Starting phenix.real_space_refine on Mon Nov 20 16:28:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfc_12299/11_2023/7nfc_12299.pdb" } resolution = 4.14 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 110 5.49 5 S 533 5.16 5 C 56729 2.51 5 N 15030 2.21 5 O 16667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 89069 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 28076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3562, 28076 Classifications: {'peptide': 3562} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 147, 'TRANS': 3414} Chain breaks: 34 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'UNK:plan-1': 19, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 322 Chain: "B" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3822 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 448} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3849 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 20, 'TRANS': 456} Chain breaks: 5 Chain: "F" Number of atoms: 28060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3557, 28060 Classifications: {'peptide': 3557} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 147, 'TRANS': 3409} Chain breaks: 35 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 428 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'UNK:plan-1': 19, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 321 Chain: "G" Number of atoms: 3948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3948 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain breaks: 1 Chain: "H" Number of atoms: 5150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5150 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 612} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1625 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 197} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1592 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2095 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 247} Chain: "N" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1625 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 197} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1579 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1965 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1690 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "R" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1728 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 556 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "E" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 576 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "I" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 576 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Time building chain proxies: 34.47, per 1000 atoms: 0.39 Number of scatterers: 89069 At special positions: 0 Unit cell: (239.936, 260.8, 312.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 533 16.00 P 110 15.00 O 16667 8.00 N 15030 7.00 C 56729 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: 30.78 Conformation dependent library (CDL) restraints added in 11.6 seconds 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20994 Finding SS restraints... Secondary structure from input PDB file: 535 helices and 40 sheets defined 64.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 51 through 70 removed outlier: 3.785A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 94 removed outlier: 4.163A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.847A pdb=" N VAL A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.563A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 172 through 179 removed outlier: 4.172A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 4.587A pdb=" N GLU A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.657A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 4.187A pdb=" N THR A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 333 through 349 removed outlier: 4.921A pdb=" N MET A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 376 removed outlier: 3.600A pdb=" N ALA A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 4.000A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.736A pdb=" N VAL A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 450 through 469 Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 526 through 536 removed outlier: 3.917A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 547 removed outlier: 4.558A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 616 through 634 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.609A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.875A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.714A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.793A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.629A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 4.002A pdb=" N MET A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 798 removed outlier: 4.122A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 840 removed outlier: 3.632A pdb=" N LEU A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.989A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 906 through 909 removed outlier: 3.574A pdb=" N VAL A 909 " --> pdb=" O PHE A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 923 through 944 Processing helix chain 'A' and resid 959 through 974 Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 978 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.626A pdb=" N LEU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 Processing helix chain 'A' and resid 1045 through 1052 removed outlier: 3.610A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1069 Processing helix chain 'A' and resid 1071 through 1090 removed outlier: 4.460A pdb=" N ARG A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1099 Processing helix chain 'A' and resid 1100 through 1116 Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1142 through 1147 Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.520A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1198 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1205 through 1215 removed outlier: 3.637A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1223 removed outlier: 3.659A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 4.243A pdb=" N LEU A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1273 Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.590A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1277 through 1282' Processing helix chain 'A' and resid 1287 through 1300 removed outlier: 3.817A pdb=" N LEU A1291 " --> pdb=" O GLN A1287 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A1298 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1352 Processing helix chain 'A' and resid 1353 through 1355 No H-bonds generated for 'chain 'A' and resid 1353 through 1355' Processing helix chain 'A' and resid 1356 through 1361 removed outlier: 3.609A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1367 through 1378 Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.650A pdb=" N ILE A1382 " --> pdb=" O PRO A1379 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A1383 " --> pdb=" O ALA A1380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1379 through 1383' Processing helix chain 'A' and resid 1389 through 1409 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 4.054A pdb=" N GLU A1430 " --> pdb=" O GLN A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1461 Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 5.034A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1492 No H-bonds generated for 'chain 'A' and resid 1490 through 1492' Processing helix chain 'A' and resid 1504 through 1520 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 4.185A pdb=" N ARG A1527 " --> pdb=" O GLY A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.666A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1586 Processing helix chain 'A' and resid 1590 through 1607 Processing helix chain 'A' and resid 1612 through 1625 Processing helix chain 'A' and resid 1626 through 1629 removed outlier: 3.774A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1626 through 1629' Processing helix chain 'A' and resid 1638 through 1656 Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.539A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1695 removed outlier: 3.619A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1699 Processing helix chain 'A' and resid 1708 through 1722 Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 3.979A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1806 removed outlier: 4.100A pdb=" N ARG A1806 " --> pdb=" O TYR A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1831 removed outlier: 4.205A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR A1826 " --> pdb=" O ARG A1822 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1843 removed outlier: 3.941A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 4.060A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A1852 " --> pdb=" O ILE A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1884 removed outlier: 4.386A pdb=" N VAL A1879 " --> pdb=" O LYS A1875 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1884 " --> pdb=" O MET A1880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1924 removed outlier: 3.769A pdb=" N LEU A1915 " --> pdb=" O LEU A1911 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1953 Processing helix chain 'A' and resid 2093 through 2108 removed outlier: 4.223A pdb=" N LEU A2097 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2135 removed outlier: 3.623A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2154 through 2159 removed outlier: 4.091A pdb=" N ARG A2158 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Proline residue: A2159 - end of helix Processing helix chain 'A' and resid 2160 through 2173 