASP B2481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2480 through 2484' Processing helix chain 'B' and resid 2485 through 2490 Processing helix chain 'B' and resid 2499 through 2502 Processing helix chain 'B' and resid 2503 through 2508 Processing helix chain 'B' and resid 2516 through 2518 No H-bonds generated for 'chain 'B' and resid 2516 through 2518' Processing helix chain 'B' and resid 2519 through 2528 removed outlier: 3.625A pdb=" N ALA B2524 " --> pdb=" O MET B2520 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA B2525 " --> pdb=" O TYR B2521 " (cutoff:3.500A) Processing helix chain 'B' and resid 2536 through 2552 removed outlier: 3.523A pdb=" N SER B2546 " --> pdb=" O ASN B2542 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B2547 " --> pdb=" O ASN B2543 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B2548 " --> pdb=" O LEU B2544 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B2549 " --> pdb=" O ILE B2545 " (cutoff:3.500A) Processing helix chain 'B' and resid 2552 through 2565 removed outlier: 3.608A pdb=" N THR B2556 " --> pdb=" O HIS B2552 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B2561 " --> pdb=" O LEU B2557 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B2562 " --> pdb=" O PHE B2558 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B2563 " --> pdb=" O ILE B2559 " (cutoff:3.500A) Processing helix chain 'B' and resid 2595 through 2613 removed outlier: 4.378A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2634 removed outlier: 3.842A pdb=" N VAL B2620 " --> pdb=" O MET B2616 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B2621 " --> pdb=" O VAL B2617 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B2634 " --> pdb=" O LEU B2630 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2640 removed outlier: 3.865A pdb=" N LYS B2639 " --> pdb=" O ALA B2635 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B2640 " --> pdb=" O THR B2636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2635 through 2640' Processing helix chain 'B' and resid 2653 through 2659 Processing helix chain 'B' and resid 2723 through 2728 Processing helix chain 'B' and resid 2729 through 2742 removed outlier: 3.936A pdb=" N GLN B2733 " --> pdb=" O GLN B2729 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B2742 " --> pdb=" O LEU B2738 " (cutoff:3.500A) Processing helix chain 'B' and resid 2743 through 2747 removed outlier: 3.782A pdb=" N LYS B2747 " --> pdb=" O GLU B2744 " (cutoff:3.500A) Processing helix chain 'B' and resid 2776 through 2780 Processing helix chain 'B' and resid 2786 through 2791 removed outlier: 3.722A pdb=" N TYR B2791 " --> pdb=" O ALA B2787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2809 removed outlier: 3.759A pdb=" N GLN B2802 " --> pdb=" O ALA B2798 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B2804 " --> pdb=" O GLN B2800 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B2809 " --> pdb=" O MET B2805 " (cutoff:3.500A) Processing helix chain 'B' and resid 2815 through 2826 removed outlier: 3.954A pdb=" N ASN B2826 " --> pdb=" O ASP B2822 " (cutoff:3.500A) Processing helix chain 'B' and resid 2830 through 2835 removed outlier: 4.209A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) Processing helix chain 'B' and resid 2841 through 2867 removed outlier: 3.601A pdb=" N ILE B2861 " --> pdb=" O ALA B2857 " (cutoff:3.500A) Processing helix chain 'B' and resid 2911 through 2918 Processing helix chain 'B' and resid 2926 through 2936 removed outlier: 3.959A pdb=" N GLU B2936 " --> pdb=" O GLU B2932 " (cutoff:3.500A) Processing helix chain 'B' and resid 2941 through 2953 removed outlier: 3.675A pdb=" N LEU B2945 " --> pdb=" O SER B2941 