removed outlier: 5.002A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2181 through 2194 Processing helix chain 'A' and resid 2205 through 2223 removed outlier: 3.500A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2245 removed outlier: 3.769A pdb=" N TRP A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2262 removed outlier: 3.905A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2282 Processing helix chain 'A' and resid 2300 through 2309 removed outlier: 3.587A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2329 removed outlier: 3.856A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2330 through 2333 Processing helix chain 'A' and resid 2338 through 2351 Processing helix chain 'A' and resid 2359 through 2371 removed outlier: 3.744A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 3.645A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2403 removed outlier: 3.564A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2410 removed outlier: 4.523A pdb=" N GLY A2407 " --> pdb=" O ARG A2404 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET A2408 " --> pdb=" O VAL A2405 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A2409 " --> pdb=" O GLU A2406 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A2410 " --> pdb=" O GLY A2407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2404 through 2410' Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.656A pdb=" N HIS A2426 " --> pdb=" O GLN A2422 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.819A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2466 through 2485 Processing helix chain 'A' and resid 2492 through 2510 Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2543 removed outlier: 3.713A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2564 Processing helix chain 'A' and resid 2565 through 2569 removed outlier: 3.838A pdb=" N MET A2568 " --> pdb=" O MET A2565 " (cutoff:3.500A) Processing helix chain 'A' and resid 2723 through 2731 removed outlier: 3.515A pdb=" N ARG A2731 " --> pdb=" O ARG A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2732 through 2735 removed outlier: 3.636A pdb=" N ASP A2735 " --> pdb=" O PHE A2732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2732 through 2735' Processing helix chain 'A' and resid 2737 through 2765 removed outlier: 3.895A pdb=" N GLN A2765 " --> pdb=" O LEU A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2821 through 2824 removed outlier: 3.593A pdb=" N LYS A2824 " --> pdb=" O ASP A2821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2821 through 2824' Processing helix chain 'A' and resid 2825 through 2847 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.924A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2866 through 2870 removed outlier: 4.183A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 removed outlier: 3.671A pdb=" N VAL A2876 " --> pdb=" O ASP A2872 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2901 Processing helix chain 'A' and resid 2919 through 2933 removed outlier: 3.517A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2945 removed outlier: 3.794A pdb=" N ARG A2940 " --> pdb=" O TYR A2936 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.779A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2977 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3016 Processing helix chain 'A' and resid 3034 through 3054 Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3059 through 3070 removed outlier: 3.936A pdb=" N HIS A3070 " --> pdb=" O ASP A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3072 through 3082 Processing helix chain 'A' and resid 3082 through 3093 Processing helix chain 'A' and resid 3095 through 3117 Processing helix chain 'A' and resid 3121 through 3144 removed outlier: 3.876A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) Processing helix chain 'A' and resid 3149 through 3153 Processing helix chain 'A' and resid 3155 through 3162 removed outlier: 4.492A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3162 through 3168 removed outlier: 4.176A pdb=" N ARG A3167 " --> pdb=" O THR A3163 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A3168 " --> pdb=" O TRP A3164 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 4.137A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3249 Processing helix chain 'A' and resid 3255 through 3267 removed outlier: 3.941A pdb=" N LYS A3267 " --> pdb=" O HIS A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3287 Processing helix chain 'A' and resid 3291 through 3299 Processing helix chain 'A' and resid 3300 through 3308 Processing helix chain 'A' and resid 3309 through 3311 No H-bonds generated for 'chain 'A' and resid 3309 through 3311' Processing helix chain 'A' and resid 3319 through 3344 removed outlier: 3.737A pdb=" N PHE A3323 " --> pdb=" O ASN A3319 " (cutoff:3.500A) Processing helix chain 'A' and resid 3347 through 3352 Processing helix chain 'A' and resid 3355 through 3364 removed outlier: 3.969A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3394 removed outlier: 3.550A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3408 through 3427 Processing helix chain 'A' and resid 3442 through 3456 removed outlier: 3.789A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3475 Processing helix chain 'A' and resid 3475 through 3483 removed outlier: 3.965A pdb=" N THR A3479 " --> pdb=" O TYR A3475 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A3481 " --> pdb=" O GLU A3477 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.752A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3525 removed outlier: 3.884A pdb=" N GLN A3515 " --> pdb=" O ALA A3511 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3537 Processing helix chain 'A' and resid 3547 through 3562 removed outlier: 4.142A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A3552 " --> pdb=" O GLY A3548 " (cutoff:3.500A) Processing helix chain 'A' and resid 3565 through 3579 Processing helix chain 'A' and resid 3580 through 3597 removed outlier: 3.769A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A3590 " --> pdb=" O LYS A3586 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A3591 " --> pdb=" O ASP A3587 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A3592 " --> pdb=" O TRP A3588 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG A3593 " --> pdb=" O SER A3589 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3618 Processing helix chain 'A' and resid 3627 through 3644 removed outlier: 3.835A pdb=" N GLN A3634 " --> pdb=" O ARG A3630 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS A3638 " --> pdb=" O GLN A3634 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A3639 " --> pdb=" O THR A3635 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A3643 " --> pdb=" O GLU A3639 " (cutoff:3.500A) Processing helix chain 'A' and resid 3658 through 3670 removed outlier: 3.531A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A3670 " --> pdb=" O LEU A3666 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3689 removed outlier: 3.934A pdb=" N SER A3688 " --> pdb=" O SER A3684 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A3689 " --> pdb=" O PRO A3685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3684 through 3689' Processing helix chain 'A' and resid 3758 through 3777 Processing helix chain 'A' and resid 3778 through 3784 Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3821 through 3831 removed outlier: 4.067A pdb=" N LEU A3829 " --> pdb=" O LYS A3825 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A3831 " --> pdb=" O ALA A3827 " (cutoff:3.500A) Processing helix chain 'A' and resid 3833 through 3839 removed outlier: 4.345A pdb=" N CYS A3837 " --> pdb=" O ARG A3833 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3861 Processing helix chain 'A' and resid 3863 through 3878 Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3991 Processing helix chain 'A' and resid 3992 through 3996 Proline residue: A3995 - end of helix No H-bonds generated for 'chain 'A' and resid 3992 through 3996' Processing helix chain 'A' and resid 3997 through 4003 Processing helix chain 'A' and resid 4039 through 4053 removed outlier: 3.973A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4066 Processing helix chain 'A' and resid 4073 through 4082 Processing helix chain 'A' and resid 4085 through 4090 Processing helix chain 'A' and resid 4091 through 4093 No H-bonds generated for 'chain 'A' and resid 4091 through 4093' Processing helix chain 'A' and resid 4099 through 4111 Processing helix chain 'A' and resid 4112 through 4119 removed outlier: 3.682A pdb=" N ILE A4116 " --> pdb=" O THR A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 6005 through 6019 Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 142 through 156 Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.897A pdb=" N ASP B 219 " --> pdb=" O PHE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.041A pdb=" N LYS B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.707A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 388 removed outlier: 3.842A pdb=" N LYS B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.701A pdb=" N LYS B 443 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.944A pdb=" N GLU B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 87 through 98 removed outlier: 3.695A pdb=" N ILE C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 125 removed outlier: 3.583A pdb=" N ALA C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 199 through 217 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.514A pdb=" N ASP C 288 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 332 Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.578A pdb=" N LEU C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 445 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 484 through 500 removed outlier: 3.785A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 517 removed outlier: 4.490A pdb=" N MET C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 4.175A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'F' and resid 11 through 22 Processing helix chain 'F' and resid 27 through 46 Processing helix chain 'F' and resid 51 through 70 removed outlier: 3.943A pdb=" N VAL F 58 " --> pdb=" O GLN F 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 94 removed outlier: 4.026A pdb=" N CYS F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 Proline residue: F 102 - end of helix Processing helix chain 'F' and resid 103 through 117 Processing helix chain 'F' and resid 117 through 122 removed outlier: 4.115A pdb=" N ALA F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 141 Processing helix chain 'F' and resid 149 through 161 Processing helix chain 'F' and resid 168 through 172 Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 186 through 209 removed outlier: 3.617A pdb=" N ASN F 195 " --> pdb=" O ASN F 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 232 removed outlier: 3.740A pdb=" N LEU F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY F 222 " --> pdb=" O PRO F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.058A pdb=" N THR F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.635A pdb=" N SER F 269 " --> pdb=" O TYR F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 289 through 301 Processing helix chain 'F' and resid 305 through 329 removed outlier: 3.834A pdb=" N LYS F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 349 removed outlier: 4.379A pdb=" N ASN F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET F 342 " --> pdb=" O LEU F 338 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU F 343 " --> pdb=" O GLN F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 376 removed outlier: 3.608A pdb=" N ALA F 370 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Proline residue: F 372 - end of helix removed outlier: 3.744A pdb=" N VAL F 375 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 395 removed outlier: 4.424A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE F 383 " --> pdb=" O LYS F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 424 Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 431 through 445 Processing helix chain 'F' and resid 450 through 469 Processing helix chain 'F' and resid 471 through 493 removed outlier: 3.643A pdb=" N LYS F 493 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 536 removed outlier: 3.996A pdb=" N LEU F 530 " --> pdb=" O ASP F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 547 removed outlier: 4.523A pdb=" N SER F 543 " --> pdb=" O GLN F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 579 Processing helix chain 'F' and resid 616 through 634 Processing helix chain 'F' and resid 644 through 660 removed outlier: 4.722A pdb=" N SER F 648 " --> pdb=" O PRO F 644 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER F 650 " --> pdb=" O VAL F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 680 removed outlier: 3.996A pdb=" N TYR F 667 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 680 " --> pdb=" O ASN F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 718 Processing helix chain 'F' and resid 719 through 721 No H-bonds generated for 'chain 'F' and resid 719 through 721' Processing helix chain 'F' and resid 725 through 735 Processing helix chain 'F' and resid 737 through 742 removed outlier: 3.678A pdb=" N ILE F 741 " --> pdb=" O PRO F 737 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 742 " --> pdb=" O HIS F 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 737 through 742' Processing helix chain 'F' and resid 743 through 747 removed outlier: 6.107A pdb=" N ARG F 746 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 759 Processing helix chain 'F' and resid 762 through 780 Processing helix chain 'F' and resid 781 through 786 removed outlier: 3.971A pdb=" N MET F 785 " --> pdb=" O ASP F 781 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 793 Processing helix chain 'F' and resid 794 through 798 removed outlier: 3.756A pdb=" N GLY F 798 " --> pdb=" O CYS F 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 848 through 863 removed outlier: 3.628A pdb=" N GLY F 863 " --> pdb=" O LEU F 859 " (cutoff:3.500A) Processing helix chain 'F' and resid 863 through 868 Processing helix chain 'F' and resid 869 through 871 No H-bonds generated for 'chain 'F' and resid 869 through 871' Processing helix chain 'F' and resid 910 through 920 Processing helix chain 'F' and resid 923 through 944 Processing helix chain 'F' and resid 945 through 947 No H-bonds generated for 'chain 'F' and resid 945 through 947' Processing helix chain 'F' and resid 958 through 974 Proline residue: F 967 - end of helix removed outlier: 3.583A pdb=" N CYS F 974 " --> pdb=" O LEU F 970 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 995 removed outlier: 3.521A pdb=" N ARG F 981 " --> pdb=" O ASP F 977 " (cutoff:3.500A) Proline residue: F 986 - end of helix Processing helix chain 'F' and resid 1004 through 1017 removed outlier: 4.293A pdb=" N GLY F1016 " --> pdb=" O ALA F1012 " (cutoff:3.500A) Processing helix chain 'F' and resid 1022 through 1044 Processing helix chain 'F' and resid 1045 through 1052 Processing helix chain 'F' and resid 1055 through 1069 Processing helix chain 'F' and resid 1071 through 1090 removed outlier: 4.562A pdb=" N ARG F1087 " --> pdb=" O ASN F1083 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU F1088 " --> pdb=" O ASN F1084 " (cutoff:3.500A) Processing helix chain 'F' and resid 1092 through 1099 removed outlier: 3.509A pdb=" N VAL F1096 " --> pdb=" O GLU F1092 " (cutoff:3.500A) Processing helix chain 'F' and resid 1100 through 1116 Processing helix chain 'F' and resid 1122 through 1141 Processing helix chain 'F' and resid 1142 through 1147 Processing helix chain 'F' and resid 1164 through 1175 Processing helix chain 'F' and resid 1180 through 1195 Processing helix chain 'F' and resid 1205 through 1215 removed outlier: 4.122A pdb=" N GLU F1214 " --> pdb=" O ASP F1210 " (cutoff:3.500A) Processing helix chain 'F' and resid 1217 through 1222 removed outlier: 3.930A pdb=" N ILE F1221 " --> pdb=" O VAL F1217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1231 through 1237 removed outlier: 3.841A pdb=" N ILE F1235 " --> pdb=" O GLN F1231 " (cutoff:3.500A) Processing helix chain 'F' and resid 1250 through 1273 Processing helix chain 'F' and resid 1277 through 1282 removed outlier: 3.783A pdb=" N VAL F1281 " --> pdb=" O GLY F1277 " (cutoff:3.500A) Processing helix chain 'F' and resid 1287 through 1301 removed outlier: 4.057A pdb=" N LEU F1291 " --> pdb=" O GLN F1287 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F1298 " --> pdb=" O VAL F1294 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F1299 " --> pdb=" O ALA F1295 " (cutoff:3.500A) Processing helix chain 'F' and resid 1326 through 1352 removed outlier: 3.562A pdb=" N TYR F1330 " --> pdb=" O GLU F1326 " (cutoff:3.500A) Processing helix chain 'F' and resid 1353 through 1356 Processing helix chain 'F' and resid 1357 through 1362 removed outlier: 3.522A pdb=" N ASP F1362 " --> pdb=" O LEU F1358 " (cutoff:3.500A) Processing helix chain 'F' and resid 1367 through 1378 removed outlier: 3.691A pdb=" N VAL F1371 " --> pdb=" O HIS F1367 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F1373 " --> pdb=" O MET F1369 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN F1374 " --> pdb=" O ARG F1370 " (cutoff:3.500A) Processing helix chain 'F' and resid 1379 through 1383 Processing helix chain 'F' and resid 1389 through 1409 Proline residue: F1396 - end of helix Processing helix chain 'F' and resid 1411 through 1423 Processing helix chain 'F' and resid 1442 through 1461 Processing helix chain 'F' and resid 1476 through 1489 removed outlier: 4.954A pdb=" N GLU F1482 " --> pdb=" O SER F1478 " (cutoff:3.500A) Processing helix chain 'F' and resid 1490 through 1492 No H-bonds generated for 'chain 'F' and resid 1490 through 1492' Processing helix chain 'F' and resid 1504 through 1521 Processing helix chain 'F' and resid 1523 through 1533 removed outlier: 3.814A pdb=" N ARG F1527 " --> pdb=" O GLY F1523 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU F1533 " --> pdb=" O VAL F1529 " (cutoff:3.500A) Processing helix chain 'F' and resid 1554 through 1563 Processing helix chain 'F' and resid 1563 through 1574 removed outlier: 3.776A pdb=" N LYS F1573 " --> pdb=" O THR F1569 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F1574 " --> pdb=" O GLU F1570 " (cutoff:3.500A) Processing helix chain 'F' and resid 1576 through 1585 Processing helix chain 'F' and resid 1586 through 1588 No H-bonds generated for 'chain 'F' and resid 1586 through 1588' Processing helix chain 'F' and resid 1590 through 1607 Processing helix chain 'F' and resid 1612 through 1625 Processing helix chain 'F' and resid 1626 through 1629 removed outlier: 4.111A pdb=" N CYS F1629 " --> pdb=" O TRP F1626 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1626 through 1629' Processing helix chain 'F' and resid 1638 through 1656 Processing helix chain 'F' and resid 1667 through 1681 removed outlier: 3.626A pdb=" N VAL F1671 " --> pdb=" O SER F1667 " (cutoff:3.500A) Processing helix chain 'F' and resid 1685 through 1694 Processing helix chain 'F' and resid 1695 through 1699 Processing helix chain 'F' and resid 1708 through 1722 removed outlier: 3.569A pdb=" N PHE F1722 " --> pdb=" O ILE F1718 " (cutoff:3.500A) Processing helix chain 'F' and resid 1733 through 1754 Processing helix chain 'F' and resid 1755 through 1767 Processing helix chain 'F' and resid 1774 through 1787 removed outlier: 3.601A pdb=" N PHE F1778 " --> pdb=" O MET F1774 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG F1787 " --> pdb=" O ARG F1783 " (cutoff:3.500A) Processing helix chain 'F' and resid 1790 through 1804 Processing helix chain 