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B2946 " --> pdb=" O GLN B2942 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR B2947 " --> pdb=" O GLU B2943 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B2948 " --> pdb=" O THR B2944 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B2949 " --> pdb=" O LEU B2945 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B2950 " --> pdb=" O LEU B2946 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B2951 " --> pdb=" O THR B2947 " (cutoff:3.500A) Processing helix chain 'B' and resid 2971 through 2979 removed outlier: 3.574A pdb=" N GLU B2975 " --> pdb=" O GLN B2971 " (cutoff:3.500A) Processing helix chain 'B' and resid 3000 through 3017 removed outlier: 3.947A pdb=" N LEU B3017 " --> pdb=" O LEU B3013 " (cutoff:3.500A) Processing helix chain 'B' and resid 3027 through 3038 removed outlier: 4.022A pdb=" N VAL B3032 " --> pdb=" O VAL B3028 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN B3033 " --> pdb=" O GLY B3029 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B3038 " --> pdb=" O LEU B3034 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3046 Processing sheet with id=AA1, first strand: chain 'A' and resid 2687 through 2691 removed outlier: 6.218A pdb=" N LYS A2687 " --> pdb=" O VAL A2705 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A2705 " --> pdb=" O LYS A2687 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A2713 " --> pdb=" O TRP A2769 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A2765 " --> pdb=" O LYS A2717 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2773 through 2775 removed outlier: 3.861A pdb=" N ILE A2878 " --> pdb=" O VAL A2774 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2687 through 2691 removed outlier: 6.208A pdb=" N LYS B2687 " --> pdb=" O VAL B2705 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B2705 " --> pdb=" O LYS B2687 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B2713 " --> pdb=" O TRP B2769 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B2765 " --> pdb=" O LYS B2717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2773 through 2775 removed outlier: 3.874A pdb=" N ILE B2878 " --> pdb=" O VAL B2774 " (cutoff:3.500A) 1822 hydrogen bonds defined for protein. 5295 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: 17.39 Time building geometry restraints manager: 12.56 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: 11280 1.34 - 1.46: 3669 1.46 - 1.58: 15656 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 30759 Sorted by residual: bond pdb=" C LEU B2517 " pdb=" N PRO B2518 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.49e+00 bond pdb=" C LEU A2517 " pdb=" N PRO A2518 " ideal model delta sigma weight residual 1.334 1.353 -0.019 8.40e-03 1.42e+04 5.28e+00 bond pdb=" N TRP B 164 " pdb=" CA TRP B 164 " ideal model delta sigma weight residual 1.459 1.471 -0.013 1.16e-02 7.43e+03 1.19e+00 bond pdb=" C LEU A 456 " pdb=" O LEU A 456 " ideal model delta sigma weight residual 1.234 1.245 -0.011 1.07e-02 8.73e+03 1.13e+00 bond pdb=" N GLU A 518 " pdb=" CA GLU A 518 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.75e-01 ... (remaining 30754 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.21: 448 107.21 - 113.90: 17628 113.90 - 120.59: 13369 120.59 - 127.28: 10589 127.28 - 133.98: 115 Bond angle restraints: 42149 Sorted by residual: angle pdb=" N ILE A 144 " pdb=" CA ILE A 144 " pdb=" C ILE A 144 " ideal model delta sigma weight residual 113.53 109.32 4.21 9.80e-01 1.04e+00 1.85e+01 angle pdb=" N ARG A 493 " pdb=" CA ARG A 493 " pdb=" C ARG A 493 " ideal model delta sigma weight residual 108.24 112.86 -4.62 1.32e+00 5.74e-01 1.22e+01 angle pdb=" CA ILE B1256 " pdb=" C ILE B1256 " pdb=" N PRO B1257 " ideal model delta sigma weight residual 120.83 118.84 1.99 6.10e-01 2.69e+00 1.06e+01 angle pdb=" CA ILE A1256 " pdb=" C ILE A1256 " pdb=" N PRO A1257 " ideal model delta sigma weight residual 120.83 118.87 1.96 6.10e-01 2.69e+00 1.03e+01 angle pdb=" N SER A1695 " pdb=" CA SER A1695 " pdb=" C SER A1695 " ideal model delta sigma weight residual 114.56 110.63 3.93 1.27e+00 6.20e-01 9.60e+00 ... (remaining 42144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 17896 17.36 - 34.72: 460 34.72 - 52.07: 130 52.07 - 69.43: 13 69.43 - 86.79: 4 Dihedral angle restraints: 18503 sinusoidal: 3600 harmonic: 14903 Sorted by residual: dihedral pdb=" N LYS B2363 " pdb=" CA LYS B2363 " pdb=" CB LYS B2363 " pdb=" CG LYS B2363 " ideal model delta sinusoidal sigma weight residual -60.00 -119.80 59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS A2363 " pdb=" CA LYS A2363 " pdb=" CB LYS A2363 " pdb=" CG LYS A2363 " ideal model delta sinusoidal sigma weight residual -60.00 -118.89 58.89 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASP A2708 " pdb=" CA ASP A2708 " pdb=" CB ASP A2708 " pdb=" CG ASP A2708 " ideal model delta sinusoidal sigma weight residual 60.00 118.32 -58.32 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 18500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2944 0.027 - 0.054: 1788 0.054 - 0.081: 481 0.081 - 0.108: 164 0.108 - 0.135: 28 Chirality restraints: 5405 Sorted by residual: chirality pdb=" CA ILE A2669 " pdb=" N ILE A2669 " pdb=" C ILE A2669 " pdb=" CB ILE A2669 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE B2669 " pdb=" N ILE B2669 " pdb=" C ILE B2669 " pdb=" CB ILE B2669 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CB ILE B3040 " pdb=" CA ILE B3040 " pdb=" CG1 ILE B3040 " pdb=" CG2 ILE B3040 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 5402 not shown) Planarity restraints: 5733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A2221 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A2222 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A2222 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A2222 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B2517 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B2518 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B2518 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B2518 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B2221 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B2222 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B2222 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B2222 " 0.017 5.00e-02 4.00e+02 ... (remaining 5730 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6715 2.77 - 3.30: 29639 3.30 - 3.84: 49180 3.84 - 4.37: 48154 4.37 - 4.90: 84621 Nonbonded interactions: 218309 Sorted by model distance: nonbonded pdb=" O LEU B2212 " pdb=" OG SER B2215 " model vdw 2.240 2.440 nonbonded pdb=" O LEU A2212 " pdb=" OG SER A2215 " model vdw 2.240 2.440 nonbonded pdb=" O GLN A2133 " pdb=" NH1 ARG A2138 " model vdw 2.268 2.520 nonbonded pdb=" O GLN B2133 " pdb=" NH1 ARG B2138 " model vdw 2.269 2.520 nonbonded pdb=" ND2 ASN A2782 " pdb=" OD1 ASP A2785 " model vdw 2.285 2.520 ... (remaining 218304 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' and (resid 2 through 129 or resid 142 through 3054)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 5.170 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 90.340 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 : 0.001 0.020 30759 Z= 0.095 Angle : 0.487 6.947 42149 Z= 0.295 Chirality : 0.037 0.135 5405 Planarity : 0.002 0.030 5733 Dihedral : 9.309 86.788 8677 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.95 % Allowed : 12.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.11 (0.10), residues: 4951 helix: -1.24 (0.08), residues: 3098 sheet: -0.32 (0.66), residues: 62 loop : -3.55 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B3052 HIS 0.002 0.000 HIS A2555 PHE 0.005 0.000 PHE B2558 TYR 0.005 0.000 TYR A2334 ARG 0.002 0.000 ARG B2339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 512 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2147 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7914 (tt) REVERT: A 2148 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8968 (mmtm) REVERT: A 2179 ILE cc_start: 0.8609 (tt) cc_final: 0.8349 (tp) REVERT: A 2216 ASP cc_start: 0.6502 (p0) cc_final: 0.6273 (p0) REVERT: A 2257 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: A 2313 LYS cc_start: 0.9067 (mttt) cc_final: 0.8588 (mmmm) REVERT: A 2317 LYS cc_start: 0.9095 (tppt) cc_final: 0.8808 (mmpt) REVERT: A 2384 MET cc_start: 0.8345 (tpt) cc_final: 0.7877 (tpt) REVERT: A 2565 ASN cc_start: 0.8280 (m110) cc_final: 0.8074 (m110) REVERT: A 2607 CYS cc_start: 0.8852 (t) cc_final: 0.8592 (p) REVERT: A 2700 LYS cc_start: 0.8554 (mppt) cc_final: 0.8303 (tppt) REVERT: A 2799 PHE cc_start: 0.9117 (m-80) cc_final: 0.8656 (m-80) REVERT: A 2862 VAL cc_start: 0.9171 (t) cc_final: 0.8895 (m) REVERT: A 2909 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7765 (tpp-160) REVERT: A 2913 ASP cc_start: 0.7947 (m-30) cc_final: 0.7536 (p0) REVERT: A 2950 GLU cc_start: 0.8051 (pt0) cc_final: 0.7698 (tp30) REVERT: A 2958 PHE cc_start: 0.7497 (p90) cc_final: 0.7257 (p90) REVERT: A 2959 ASP cc_start: 0.8745 (t0) cc_final: 0.8308 (p0) REVERT: A 2969 TYR cc_start: 0.9240 (p90) cc_final: 0.8930 (p90) REVERT: A 3007 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9164 (mm-30) REVERT: B 2147 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8290 (tt) REVERT: B 2179 ILE cc_start: 0.8801 (tt) cc_final: 0.8601 (tp) REVERT: B 2216 ASP cc_start: 0.6189 (p0) cc_final: 0.5989 (p0) REVERT: B 2313 LYS cc_start: 0.8991 (mttt) cc_final: 0.8504 (mmtm) REVERT: B 2317 LYS cc_start: 0.8941 (tppt) cc_final: 0.8573 (mmtm) REVERT: B 2347 GLU cc_start: 0.7866 (pt0) cc_final: 0.7516 (tm-30) REVERT: B 2384 MET cc_start: 0.8472 (tpt) cc_final: 0.8111 (tpt) REVERT: B 2479 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 2481 ASP cc_start: 0.8516 (m-30) cc_final: 0.7838 (m-30) REVERT: B 2565 ASN cc_start: 0.8424 (m110) cc_final: 0.8198 (m110) REVERT: B 2607 CYS cc_start: 0.9039 (t) cc_final: 0.8726 (p) REVERT: B 2616 MET cc_start: 0.8720 (ppp) cc_final: 0.8447 (ppp) REVERT: B 2630 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9181 (mt) REVERT: B 2640 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 2700 LYS cc_start: 0.8775 (mppt) cc_final: 0.8371 (tppt) REVERT: B 2727 VAL cc_start: 0.7490 (m) cc_final: 0.6906 (m) REVERT: B 2734 MET cc_start: 0.8775 (mmm) cc_final: 0.8128 (mmm) REVERT: B 2742 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8030 (t0) REVERT: B 2862 VAL cc_start: 0.9178 (t) cc_final: 0.8828 (m) REVERT: B 2873 VAL cc_start: 0.9038 (m) cc_final: 0.8744 (t) REVERT: B 2906 VAL cc_start: 0.8879 (t) cc_final: 0.8671 (p) REVERT: B 2913 ASP cc_start: 0.8061 (m-30) cc_final: 0.7509 (p0) REVERT: B 2950 GLU cc_start: 0.8073 (pt0) cc_final: 0.7799 (tp30) REVERT: B 2958 PHE cc_start: 0.7558 (p90) cc_final: 0.6945 (p90) REVERT: B 2959 ASP cc_start: 0.8725 (t0) cc_final: 0.8287 (p0) REVERT: B 2969 TYR cc_start: 0.9222 (p90) cc_final: 0.8814 (p90) REVERT: B 3007 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9125 (mm-30) REVERT: B 3017 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8518 (pp) outliers start: 75 outliers final: 16 residues processed: 557 average time/residue: 0.4062 time to fit residues: 362.3016 Evaluate side-chains 392 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 367 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 2.9990 chunk 386 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 132 optimal weight: 0.0770 chunk 260 optimal weight: 40.0000 chunk 206 optimal weight: 0.9990 chunk 399 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 463 optimal weight: 1.