'F' and resid 1816 through 1831 removed outlier: 3.976A pdb=" N VAL F1820 " --> pdb=" O ARG F1816 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU F1825 " --> pdb=" O ASP F1821 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR F1826 " --> pdb=" O ARG F1822 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS F1830 " --> pdb=" O THR F1826 " (cutoff:3.500A) Processing helix chain 'F' and resid 1834 through 1849 removed outlier: 3.622A pdb=" N GLU F1838 " --> pdb=" O ASP F1834 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL F1845 " --> pdb=" O SER F1841 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP F1846 " --> pdb=" O THR F1842 " (cutoff:3.500A) Processing helix chain 'F' and resid 1850 through 1852 No H-bonds generated for 'chain 'F' and resid 1850 through 1852' Processing helix chain 'F' and resid 1863 through 1884 removed outlier: 4.443A pdb=" N VAL F1879 " --> pdb=" O LYS F1875 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET F1880 " --> pdb=" O ILE F1876 " (cutoff:3.500A) Processing helix chain 'F' and resid 1910 through 1925 removed outlier: 3.927A pdb=" N THR F1914 " --> pdb=" O GLU F1910 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA F1922 " --> pdb=" O LEU F1918 " (cutoff:3.500A) Processing helix chain 'F' and resid 1935 through 1953 removed outlier: 3.678A pdb=" N CYS F1953 " --> pdb=" O ILE F1949 " (cutoff:3.500A) Processing helix chain 'F' and resid 2094 through 2108 Processing helix chain 'F' and resid 2125 through 2135 removed outlier: 3.767A pdb=" N ASN F2135 " --> pdb=" O GLY F2131 " (cutoff:3.500A) Processing helix chain 'F' and resid 2139 through 2153 Processing helix chain 'F' and resid 2157 through 2159 No H-bonds generated for 'chain 'F' and resid 2157 through 2159' Processing helix chain 'F' and resid 2160 through 2173 removed outlier: 5.610A pdb=" N SER F2166 " --> pdb=" O LYS F2162 " (cutoff:3.500A) Proline residue: F2167 - end of helix Processing helix chain 'F' and resid 2181 through 2196 removed outlier: 4.342A pdb=" N TRP F2196 " --> pdb=" O THR F2192 " (cutoff:3.500A) Processing helix chain 'F' and resid 2205 through 2223 Processing helix chain 'F' and resid 2229 through 2246 removed outlier: 3.548A pdb=" N LYS F2246 " --> pdb=" O VAL F2242 " (cutoff:3.500A) Processing helix chain 'F' and resid 2253 through 2261 Processing helix chain 'F' and resid 2270 through 2283 removed outlier: 3.563A pdb=" N ASN F2283 " --> pdb=" O ILE F2279 " (cutoff:3.500A) Processing helix chain 'F' and resid 2300 through 2309 Processing helix chain 'F' and resid 2312 through 2330 removed outlier: 3.756A pdb=" N TYR F2316 " --> pdb=" O TYR F2312 " (cutoff:3.500A) Processing helix chain 'F' and resid 2331 through 2334 Processing helix chain 'F' and resid 2338 through 2351 Processing helix chain 'F' and resid 2358 through 2369 removed outlier: 3.971A pdb=" N VAL F2362 " --> pdb=" O ASP F2358 " (cutoff:3.500A) Processing helix chain 'F' and resid 2371 through 2377 removed outlier: 3.533A pdb=" N LEU F2374 " --> pdb=" O PHE F2371 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F2376 " --> pdb=" O PRO F2373 " (cutoff:3.500A) Processing helix chain 'F' and resid 2378 through 2386 Processing helix chain 'F' and resid 2387 through 2389 No H-bonds generated for 'chain 'F' and resid 2387 through 2389' Processing helix chain 'F' and resid 2391 through 2403 removed outlier: 3.685A pdb=" N THR F2395 " --> pdb=" O GLY F2391 " (cutoff:3.500A) Processing helix chain 'F' and resid 2405 through 2410 removed outlier: 4.153A pdb=" N MET F2408 " --> pdb=" O VAL F2405 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F2409 " --> pdb=" O GLU F2406 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU F2410 " --> pdb=" O GLY F2407 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2405 through 2410' Processing helix chain 'F' and resid 2411 through 2418 Processing helix chain 'F' and resid 2419 through 2426 removed outlier: 3.640A pdb=" N VAL F2423 " --> pdb=" O ASP F2419 " (cutoff:3.500A) Processing helix chain 'F' and resid 2428 through 2443 Processing helix chain 'F' and resid 2444 through 2446 No H-bonds generated for 'chain 'F' and resid 2444 through 2446' Processing helix chain 'F' and resid 2447 through 2459 removed outlier: 3.817A pdb=" N GLU F2453 " --> pdb=" O VAL F2449 " (cutoff:3.500A) Proline residue: F2457 - end of helix Processing helix chain 'F' and resid 2460 through 2462 No H-bonds generated for 'chain 'F' and resid 2460 through 2462' Processing helix chain 'F' and resid 2466 through 2485 Processing helix chain 'F' and resid 2492 through 2510 Processing helix chain 'F' and resid 2514 through 2527 Processing helix chain 'F' and resid 2534 through 2545 removed outlier: 3.719A pdb=" N ASN F2543 " --> pdb=" O LEU F2539 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER F2544 " --> pdb=" O LEU F2540 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F2545 " --> pdb=" O ALA F2541 " (cutoff:3.500A) Processing helix chain 'F' and resid 2553 through 2565 removed outlier: 3.782A pdb=" N MET F2565 " --> pdb=" O PHE F2561 " (cutoff:3.500A) Processing helix chain 'F' and resid 2723 through 2731 Processing helix chain 'F' and resid 2737 through 2765 removed outlier: 3.522A pdb=" N LEU F2761 " --> pdb=" O ILE F2757 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F2765 " --> pdb=" O LEU F2761 " (cutoff:3.500A) Processing helix chain 'F' and resid 2786 through 2799 Proline residue: F2793 - end of helix removed outlier: 3.596A pdb=" N GLN F2799 " --> pdb=" O GLN F2795 " (cutoff:3.500A) Processing helix chain 'F' and resid 2801 through 2821 removed outlier: 3.970A pdb=" N ASP F2821 " --> pdb=" O LEU F2817 " (cutoff:3.500A) Processing helix chain 'F' and resid 2822 through 2824 No H-bonds generated for 'chain 'F' and resid 2822 through 2824' Processing helix chain 'F' and resid 2825 through 2847 Processing helix chain 'F' and resid 2851 through 2865 removed outlier: 3.682A pdb=" N HIS F2865 " --> pdb=" O ILE F2861 " (cutoff:3.500A) Processing helix chain 'F' and resid 2866 through 2870 removed outlier: 4.152A pdb=" N SER F2870 " --> pdb=" O ALA F2867 " (cutoff:3.500A) Processing helix chain 'F' and resid 2872 through 2883 Processing helix chain 'F' and resid 2885 through 2901 Processing helix chain 'F' and resid 2919 through 2933 Processing helix chain 'F' and resid 2936 through 2945 removed outlier: 3.795A pdb=" N ARG F2940 " --> pdb=" O TYR F2936 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY F2941 " --> pdb=" O ASP F2937 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER F2945 " --> pdb=" O GLY F2941 " (cutoff:3.500A) Processing helix chain 'F' and resid 2950 through 2962 removed outlier: 4.000A pdb=" N GLN F2954 " --> pdb=" O LYS F2950 " (cutoff:3.500A) Processing helix chain 'F' and resid 2965 through 2977 Processing helix chain 'F' and resid 2987 through 3005 Processing helix chain 'F' and resid 3007 through 3016 Processing helix chain 'F' and resid 3029 through 3033 Processing helix chain 'F' and resid 3034 through 3054 Proline residue: F3042 - end of helix Processing helix chain 'F' and resid 3059 through 3070 removed outlier: 3.831A pdb=" N HIS F3070 " --> pdb=" O ASP F3066 " (cutoff:3.500A) Processing helix chain 'F' and resid 3071 through 3093 removed outlier: 3.526A pdb=" N SER F3083 " --> pdb=" O GLU F3079 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN F3084 " --> pdb=" O LEU F3080 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU F3085 " --> pdb=" O HIS F3081 " (cutoff:3.500A) Processing helix chain 'F' and resid 3095 through 3117 Processing helix chain 'F' and resid 3121 through 3144 removed outlier: 3.699A pdb=" N ILE F3138 " --> pdb=" O ALA F3134 " (cutoff:3.500A) Processing helix chain 'F' and resid 3149 through 3153 removed outlier: 3.511A pdb=" N SER F3153 " --> pdb=" O ASN F3150 " (cutoff:3.500A) Processing helix chain 'F' and resid 3156 through 3162 Processing helix chain 'F' and resid 3162 through 3168 removed outlier: 3.739A pdb=" N ARG F3167 " --> pdb=" O THR F3163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR F3168 " --> pdb=" O TRP F3164 " (cutoff:3.500A) Processing helix chain 'F' and resid 3175 through 3197 removed outlier: 4.019A pdb=" N TRP F3179 " --> pdb=" O PRO F3175 " (cutoff:3.500A) Processing helix chain 'F' and resid 3227 through 3250 Processing helix chain 'F' and resid 3255 through 3266 Processing helix chain 'F' and resid 3269 through 3287 Processing helix chain 'F' and resid 3291 through 3299 Processing helix chain 'F' and resid 3304 through 3311 removed outlier: 5.841A pdb=" N GLU F3309 " --> pdb=" O LEU F3306 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F3310 " --> pdb=" O LEU F3307 " (cutoff:3.500A) Processing helix chain 'F' and resid 3312 through 3317 Processing helix chain 'F' and resid 3319 through 3344 removed outlier: 3.677A pdb=" N PHE F3323 " --> pdb=" O ASN F3319 " (cutoff:3.500A) Processing helix chain 'F' and resid 3347 through 3352 removed outlier: 3.534A pdb=" N ILE F3351 " --> pdb=" O CYS F3347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU F3352 " --> pdb=" O LEU F3348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3347 through 3352' Processing helix chain 'F' and resid 3355 through 3364 removed outlier: 3.841A pdb=" N ILE F3359 " --> pdb=" O LYS F3355 " (cutoff:3.500A) Processing helix chain 'F' and resid 3369 through 3393 Processing helix chain 'F' and resid 3408 through 3427 removed outlier: 3.521A pdb=" N GLU F3427 " --> pdb=" O GLN F3423 " (cutoff:3.500A) Processing helix chain 'F' and resid 3442 through 3456 removed outlier: 3.884A pdb=" N LEU F3456 " --> pdb=" O LYS F3452 " (cutoff:3.500A) Processing helix chain 'F' and resid 3458 through 3463 Processing helix chain 'F' and resid 3464 through 3475 Processing helix chain 'F' and resid 3475 through 3483 removed outlier: 4.719A pdb=" N SER F3481 " --> pdb=" O GLU F3477 " (cutoff:3.500A) Processing helix chain 'F' and