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2177 GLN A2195 HIS A2254 HIS ** A2282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 GLN A2397 GLN A2399 GLN A2469 ASN A2494 ASN ** A2542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2896 GLN ** A2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2971 GLN A3014 GLN A3033 ASN B2177 GLN B2195 HIS B2254 HIS B2282 ASN B2397 GLN B2399 GLN B2469 ASN B2494 ASN ** B2542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2641 GLN ** B2673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2724 GLN ** B2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2896 GLN B2971 GLN B3014 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 30759 Z= 0.137 Angle : 0.493 10.031 42149 Z= 0.252 Chirality : 0.039 0.217 5405 Planarity : 0.002 0.034 5733 Dihedral : 2.661 13.794 5191 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4951 helix: 0.05 (0.09), residues: 3124 sheet: 0.53 (0.69), residues: 58 loop : -3.03 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B2205 HIS 0.003 0.001 HIS A2552 PHE 0.016 0.001 PHE B2189 TYR 0.022 0.001 TYR A2514 ARG 0.011 0.001 ARG B2723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2148 LYS cc_start: 0.9272 (mmtt) cc_final: 0.8976 (mmtm) REVERT: A 2179 ILE cc_start: 0.8853 (tt) cc_final: 0.8518 (tp) REVERT: A 2216 ASP cc_start: 0.7155 (p0) cc_final: 0.6854 (p0) REVERT: A 2306 SER cc_start: 0.8386 (m) cc_final: 0.8061 (p) REVERT: A 2384 MET cc_start: 0.8944 (tpt) cc_final: 0.8691 (tpt) REVERT: A 2509 MET cc_start: 0.8269 (mpp) cc_final: 0.7413 (ppp) REVERT: A 2565 ASN cc_start: 0.8517 (m110) cc_final: 0.8273 (m110) REVERT: A 2616 MET cc_start: 0.8953 (ppp) cc_final: 0.8706 (ppp) REVERT: A 2638 TRP cc_start: 0.7807 (t60) cc_final: 0.7496 (t60) REVERT: A 2728 MET cc_start: 0.8910 (ptm) cc_final: 0.8636 (tmm) REVERT: A 2734 MET cc_start: 0.8816 (mmm) cc_final: 0.8097 (mmm) REVERT: A 2743 THR cc_start: 0.8512 (t) cc_final: 0.7889 (t) REVERT: A 2799 PHE cc_start: 0.9136 (m-80) cc_final: 0.8623 (m-80) REVERT: A 2862 VAL cc_start: 0.9120 (t) cc_final: 0.8755 (p) REVERT: A 2885 LEU cc_start: 0.8795 (mt) cc_final: 0.8542 (mt) REVERT: A 2913 ASP cc_start: 0.8361 (m-30) cc_final: 0.7806 (p0) REVERT: A 2935 MET cc_start: 0.9109 (tpt) cc_final: 0.8200 (tpp) REVERT: A 2938 MET cc_start: 0.8804 (pmm) cc_final: 0.8509 (pmm) REVERT: A 2950 GLU cc_start: 0.8427 (pt0) cc_final: 0.7666 (tp30) REVERT: A 2958 PHE cc_start: 0.6909 (p90) cc_final: 0.6620 (p90) REVERT: A 2960 TRP cc_start: 0.7431 (p-90) cc_final: 0.7126 (p-90) REVERT: A 3011 MET cc_start: 0.9057 (tpp) cc_final: 0.8484 (tmm) REVERT: B 2216 ASP cc_start: 0.6480 (p0) cc_final: 0.6194 (p0) REVERT: B 2224 MET cc_start: 0.9021 (mmp) cc_final: 0.8752 (mmm) REVERT: B 2276 PHE cc_start: 0.6876 (m-80) cc_final: 0.6249 (m-80) REVERT: B 2347 GLU cc_start: 0.8325 (pt0) cc_final: 0.8002 (tm-30) REVERT: B 2384 MET cc_start: 0.8557 (tpt) cc_final: 0.8183 (tpt) REVERT: B 2509 MET cc_start: 0.7899 (ppp) cc_final: 0.7630 (ppp) REVERT: B 2565 ASN cc_start: 0.8583 (m110) cc_final: 0.8232 (m110) REVERT: B 2607 CYS cc_start: 0.8816 (t) cc_final: 0.8583 (p) REVERT: B 2616 MET cc_start: 0.8887 (ppp) cc_final: 0.8677 (ppp) REVERT: B 2621 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 