resid 3495 through 3497 No H-bonds generated for 'chain 'F' and resid 3495 through 3497' Processing helix chain 'F' and resid 3498 through 3506 removed outlier: 3.624A pdb=" N MET F3502 " --> pdb=" O TRP F3498 " (cutoff:3.500A) Processing helix chain 'F' and resid 3511 through 3525 removed outlier: 3.722A pdb=" N GLN F3515 " --> pdb=" O ALA F3511 " (cutoff:3.500A) Processing helix chain 'F' and resid 3529 through 3536 Processing helix chain 'F' and resid 3547 through 3562 removed outlier: 4.047A pdb=" N ASN F3551 " --> pdb=" O THR F3547 " (cutoff:3.500A) Processing helix chain 'F' and resid 3564 through 3579 removed outlier: 3.955A pdb=" N ILE F3568 " --> pdb=" O GLN F3564 " (cutoff:3.500A) Processing helix chain 'F' and resid 3580 through 3597 removed outlier: 3.643A pdb=" N LEU F3584 " --> pdb=" O ASN F3580 " (cutoff:3.500A) Processing helix chain 'F' and resid 3605 through 3617 Processing helix chain 'F' and resid 3627 through 3644 removed outlier: 3.781A pdb=" N GLN F3634 " --> pdb=" O ARG F3630 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS F3638 " --> pdb=" O GLN F3634 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU F3639 " --> pdb=" O THR F3635 " (cutoff:3.500A) Processing helix chain 'F' and resid 3658 through 3670 removed outlier: 3.941A pdb=" N MET F3670 " --> pdb=" O LEU F3666 " (cutoff:3.500A) Processing helix chain 'F' and resid 3684 through 3689 Processing helix chain 'F' and resid 3758 through 3777 Processing helix chain 'F' and resid 3778 through 3784 Processing helix chain 'F' and resid 3812 through 3818 Processing helix chain 'F' and resid 3821 through 3831 removed outlier: 3.557A pdb=" N LEU F3829 " --> pdb=" O LYS F3825 " (cutoff:3.500A) Processing helix chain 'F' and resid 3834 through 3843 removed outlier: 5.368A pdb=" N LYS F3840 " --> pdb=" O PRO F3836 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP F3841 " --> pdb=" O CYS F3837 " (cutoff:3.500A) Processing helix chain 'F' and resid 3853 through 3861 removed outlier: 4.046A pdb=" N LEU F3857 " --> pdb=" O GLY F3853 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F3859 " --> pdb=" O TYR F3855 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F3860 " --> pdb=" O MET F3856 " (cutoff:3.500A) Processing helix chain 'F' and resid 3863 through 3878 Processing helix chain 'F' and resid 3881 through 3890 Processing helix chain 'F' and resid 3893 through 3918 Processing helix chain 'F' and resid 3924 through 3926 No H-bonds generated for 'chain 'F' and resid 3924 through 3926' Processing helix chain 'F' and resid 3964 through 3969 Processing helix chain 'F' and resid 3978 through 3991 Processing helix chain 'F' and resid 3992 through 3996 Proline residue: F3995 - end of helix No H-bonds generated for 'chain 'F' and resid 3992 through 3996' Processing helix chain 'F' and resid 3997 through 4002 Processing helix chain 'F' and resid 4039 through 4053 removed outlier: 3.594A pdb=" N LYS F4043 " --> pdb=" O TYR F4039 " (cutoff:3.500A) Processing helix chain 'F' and resid 4055 through 4069 removed outlier: 4.938A pdb=" N GLY F4067 " --> pdb=" O GLU F4063 " (cutoff:3.500A) Processing helix chain 'F' and resid 4073 through 4083 Processing helix chain 'F' and resid 4085 through 4090 Processing helix chain 'F' and resid 4091 through 4093 No H-bonds generated for 'chain 'F' and resid 4091 through 4093' Processing helix chain 'F' and resid 4099 through 4111 Processing helix chain 'F' and resid 4112 through 4119 removed outlier: 3.679A pdb=" N ILE F4116 " --> pdb=" O THR F4112 " (cutoff:3.500A) Processing helix chain 'F' and resid 4121 through 4125 removed outlier: 3.735A pdb=" N GLU F4125 " --> pdb=" O GLU F4122 " (cutoff:3.500A) Processing helix chain 'F' and resid 6005 through 6019 Processing helix chain 'G' and resid 58 through 78 removed outlier: 3.904A pdb=" N MET G 62 " --> pdb=" O THR G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 135 Processing helix chain 'G' and resid 142 through 157 removed outlier: 3.567A pdb=" N VAL G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 197 removed outlier: 3.701A pdb=" N ALA G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 245 removed outlier: 3.874A pdb=" N LYS G 245 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 339 Processing helix chain 'G' and resid 377 through 388 Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.777A pdb=" N LYS G 443 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 469 removed outlier: 3.645A pdb=" N VAL G 459 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 493 Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'H' and resid 17 through 22 removed outlier: 3.774A pdb=" N SER H 21 " --> pdb=" O GLY H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 49 Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 107 through 125 Processing helix chain 'H' and resid 147 through 158 Processing helix chain 'H' and resid 198 through 213 Processing helix chain 'H' and resid 217 through 223 Processing helix chain 'H' and resid 226 through 233 removed outlier: 3.703A pdb=" N LEU H 231 " --> pdb=" O PHE H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 332 Processing helix chain 'H' and resid 352 through 356 Processing helix chain 'H' and resid 370 through 388 Processing helix chain 'H' and resid 447 through 459 removed outlier: 3.916A pdb=" N ASP H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 484 through 500 Processing helix chain 'H' and resid 511 through 516 removed outlier: 3.559A pdb=" N LEU H 516 " --> pdb=" O TRP H 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 537 removed outlier: 3.888A pdb=" N THR H 523 " --> pdb=" O PRO H 519 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE H 528 " --> pdb=" O THR H 524 " (cutoff:3.500A) Proline residue: H 529 - end of helix Processing helix chain 'H' and resid 594 through 606 removed outlier: 3.739A pdb=" N VAL H 602 " --> pdb=" O PHE H 598 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS H 603 " --> pdb=" O ARG H 599 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS H 605 " --> pdb=" O LEU H 601 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 606 " --> pdb=" O VAL H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 609 through 622 removed outlier: 3.553A pdb=" N SER H 613 " --> pdb=" O PHE H 609 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN H 622 " --> pdb=" O ASN H 618 " (cutoff:3.500A) Processing helix chain 'H' and resid 628 through 649 removed outlier: 4.173A pdb=" N PHE H 649 " --> pdb=" O GLU H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 669 removed outlier: 3.888A pdb=" N LYS H 669 " --> pdb=" O LYS H 665 " (cutoff:3.500A) Processing helix chain 'H' and resid 675 through 682 Processing helix chain 'H' and resid 693 through 704 removed outlier: 4.056A pdb=" N THR H 697 " --> pdb=" O GLY H 693 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE H 704 " --> pdb=" O GLU H 700 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 59 removed outlier: 4.076A pdb=" N MET K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 76 removed outlier: 4.290A pdb=" N GLU K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 200 removed outlier: 3.972A pdb=" N GLU K 125 " --> pdb=" O GLU K 121 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU K 131 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN K 200 " --> pdb=" O ASN K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.577A pdb=" N GLY L 31 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.844A pdb=" N GLU L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE L 52 " --> pdb=" O GLU L 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 52' Processing helix chain 'L' and resid 53 through 57 removed outlier: 3.631A pdb=" N ALA L 56 " --> pdb=" O SER L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 75 removed outlier: 4.630A pdb=" N GLU L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 201 Processing helix chain 'M' and resid 656 through 660 Processing helix chain 'M' and resid 674 through 685 Processing helix chain 'M' and resid 706 through 715 Processing helix chain 'M' and resid 722 through 733 removed outlier: 3.853A pdb=" N LEU M 726 " --> pdb=" O LYS M 722 " (cutoff:3.500A) Processing helix chain 'M' and resid 747 through 758 removed outlier: 3.549A pdb=" N GLU M 757 " --> pdb=" O HIS M 753 " (cutoff:3.500A) Processing helix chain 'M' and resid 770 through 781 Processing helix chain 'M' and resid 788 through 803 Processing helix chain 'M' and resid 837 through 848 removed outlier: 3.929A pdb=" N HIS M 848 " --> pdb=" O GLU M 844 " (cutoff:3.500A) Processing helix chain 'M' and resid 871 through 882 removed outlier: 3.740A pdb=" N PHE M 875 " --> pdb=" O ARG M 871 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG M 880 " --> pdb=" O LYS M 876 " (cutoff:3.500A) Processing helix chain 'M' and resid 891 through 897 removed outlier: 3.510A pdb=" N THR M 895 " --> pdb=" O GLU M 891 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER M 897 " --> pdb=" O TRP M 893 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 909 removed outlier: 3.629A pdb=" N GLN M 908 " --> pdb=" O GLU M 905 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 58 Processing helix chain 'N' and resid 64 through 75 removed outlier: 3.669A pdb=" N LEU N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 200 removed outlier: 3.725A pdb=" N VAL N 122 " --> pdb=" O ASN N 118 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU N 170 " --> pdb=" O VAL N 166 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA N 171 " --> pdb=" O SER N 167 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN N 200 " --> pdb=" O ASN N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 31 Processing helix chain 'O' and resid 51 through 57 removed outlier: 4.264A pdb=" N GLU O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 removed outlier: 4.760A pdb=" N GLU O 69 " --> pdb=" O LYS