2638 TRP cc_start: 0.7943 (t60) cc_final: 0.7524 (t60) REVERT: B 2672 ASP cc_start: 0.7279 (m-30) cc_final: 0.6920 (t0) REVERT: B 2721 ASP cc_start: 0.7996 (t0) cc_final: 0.7725 (t0) REVERT: B 2734 MET cc_start: 0.8928 (mmm) cc_final: 0.8302 (mmm) REVERT: B 2862 VAL cc_start: 0.9262 (t) cc_final: 0.8888 (p) REVERT: B 2913 ASP cc_start: 0.8194 (m-30) cc_final: 0.7850 (p0) REVERT: B 2935 MET cc_start: 0.9106 (tpt) cc_final: 0.8494 (tpp) REVERT: B 2946 LEU cc_start: 0.9138 (pp) cc_final: 0.8642 (tt) REVERT: B 2950 GLU cc_start: 0.8343 (pt0) cc_final: 0.7797 (tp30) REVERT: B 2960 TRP cc_start: 0.7213 (p-90) cc_final: 0.6826 (p-90) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.3851 time to fit residues: 254.0562 Evaluate side-chains 315 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 315 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 463 optimal weight: 0.9990 chunk 501 optimal weight: 0.6980 chunk 413 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 372 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2197 GLN A2297 GLN A2343 ASN A2399 GLN A2403 ASN ** A2542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2641 GLN A2724 GLN ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2197 GLN B2292 GLN B2343 ASN B2399 GLN B2403 ASN ** B2469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2538 HIS ** B2542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2552 HIS B2673 HIS B2684 GLN B2724 GLN ** B2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30759 Z= 0.171 Angle : 0.497 9.556 42149 Z= 0.261 Chirality : 0.039 0.217 5405 Planarity : 0.002 0.043 5733 Dihedral : 2.902 14.893 5191 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4951 helix: 0.89 (0.10), residues: 3145 sheet: 0.48 (0.67), residues: 60 loop : -2.66 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B2205 HIS 0.004 0.001 HIS B2673 PHE 0.019 0.001 PHE B2393 TYR 0.022 0.001 TYR B2514 ARG 0.007 0.001 ARG B2598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9902 Ramachandran restraints generated. 4951 Oldfield, 0 Emsley, 4951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2148 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8957 (mmtm) REVERT: A 2179 ILE cc_start: 0.8997 (tt) cc_final: 0.8731 (tp) REVERT: A 2216 ASP cc_start: 0.7424 (p0) cc_final: 0.7115 (p0) REVERT: A 2224 MET cc_start: 0.9229 (mmm) cc_final: 0.8999 (mmm) REVERT: A 2294 GLU cc_start: 0.7775 (pm20) cc_final: 0.7563 (mm-30) REVERT: A 2336 GLU cc_start: 0.9139 (pt0) cc_final: 0.8866 (pt0) REVERT: A 2384 MET cc_start: 0.9011 (tpt) cc_final: 0.8675 (tpt) REVERT: A 2393 PHE cc_start: 0.9376 (t80) cc_final: 0.9027 (t80) REVERT: A 2509 MET cc_start: 0.8240 (mpp) cc_final: 0.7344 (ppp) REVERT: A 2616 MET cc_start: 0.8994 (ppp) cc_final: 0.8696 (ppp) REVERT: A 2638 TRP cc_start: 0.7455 (t60) cc_final: 0.6718 (t60) REVERT: A 2672 ASP cc_start: 0.7659 (m-30) cc_final: 0.7064 (t0) REVERT: A 2684 GLN cc_start: 0.9530 (tm-30) cc_final: 0.9316 (tm-30) REVERT: A 2728 MET cc_start: 0.9111 (ptm) cc_final: 0.8512 (tmm) REVERT: A 2781 VAL cc_start: 0.9163 (m) cc_final: 0.8923 (p) REVERT: A 2799 PHE cc_start: 0.9132 (m-80) cc_final: 0.8600 (m-80) REVERT: A 2913 ASP cc_start: 0.8299 (m-30) cc_final: 0.7795 (p0) REVERT: A 2924 GLU cc_start: 0.9068 (mp0) cc_final: 0.8796 (mp0) REVERT: A 2935 MET cc_start: 0.9230 (tpt) cc_final: 0.8998 (tpt) REVERT: A 2950 GLU cc_start: 0.8573 (pt0) cc_final: 0.8220 (tp30) REVERT: A 2960 TRP cc_start: 0.7469 (p-90) cc_final: 0.7205 (p-90) REVERT: A 3011 MET cc_start: 0.9105 (tpp) cc_final: 0.8895 (tpp) REVERT: B 2156 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 2216 ASP cc_start: 0.7128 (p0) cc_final: 0.6761 (p0) REVERT: B 2277 GLN cc_start: 