O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 201 removed outlier: 4.161A pdb=" N ILE O 123 " --> pdb=" O PRO O 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 656 through 660 Processing helix chain 'P' and resid 674 through 685 Processing helix chain 'P' and resid 706 through 715 Processing helix chain 'P' and resid 722 through 733 removed outlier: 4.113A pdb=" N LEU P 726 " --> pdb=" O LYS P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 747 through 758 Processing helix chain 'P' and resid 770 through 781 removed outlier: 3.511A pdb=" N LEU P 774 " --> pdb=" O ASP P 770 " (cutoff:3.500A) Processing helix chain 'P' and resid 788 through 804 removed outlier: 3.558A pdb=" N MET P 792 " --> pdb=" O THR P 788 " (cutoff:3.500A) Processing helix chain 'P' and resid 805 through 808 removed outlier: 4.253A pdb=" N SER P 808 " --> pdb=" O TRP P 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 805 through 808' Processing helix chain 'P' and resid 837 through 848 Processing helix chain 'P' and resid 868 through 870 No H-bonds generated for 'chain 'P' and resid 868 through 870' Processing helix chain 'P' and resid 871 through 880 removed outlier: 3.545A pdb=" N ARG P 880 " --> pdb=" O LYS P 876 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 11 removed outlier: 3.566A pdb=" N MET Q 10 " --> pdb=" O GLN Q 6 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 61 removed outlier: 4.708A pdb=" N VAL Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU Q 61 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 78 Processing helix chain 'Q' and resid 80 through 84 removed outlier: 3.558A pdb=" N LEU Q 83 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU Q 84 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 80 through 84' Processing helix chain 'Q' and resid 135 through 167 Processing helix chain 'Q' and resid 185 through 195 Processing helix chain 'Q' and resid 207 through 222 removed outlier: 6.274A pdb=" N ASP Q 216 " --> pdb=" O MET Q 212 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU Q 217 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET Q 219 " --> pdb=" O GLN Q 215 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA Q 220 " --> pdb=" O ASP Q 216 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL Q 221 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 60 Processing helix chain 'R' and resid 68 through 78 removed outlier: 3.647A pdb=" N PHE R 72 " --> pdb=" O PRO R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 169 removed outlier: 4.251A pdb=" N MET R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS R 148 " --> pdb=" O LEU R 144 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG R 151 " --> pdb=" O GLN R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 196 Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.540A pdb=" N CYS R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 Processing sheet with id=AA1, first strand: chain 'A' and resid 1537 through 1539 removed outlier: 3.501A pdb=" N LEU A1538 " --> pdb=" O PHE A1553 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A1553 " --> pdb=" O LEU A1538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 2586 through 2587 Processing sheet with id=AA3, first strand: chain 'A' and resid 3736 through 3741 removed outlier: 4.477A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 109 removed outlier: 6.661A pdb=" N VAL B 85 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU B 107 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 83 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 42 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 88 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 35 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS B 164 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER B 37 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE B 166 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 39 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU B 168 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 41 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.544A pdb=" N VAL B 368 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 432 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 413 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 396 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 260 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU B 347 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N LYS B 262 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N GLY B 349 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 289 Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 420 removed outlier: 3.914A pdb=" N GLU B 419 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.924A pdb=" N LEU C 12 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 57 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE C 54 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 83 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 58 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL C 79 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 removed outlier: 6.057A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 247 through 253 removed outlier: 6.635A pdb=" N ALA C 366 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 11.094A pdb=" N GLU C 417 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL C 405 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 408 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 391 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N MET C 389 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL C 342 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR C 252 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY C 344 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 583 through 584 Processing sheet with id=AB7, first strand: chain 'F' and resid 893 through 895 Processing sheet with id=AB8, first strand: chain 'F' and resid 2586 through 2587 Processing sheet with id=AB9, first strand: chain 'F' and resid 3736 through 3741 removed outlier: 3.792A pdb=" N GLY F3801 " --> pdb=" O LYS F3753 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F3800 " --> pdb=" O THR F3797 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU F3802 " --> pdb=" O PRO F3795 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU F3804 " --> pdb=" O VAL F3793 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL F3793 " --> pdb=" O GLU F3804 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3810 through 3811 Processing sheet with id=AC2, first strand: chain 'G' and resid 102 through 109 removed outlier: 6.682A pdb=" N VAL G 85 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU G 107 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU G 83 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP G 109 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP G 81 " --> pdb=" O ASP G 109 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP G 36 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA G 84 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU G 38 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL G 86 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE G 40 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR G 88 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL G 42 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG G 35 " --> pdb=" O HIS G 163 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG G 165 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER G 37 " --> pdb=" O ARG G 165 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET G 167 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE G 39 " --> pdb=" O MET G 167 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE G 169 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU G 41 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET G 203 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 258 through 262 removed outlier: 3.830A pdb=" N PHE G 432 " --> pdb=" O VAL G 368 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N VAL G 394 " --> pdb=" O PRO G 415 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG G 399 " --> pdb=" O LEU G 347 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU G 347 " --> pdb=" O ARG G 399 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR G 401 " --> pdb=" O LEU G 345 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU G 345 " --> pdb=" O THR G 401 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LEU G 345 " --> pdb=" O ARG G 258 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS G 260 " --> pdb=" O LEU G 345 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU G 347 " --> pdb=" O LYS G 260 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS G 262 " --> pdb=" O LEU G 347 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY G 349 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 286 through 289 Processing sheet with id=AC5, first strand: chain 'G' and resid 296 through 303 Processing sheet with id=AC6, first strand: chain 'G' and resid 325 through 329 Processing sheet with id=AC7, first strand: chain 'G' and resid 419 through 420 removed outlier: 3.933A pdb=" N GLU G 419 " --> pdb=" O VAL G 427 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 removed outlier: 9.287A pdb=" N VAL H 57 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU H 12 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE H 59 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET H 14 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA H 9 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU H 133 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL H 11 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER H 160 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 162 " --> pdb=" O ILE H 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 134 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 247 through 253 removed outlier: 9.175A pdb=" N GLN H 360 " --> pdb=" O GLN H 423 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLN H 423 " --> pdb=" O GLN H 360 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU H 362 " --> pdb=" O TYR H 421 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 391 " --> pdb=" O ALA H 408 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N MET H 389 " --> pdb=" O PRO H 410 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL H 390 " --> pdb=" O PHE H 345 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE H 345 " --> pdb=" O VAL H 390 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE H 392 " --> pdb=" O LEU H 343 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H 341 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE H 340 " --> pdb=" O ARG H 250 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 36 through 37 removed outlier: 4.026A pdb=" N LEU K 36 " --> pdb=" O TRP K 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP K 43 " --> pdb=" O LEU K 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 2 through 3 removed outlier: 4.164A pdb=" N GLU L 2 " --> pdb=" O TRP L 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 34 through 37 removed outlier: 4.303A pdb=" N ILE L 34 " --> pdb=" O GLY L 45 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY L 45 " --> pdb=" O ILE L 34 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.037A pdb=" N LYS L 99 " --> pdb=" O PHE L 106 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE L 106 " --> pdb=" O LYS L 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'M' and resid 688 through 689 removed outlier: 6.920A pdb=" N GLU M 663 " --> pdb=" O CYS M 699 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE M 701 " --> pdb=" O GLU M 663 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS M 665 " --> pdb=" O ILE M 701 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL M 721 " --> pdb=" O TYR M 698 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL M 700 " --> pdb=" O VAL M 721 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 820 through 821 Processing sheet with id=AD7, first strand: chain 'N' and resid 34 through 37 removed outlier: 3.758A pdb=" N ILE N 34 " --> pdb=" O GLY N 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY N 45 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU N 36 " --> pdb=" O TRP N 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 100 through 101 removed outlier: 3.791A pdb=" N LEU N 101 " --> pdb=" O VAL N 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 5 removed outlier: 3.543A pdb=" N LYS O 4 " --> pdb=" O VAL O 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 8 through 9 Processing sheet with id=AE2, first strand: chain 'O' and resid 36 through 37 removed outlier: 4.221A pdb=" N LEU O 36 " --> pdb=" O TRP O 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP O 43 " --> pdb=" O LEU O 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 688 through 690 removed outlier: 6.565A pdb=" N GLU P 663 " --> pdb=" O THR P 697 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS P 699 " --> pdb=" O GLU P 663 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL P 721 " --> pdb=" O TYR P 698 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL P 700 " --> pdb=" O VAL P 721 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 26 through 28 removed outlier: 3.546A pdb=" N ALA Q 35 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU Q 36 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU Q 47 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL Q 38 " --> pdb=" O TRP Q 45 " (cutoff:3.500A) 4716 hydrogen bonds defined for protein. 13872 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: 52.84 Time building geometry restraints manager: 33.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26407 1.33 - 1.46: 15441 1.46 - 1.58: 48148 1.58 - 1.70: 216 1.70 - 1.82: 828 Bond restraints: 91040 Sorted by residual: bond pdb=" N VAL P 818 " pdb=" CA VAL P 818 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N ILE A2591 " pdb=" CA ILE A2591 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.18e-02 7.18e+03 1.07e+01 bond pdb=" N THR P 817 " pdb=" CA THR P 817 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.20e+00 bond pdb=" N ARG P 815 " pdb=" CA ARG P 815 " ideal model delta sigma weight residual 1.459 1.501 -0.043 1.41e-02 5.03e+03 9.19e+00 bond pdb=" N ILE F2591 " pdb=" CA ILE F2591 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 ... (remaining 91035 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.40: 1704 104.40 - 111.82: 44296 111.82 - 119.24: 31396 119.24 - 126.66: 44597 126.66 - 134.08: 1474 Bond angle restraints: 123467 Sorted by residual: angle pdb=" N PRO F 956 " pdb=" CA PRO F 956 " pdb=" CB PRO F 956 " ideal model delta sigma weight residual 103.08 110.77 -7.69 9.70e-01 1.06e+00 6.28e+01 angle pdb=" N VAL H 16 " pdb=" CA VAL H 16 " pdb=" C VAL H 16 " ideal model delta sigma weight residual 111.91 105.81 6.10 8.90e-01 1.26e+00 4.69e+01 angle pdb=" C SER Q 132 " pdb=" N GLN Q 133 " pdb=" CA GLN Q 133 " ideal model delta sigma weight residual 122.46 111.91 10.55 1.80e+00 3.09e-01 3.44e+01 angle pdb=" CA THR F1540 " pdb=" C THR F1540 " pdb=" O THR F1540 " ideal model delta sigma weight residual 121.51 127.93 -6.42 1.12e+00 7.97e-01 3.28e+01 angle pdb=" C ALA F 955 " pdb=" N PRO F 956 " pdb=" CA PRO F 956 " ideal model delta sigma weight residual 120.38 125.52 -5.14 1.03e+00 9.43e-01 2.49e+01 ... (remaining 123462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 53623 34.49 - 68.98: 1290 68.98 - 103.47: 191 103.47 - 137.96: 1 137.96 - 172.45: 3 Dihedral angle restraints: 55108 sinusoidal: 22969 harmonic: 32139 Sorted by residual: dihedral pdb=" CA LEU F 217 " pdb=" C LEU F 217 " pdb=" N PRO F 218 " pdb=" CA PRO F 218 " ideal model delta harmonic sigma weight residual 180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE P 847 " pdb=" C PHE P 847 " pdb=" N HIS P 848 " pdb=" CA HIS P 848 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PHE P 813 " pdb=" C PHE P 813 " pdb=" N ARG P 814 " pdb=" CA ARG P 814 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 55105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 12067 0.057 - 0.115: 1847 0.115 - 0.172: 124 0.172 - 0.229: 3 0.229 - 0.287: 3 Chirality restraints: 14044 Sorted by residual: chirality pdb=" CA PRO F 956 " pdb=" N PRO F 956 " pdb=" C PRO F 956 " pdb=" CB PRO F 956 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE F2591 " pdb=" N ILE F2591 " pdb=" C ILE F2591 " pdb=" CB ILE F2591 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE H 508 " pdb=" CA ILE H 508 " pdb=" CG1 ILE H 508 " pdb=" CG2 ILE H 508 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 14041 not shown) Planarity restraints: 15309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS P 848 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C HIS P 848 " -0.050 2.00e-02 2.50e+03 pdb=" O HIS P 848 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY P 849 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 44 " -0.196 9.50e-02 1.11e+02 8.79e-02 4.94e+00 pdb=" NE ARG H 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG H 44 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG H 44 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 44 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 814 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ARG P 814 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG P 814 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG P 815 " -0.012 2.00e-02 2.50e+03 ... (remaining 15306 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1285 2.61 - 3.18: 85802 3.18 - 3.76: 147732 3.76 - 4.33: 190514 4.33 - 4.90: 299949 Nonbonded interactions: 725282 Sorted by model distance: nonbonded pdb=" O SER A1549 " pdb=" CG2 VAL A1550 " model vdw 2.040 3.460 nonbonded pdb=" OD1 ASP G 533 " pdb=" NH2 ARG H 250 " model vdw 2.197 2.520 nonbonded pdb=" OG SER A2569 " pdb=" OD1 ASP A2571 " model vdw 2.201 2.440 nonbonded pdb=" O ALA A 266 " pdb=" OG SER A 269 " model vdw 2.205 2.440 nonbonded pdb=" O ILE F3142 " pdb=" NZ LYS F3147 " model vdw 2.207 2.520 ... (remaining 725277 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 10 through 252 or (resid 253 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 264 through 266 and (name N or name CA or \ name C or name O or name CB )) or resid 267 through 585 or (resid 586 through 61 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 613 through \ 841 or resid 848 through 955 or (resid 956 and (name N or name CA or name C or n \ ame O or name CB )) or resid 957 through 2097 or (resid 2098 through 2099 and (n \ ame N or name CA or name C or name O or name CB )) or resid 2100 through 2729 or \ (resid 2730 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 731 through 2745 or (resid 2746 and (name N or name CA or name C or name O or na \ me CB )) or resid 2747 through 3159 or (resid 3160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 3161 through 3265 or (resid 3266 and (name \ N or name CA or name C or name O or name CB )) or resid 3267 through 3295 or (re \ sid 3296 and (name N or name CA or name C or name O or name CB )) or resid 3297 \ through 3300 or (resid 3301 through 3302 and (name N or name CA or name C or nam \ e O or name CB )) or resid 3303 through 3356 or (resid 3357 and (name N or name \ CA or name C or name O or name CB )) or resid 3358 through 3880 or (resid 3881 a \ nd (name N or name CA or name C or name O or name CB )) or resid 3882 through 41 \ 07 or (resid 4108 and (name N or name CA or name C or name O or name CB )) or re \ sid 4109 through 4111 or (resid 4112 and (name N or name CA or name C or name O \ or name CB )) or resid 4113 through 6023)) selection = (chain 'F' and (resid 10 