0.8651 (mp10) cc_final: 0.8021 (mp10) REVERT: B 2306 SER cc_start: 0.9149 (m) cc_final: 0.8929 (p) REVERT: B 2336 GLU cc_start: 0.9154 (pt0) cc_final: 0.8875 (pt0) REVERT: B 2347 GLU cc_start: 0.8385 (pt0) cc_final: 0.8169 (tm-30) REVERT: B 2384 MET cc_start: 0.9203 (tpt) cc_final: 0.8970 (tpt) REVERT: B 2393 PHE cc_start: 0.9425 (t80) cc_final: 0.9094 (t80) REVERT: B 2510 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7900 (ptpp) REVERT: B 2565 ASN cc_start: 0.8708 (m110) cc_final: 0.8369 (m110) REVERT: B 2616 MET cc_start: 0.9009 (ppp) cc_final: 0.8686 (ppp) REVERT: B 2621 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 2638 TRP cc_start: 0.8079 (t60) cc_final: 0.7708 (t60) REVERT: B 2672 ASP cc_start: 0.7473 (m-30) cc_final: 0.7245 (t0) REVERT: B 2700 LYS cc_start: 0.7958 (tppt) cc_final: 0.7714 (tppt) REVERT: B 2913 ASP cc_start: 0.8270 (m-30) cc_final: 0.7892 (p0) REVERT: B 2935 MET cc_start: 0.9284 (tpt) cc_final: 0.8178 (tpp) REVERT: B 2960 TRP cc_start: 0.7705 (p-90) cc_final: 0.7474 (p-90) outliers start: 1 outliers final: 1 residues processed: 375 average time/residue: 0.3624 time to fit residues: 228.0266 Evaluate side-chains 312 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 3.647 ------------------------------------------------------------------------------- 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 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) 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 368, 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 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) 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/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients 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: 53.7795 > 50: distance: 49 - 121: 10.487 distance: 51 - 58: 16.501 distance: 52 - 118: 26.705 distance: 58 - 59: 9.902 distance: 59 - 60: 22.515 distance: 59 - 62: 15.024 distance: 60 - 61: 23.953 distance: 60 - 66: 18.126 distance: 62 - 63: 43.791 distance: 63 - 64: 47.540 distance: 63 - 65: 36.232 distance: 66 - 67: 28.447 distance: 67 - 68: 13.740 distance: 67 - 70: 10.613 distance: 68 - 69: 17.129 distance: 68 - 71: 22.902 distance: 71 - 72: 14.235 distance: 72 - 73: 31.282 distance: 73 - 74: 12.718 distance: 73 - 75: 18.315 distance: 75 - 76: 27.927 distance: 76 - 77: 29.814 distance: 77 - 78: 22.041 distance: 77 - 79: 30.129 distance: 79 - 80: 23.985 distance: 80 - 81: 30.891 distance: 80 - 83: 18.241 distance: 81 - 82: 34.893 distance: 81 - 86: 15.618 distance: 83 - 84: 12.451 distance: 83 - 85: 12.526 distance: 86 - 87: 13.305 distance: 87 - 88: 22.625 distance: 87 - 90: 8.953 distance: 88 - 89: 6.044 distance: 88 - 94: 34.433 distance: 90 - 91: 16.606 distance: 91 - 92: 23.774 distance: 91 - 93: 23.923 distance: 94 - 95: 30.687 distance: 95 - 96: 22.317 distance: 95 - 98: 16.344 distance: 96 - 97: 17.653 distance: 96 - 102: 26.293 distance: 98 - 99: 35.853 distance: 99 - 100: 21.367 distance: 99 - 101: 6.602 distance: 102 - 103: 4.609 distance: 102 - 108: 27.273 distance: 103 - 104: 6.985 distance: 103 - 106: 9.208 distance: 104 - 105: 3.703 distance: 104 - 109: 17.541 distance: 106 - 107: 18.843 distance: 107 - 108: 5.300 distance: 109 - 110: 21.878 distance: 109 - 155: 13.962 distance: 110 - 111: 14.441 distance: 110 - 113: 10.356 distance: 111 - 112: 7.513 distance: 111 - 118: 25.236 distance: 112 - 152: 3.781 distance: 113 - 114: 7.414 distance: 114 - 115: 11.304 distance: 115 - 116: 11.520 distance: 116 - 117: 23.036 distance: 118 - 119: 18.275 distance: 119 - 120: 17.267 distance: 119 - 122: 18.307 distance: 120 - 121: 15.939 distance: 120 - 126: 10.482 distance: 122 - 124: 8.164 distance: 123 - 125: 5.978