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 116 or (resid 117 through 121 and \ (name N or name CA or name C or name O or name CB )) or resid 122 through 204 o \ r (resid 205 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 06 through 208 or (resid 209 and (name N or name CA or name C or name O or name \ CB )) or resid 210 through 235 or (resid 236 and (name N or name CA or name C or \ name O or name CB )) or resid 237 through 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 247 or (resid 248 and \ (name N or name CA or name C or name O or name CB )) or resid 249 through 253 o \ r resid 264 through 658 or (resid 659 and (name N or name CA or name C or name O \ or name CB )) or resid 660 through 802 or (resid 803 and (name N or name CA or \ name C or name O or name CB )) or resid 826 through 837 or (resid 838 through 84 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 848 through \ 1436 or (resid 1437 and (name N or name CA or name C or name O or name CB )) or \ resid 1438 through 1539 or (resid 1540 and (name N or name CA or name C or name \ O or name CB )) or resid 1549 through 1550 or (resid 1551 and (name N or name CA \ or name C or name O or name CB )) or resid 1552 through 1693 or (resid 1694 and \ (name N or name CA or name C or name O or name CB )) or resid 1695 through 1959 \ or (resid 1960 through 1961 and (name N or name CA or name C or name O or name \ CB )) or resid 1962 through 3305 or (resid 3306 and (name N or name CA or name C \ or name O or name CB )) or resid 3307 through 3820 or (resid 3821 and (name N o \ r name CA or name C or name O or name CB )) or resid 3822 through 3823 or (resid \ 3824 through 3827 and (name N or name CA or name C or name O or name CB )) or r \ esid 3828 through 6023)) } ncs_group { reference = chain 'B' selection = (chain 'G' and (resid 32 through 49 or resid 58 through 210 or (resid 211 and (n \ ame N or name CA or name C or name O or name CB )) or resid 212 or (resid 213 an \ d (name N or name CA or name C or name O or name CB )) or resid 214 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 253 or (resid 254 through 255 and (name N or name CA or name C or na \ me O or name CB )) or resid 256 through 448 or resid 454 through 534)) } ncs_group { reference = (chain 'D' and (resid 12 or resid 15 through 38)) selection = (chain 'J' and (resid 12 or resid 15 through 38)) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'K' and (resid 1 through 75 or resid 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 201)) selection = (chain 'L' and (resid 1 through 75 or resid 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 201)) selection = (chain 'N' and (resid 1 through 75 or resid 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 201)) selection = chain 'O' } ncs_group { reference = (chain 'M' and (resid 654 through 812 or (resid 813 through 816 and (name N or n \ ame CA or name C or name O or name CB )) or resid 817 through 850 or (resid 851 \ and (name N or name CA or name C or name O or name CB )) or resid 852 through 89 \ 0 or resid 899 through 907)) selection = chain 'P' } ncs_group { reference = (chain 'Q' and (resid 1 through 85 or resid 93 through 145 or (resid 146 and (na \ me N or name CA or name C or name O or name CB )) or resid 147 through 148 or (r \ esid 149 and (name N or name CA or name C or name O or name CB )) or resid 150 t \ hrough 207 or (resid 208 and (name N or name CA or name C or name O or name CB ) \ ) or resid 209 through 224)) selection = (chain 'R' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 38 or (resid 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 85 or resid 93 through \ 198 or resid 206 through 224)) } 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=0.00 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: 9.930 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: 0.060 Extract box with map and model: 34.590 Check model and map are aligned: 1.070 Set scattering table: 0.620 Process input model: 205.740 Find NCS groups from input model: 5.310 Set up NCS constraints: 0.550 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 260.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.003 0.047 91040 Z= 0.193 Angle : 0.603 10.551 123467 Z= 0.331 Chirality : 0.039 0.287 14044 Planarity : 0.004 0.088 15309 Dihedral : 15.548 172.453 34114 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.57 % 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: 0.21 (0.09), residues: 10691 helix: 1.44 (0.07), residues: 6143 sheet: -0.73 (0.26), residues: 416 loop : -1.84 (0.10), residues: 4132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1127 time to evaluate : 7.889 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: 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: 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: 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 outliers start: 6 outliers final: 0 residues processed: 1131 average time/residue: 0.8728 time to fit residues: 1684.3323 Evaluate side-chains 672 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 7.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 923 optimal weight: 9.9990 chunk 829 optimal weight: 9.9990 chunk 460 optimal weight: 7.9990 chunk 283 optimal weight: 0.0070 chunk 559 optimal weight: 0.9980 chunk 442 optimal weight: 7.9990 chunk 857 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 521 optimal weight: 0.6980 chunk 638 optimal weight: 8.9990 chunk 993 optimal weight: 30.0000 overall best weight: 3.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN ** A1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3660 ASN ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1426 GLN ** F1465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2217 ASN F2291 GLN ** F2348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2587 GLN ** F2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3327 ASN F3664 ASN ** F3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 GLN ** H 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 680 GLN ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 91040 Z= 0.254 Angle : 0.628 12.876 123467 Z= 0.331 Chirality : 0.040 0.226 14044 Planarity : 0.005 0.102 15309 Dihedral : 11.310 178.854 12725 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.08 % Rotamer: Outliers : 0.12 % Allowed : 5.42 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.22 % 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: 0.05 (0.08), residues: 10691 helix: 1.26 (0.07), residues: 6205 sheet: -0.85 (0.25), residues: 413 loop : -1.87 (0.10), residues: 4073 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 788 time to evaluate : 8.150 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 798 average time/residue: 0.8491 time to fit residues: 1180.8592 Evaluate side-chains 592 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 587 time to evaluate : 7.930 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.7652 time to fit residues: 18.8706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 552 optimal weight: 0.9990 chunk 308 optimal weight: 0.6980 chunk 826 optimal weight: 4.9990 chunk 676 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 995 optimal weight: 5.9990 chunk 1075 optimal weight: 20.0000 chunk 886 optimal weight: 6.9990 chunk 986 optimal weight: 0.0980 chunk 339 optimal weight: 0.8980 chunk 798 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 982 GLN A1043 GLN ** A1069 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1687 HIS ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3185 ASN ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 442 GLN ** F 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 982 GLN F1043 GLN ** F1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1350 ASN F1509 GLN ** F1568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2103 HIS ** F2233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2291 GLN ** F2348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2464 HIS F2587 GLN F2807 GLN F2834 GLN ** F2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3327 ASN F3664 ASN ** F3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F3924 HIS F3927 ASN ** F4055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4068 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 ASN G 405 ASN ** H 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 680 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 HIS ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 91040 Z= 0.162 Angle : 0.585 13.955 123467 Z= 0.299 Chirality : 0.040 0.218 14044 Planarity : 0.004 0.080 15309 Dihedral : 11.255 174.116 12725 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % 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: 0.08 (0.08), residues: 10691 helix: 1.29 (0.07), residues: 6213 sheet: -0.99 (0.25), residues: 406 loop : -1.85 (0.10), residues: 4072 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21382 Ramachandran restraints generated. 10691 Oldfield, 0 Emsley, 10691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 791 time to evaluate : 8.093 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 798 average time/residue: 0.9242 time to fit residues: 1302.1013 Evaluate side-chains 604 residues out of total 9778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 602 time to evaluate : 8.139 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7569 time to fit residues: 13.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 983 optimal weight: 10.0000 chunk 748 optimal weight: 4.9990 chunk 516 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 474 optimal weight: 10.0000 chunk 668 optimal weight: 0.9980 chunk 998 optimal weight: 7.9990 chunk 1057 optimal weight: 50.0000 chunk 521 optimal weight: 9.9990 chunk 946 optimal weight: 6.9990 chunk 284 optimal weight: 0.8980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: