Starting phenix.real_space_refine on Mon Mar 25 14:32:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zcs_6913/03_2024/5zcs_6913.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 258 5.16 5 C 30920 2.51 5 N 8880 2.21 5 O 9118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2178, 17347 Classifications: {'peptide': 2178} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 85, 'TRANS': 2092} Chain breaks: 19 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 17347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2178, 17347 Classifications: {'peptide': 2178} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 85, 'TRANS': 2092} Chain breaks: 19 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "D" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 4362 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 793} Link IDs: {'CIS': 8, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 842} Chain breaks: 3 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 2817 Unresolved non-hydrogen angles: 3639 Unresolved non-hydrogen dihedrals: 2303 Unresolved non-hydrogen chiralities: 265 Planarities with less than four sites: {'GLN:plan1': 33, 'ARG:plan': 49, 'TYR:plan': 24, 'ASN:plan1': 45, 'TRP:plan': 13, 'HIS:plan': 35, 'PHE:plan': 23, 'GLU:plan': 51, 'ASP:plan': 44, 'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 1499 Chain: "F" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 4362 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 793} Link IDs: {'CIS': 8, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 842} Chain breaks: 3 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 2817 Unresolved non-hydrogen angles: 3639 Unresolved non-hydrogen dihedrals: 2303 Unresolved non-hydrogen chiralities: 265 Planarities with less than four sites: {'GLN:plan1': 33, 'ARG:plan': 49, 'TYR:plan': 24, 'ASN:plan1': 45, 'TRP:plan': 13, 'HIS:plan': 35, 'PHE:plan': 23, 'GLU:plan': 51, 'ASP:plan': 44, 'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 1499 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 423 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 79} Link IDs: {'TRANS': 85} Chain breaks: 3 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 86} Unresolved non-hydrogen planarities: 86 Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 423 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 79} Link IDs: {'TRANS': 85} Chain breaks: 3 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 86} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 24.27, per 1000 atoms: 0.49 Number of scatterers: 49176 At special positions: 0 Unit cell: (227.25, 225.23, 149.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 258 16.00 O 9118 8.00 N 8880 7.00 C 30920 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: 18.32 Conformation dependent library (CDL) restraints added in 10.1 seconds 13112 Ramachandran restraints generated. 6556 Oldfield, 0 Emsley, 6556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13204 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 20 sheets defined 59.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.031A pdb=" N LYS A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.947A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 101 through 108 removed outlier: 4.182A pdb=" N GLY A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 140 through 151 removed outlier: 4.078A pdb=" N VAL A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.937A pdb=" N PHE A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 184 " --> pdb=" O THR A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.827A pdb=" N ASN A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.534A pdb=" N ALA A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.875A pdb=" N THR A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 223' Processing helix chain 'A' and resid 234 through 246 removed outlier: 4.227A pdb=" N PHE A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.928A pdb=" N GLU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 4.181A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.777A pdb=" N GLU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.718A pdb=" N ALA A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.673A pdb=" N ASN A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.537A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Proline residue: A 453 - end of helix removed outlier: 3.715A pdb=" N LEU A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 458 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 498 through 504 removed outlier: 4.190A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.969A pdb=" N MET A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.627A pdb=" N ARG A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 4.387A pdb=" N ILE A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 579 through 590 removed outlier: 3.727A pdb=" N THR A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.699A pdb=" N CYS A 606 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 607 " --> pdb=" O ARG A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 607' Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.037A pdb=" N THR A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 removed outlier: 3.790A pdb=" N LEU A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 Processing helix chain 'A' and resid 680 through 684 removed outlier: 4.151A pdb=" N PHE A 683 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP A 684 " --> pdb=" O GLU A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 684' Processing helix chain 'A' and resid 689 through 698 removed outlier: 4.491A pdb=" N GLN A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 718 removed outlier: 3.752A pdb=" N VAL A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.597A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 733 " --> pdb=" O PHE A 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 733' Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.671A pdb=" N LYS A 750 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 removed outlier: 3.770A pdb=" N LEU A 767 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 removed outlier: 4.507A pdb=" N ILE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 removed outlier: 5.770A pdb=" N LYS A 782 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 783 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 784' Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.897A pdb=" N LEU A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 802 " --> pdb=" O VAL A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 3.877A pdb=" N VAL A 817 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.699A pdb=" N TRP A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 847 " --> pdb=" O THR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 removed outlier: 4.215A pdb=" N THR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 removed outlier: 3.751A pdb=" N ASN A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 875 " --> pdb=" O PHE A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 891 removed outlier: 3.856A pdb=" N GLU A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.006A pdb=" N VAL A 901 " --> pdb=" O TYR A 897 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.652A pdb=" N ASN A 940 " --> pdb=" O ASN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 947 Processing helix chain 'A' and resid 968 through 981 removed outlier: 4.593A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 removed outlier: 4.247A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.809A pdb=" N VAL A1003 " --> pdb=" O ASN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1020 removed outlier: 4.185A pdb=" N GLN A1015 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1030 Processing helix chain 'A' and resid 1031 through 1038 removed outlier: 3.899A pdb=" N VAL A1035 " --> pdb=" O MET A1031 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A1038 " --> pdb=" O ILE A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 3.714A pdb=" N THR A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.896A pdb=" N GLY A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 4.087A pdb=" N LEU A1069 " --> pdb=" O GLU A1066 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A1070 " --> pdb=" O PHE A1067 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1071 through 1073 No H-bonds generated for 'chain 'A' and resid 1071 through 1073' Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 3.673A pdb=" N ARG A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.844A pdb=" N ILE A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1123 Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.684A pdb=" N LEU A1142 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1156 removed outlier: 3.995A pdb=" N ILE A1155 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A1156 " --> pdb=" O SER A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1152 through 1156' Processing helix chain 'A' and resid 1157 through 1166 removed outlier: 4.109A pdb=" N ARG A1161 " --> pdb=" O HIS A1157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A1165 " --> pdb=" O ARG A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 Processing helix chain 'A' and resid 1175 through 1185 removed outlier: 3.904A pdb=" N SER A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A1185 " --> pdb=" O VAL A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1191 through 1203 removed outlier: 4.296A pdb=" N VAL A1195 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN A1196 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL A1200 " --> pdb=" O ASN A1196 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1219 removed outlier: 3.770A pdb=" N LEU A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A1216 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A1217 " --> pdb=" O ILE A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.637A pdb=" N LEU A1265 " --> pdb=" O THR A1262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A1266 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A1267 " --> pdb=" O ASN A1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1262 through 1267' Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 4.036A pdb=" N LEU A1284 " --> pdb=" O TRP A1280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A1285 " --> pdb=" O LEU A1281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1301 removed outlier: 3.648A pdb=" N LEU A1300 " --> pdb=" O SER A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1308 removed outlier: 3.827A pdb=" N GLN A1308 " --> pdb=" O TRP A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1316 removed outlier: 3.529A pdb=" N MET A1313 " --> pdb=" O TYR A1310 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A1314 " --> pdb=" O ASN A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1327 removed outlier: 4.122A pdb=" N VAL A1323 " --> pdb=" O ASN A1319 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A1324 " --> pdb=" O ALA A1320 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS A1325 " --> pdb=" O ALA A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1343 Processing helix chain 'A' and resid 1350 through 1360 Processing helix chain 'A' and resid 1373 through 1377 removed outlier: 3.698A pdb=" N ASP A1376 " --> pdb=" O PRO A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1390 removed outlier: 3.775A pdb=" N ARG A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1405 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.887A pdb=" N ALA A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.783A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1453 " --> pdb=" O TRP A1449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1453' Processing helix chain 'A' and resid 1459 through 1468 Processing helix chain 'A' and resid 1473 through 1481 Processing helix chain 'A' and resid 1481 through 1486 removed outlier: 3.914A pdb=" N GLU A1485 " --> pdb=" O MET A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1498 removed outlier: 4.226A pdb=" N LEU A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A1494 " --> pdb=" O TRP A1490 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A1498 " --> pdb=" O HIS A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1522 removed outlier: 4.259A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1520 " --> pdb=" O ALA A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1534 removed outlier: 3.656A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1554 removed outlier: 4.408A pdb=" N ALA A1548 " --> pdb=" O ALA A1544 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1549 " --> pdb=" O PHE A1545 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS A1553 " --> pdb=" O VAL A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1566 removed outlier: 3.702A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1570 removed outlier: 3.873A pdb=" N LEU A1570 " --> pdb=" O ALA A1567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1567 through 1570' Processing helix chain 'A' and resid 1572 through 1577 removed outlier: 4.206A pdb=" N THR A1576 " --> pdb=" O ASP A1572 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1572 through 1577' Processing helix chain 'A' and resid 1586 through 1597 removed outlier: 3.826A pdb=" N VAL A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS A1594 " --> pdb=" O MET A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1619 removed outlier: 3.673A pdb=" N ARG A1616 " --> pdb=" O ARG A1612 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A1619 " --> pdb=" O ILE A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.521A pdb=" N GLY A1625 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1637 removed outlier: 4.164A pdb=" N ASP A1632 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLN A1634 " --> pdb=" O GLU A1631 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A1635 " --> pdb=" O ASP A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1642 removed outlier: 3.559A pdb=" N SER A1641 " --> pdb=" O MET A1638 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A1642 " --> pdb=" O VAL A1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1638 through 1642' Processing helix chain 'A' and resid 1645 through 1649 Processing helix chain 'A' and resid 1652 through 1662 removed outlier: 3.660A pdb=" N TYR A1656 " --> pdb=" O THR A1652 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A1662 " --> pdb=" O SER A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.803A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1707 removed outlier: 3.817A pdb=" N THR A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A1707 " --> pdb=" O ASN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1725 removed outlier: 3.594A pdb=" N GLN A1718 " --> pdb=" O PHE A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 Processing helix chain 'A' and resid 1736 through 1751 removed outlier: 3.732A pdb=" N LYS A1740 " --> pdb=" O ASP A1736 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1755 removed outlier: 3.592A pdb=" N GLY A1755 " --> pdb=" O LEU A1752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1752 through 1755' Processing helix chain 'A' and resid 1757 through 1762 removed outlier: 4.038A pdb=" N LEU A1761 " --> pdb=" O TRP A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1781 removed outlier: 3.628A pdb=" N LEU A1773 " --> pdb=" O ILE A1769 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A1774 " --> pdb=" O PRO A1770 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A1779 " --> pdb=" O TYR A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1790 removed outlier: 3.534A pdb=" N ALA A1789 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1812 removed outlier: 3.701A pdb=" N ALA A1800 " --> pdb=" O MET A1796 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1801 " --> pdb=" O ASN A1797 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1878 removed outlier: 3.606A pdb=" N THR A1876 " --> pdb=" O ASP A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1893 removed outlier: 4.333A pdb=" N PHE A1889 " --> pdb=" O VAL A1885 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG A1890 " --> pdb=" O GLN A1886 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A1891 " --> pdb=" O GLY A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1903 removed outlier: 4.287A pdb=" N ASP A1902 " --> pdb=" O ASN A1898 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1903 " --> pdb=" O ASN A1899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1898 through 1903' Processing helix chain 'A' and resid 1904 through 1914 removed outlier: 4.300A pdb=" N LEU A1909 " --> pdb=" O ARG A1905 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP A1910 " --> pdb=" O VAL A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1923 Processing helix chain 'A' and resid 1923 through 1928 removed outlier: 3.513A pdb=" N LYS A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1965 removed outlier: 4.014A pdb=" N THR A1962 " --> pdb=" O HIS A1958 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A1963 " --> pdb=" O GLN A1959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1971 removed outlier: 3.897A pdb=" N ALA A1971 " --> pdb=" O HIS A1968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1968 through 1971' Processing helix chain 'A' and resid 1972 through 1977 removed outlier: 3.662A pdb=" N LEU A1976 " --> pdb=" O LEU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1998 removed outlier: 4.572A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A1989 " --> pdb=" O THR A1985 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA A1990 " --> pdb=" O ALA A1986 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A1991 " --> pdb=" O ARG A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2001 No H-bonds generated for 'chain 'A' and resid 1999 through 2001' Processing helix chain 'A' and resid 2005 through 2021 removed outlier: 3.587A pdb=" N MET A2011 " --> pdb=" O GLN A2007 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2041 removed outlier: 4.070A pdb=" N MET A2026 " --> pdb=" O LEU A2022 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP A2027 " --> pdb=" O TRP A2023 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS A2028 " --> pdb=" O HIS A2024 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU A2029 " --> pdb=" O GLU A2025 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A2034 " --> pdb=" O GLY A2030 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A2036 " --> pdb=" O GLU A2032 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A2038 " --> pdb=" O ALA A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2056 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2077 through 2087 removed outlier: 4.219A pdb=" N GLN A2082 " --> pdb=" O LEU A2078 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU A2083 " --> pdb=" O MET A2079 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP A2084 " --> pdb=" O GLU A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2113 removed outlier: 3.750A pdb=" N ARG A2109 " --> pdb=" O TYR A2105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A2110 " --> pdb=" O HIS A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2127 removed outlier: 3.943A pdb=" N VAL A2126 " --> pdb=" O GLU A2122 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2131 Processing helix chain 'A' and resid 2200 through 2209 removed outlier: 4.017A pdb=" N LEU A2204 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A2205 " --> pdb=" O LEU A2201 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN A2206 " --> pdb=" O PHE A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2217 removed outlier: 3.720A pdb=" N ARG A2217 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2254 removed outlier: 3.667A pdb=" N ARG A2251 " --> pdb=" O HIS A2247 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A2252 " --> pdb=" O ALA A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2265 through 2272 Processing helix chain 'A' and resid 2287 through 2291 removed outlier: 3.761A pdb=" N ALA A2290 " --> pdb=" O PHE A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2303 removed outlier: 3.729A pdb=" N LEU A2302 " --> pdb=" O ASP A2298 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A2303 " --> pdb=" O LEU A2299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2298 through 2303' Processing helix chain 'A' and resid 2310 through 2323 removed outlier: 3.637A pdb=" N ASP A2315 " --> pdb=" O GLU A2311 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A2321 " --> pdb=" O ARG A2317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A2323 " --> pdb=" O ASN A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2335 Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2380 through 2386 Processing helix chain 'A' and resid 2396 through 2409 removed outlier: 3.789A pdb=" N THR A2402 " --> pdb=" O ILE A2398 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A2403 " --> pdb=" O THR A2399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A2404 " --> pdb=" O CYS A2400 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU A2405 " --> pdb=" O HIS A2401 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A2406 " --> pdb=" O THR A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2415 Processing helix chain 'A' and resid 2417 through 2422 removed outlier: 4.118A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A2422 " --> pdb=" O LEU A2418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2417 through 2422' Processing helix chain 'A' and resid 2427 through 2431 removed outlier: 4.040A pdb=" N ARG A2430 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2510 removed outlier: 3.697A pdb=" N ILE A2498 " --> pdb=" O ASN A2494 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A2501 " --> pdb=" O ALA A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2528 removed outlier: 3.564A pdb=" N LEU A2528 " --> pdb=" O GLN A2524 " (cutoff:3.500A) Processing helix chain 'A' and resid 2529 through 2534 removed outlier: 3.853A pdb=" N SER A2534 " --> pdb=" O LYS A2530 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.032A pdb=" N LYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.947A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 101 through 108 removed outlier: 4.182A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.078A pdb=" N VAL B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.938A pdb=" N PHE B 183 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE B 184 " --> pdb=" O THR B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.828A pdb=" N ASN B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 197 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.534A pdb=" N ALA B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.874A pdb=" N THR B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 223' Processing helix chain 'B' and resid 234 through 246 removed outlier: 4.226A pdb=" N PHE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.928A pdb=" N GLU B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 removed outlier: 4.182A pdb=" N GLU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 375 removed outlier: 3.777A pdb=" N GLU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.718A pdb=" N ALA B 401 " --> pdb=" O PRO B 397 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 421 removed outlier: 3.674A pdb=" N ASN B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 438 Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.538A pdb=" N VAL B 450 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 3.715A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 457 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 458 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 498 through 504 removed outlier: 4.189A pdb=" N LYS B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.969A pdb=" N MET B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.628A pdb=" N ARG B 526 " --> pdb=" O TYR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 removed outlier: 4.386A pdb=" N ILE B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 579 through 590 removed outlier: 3.727A pdb=" N THR B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.698A pdb=" N CYS B 606 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 607 " --> pdb=" O ARG B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 621 through 630 removed outlier: 4.037A pdb=" N THR B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 664 removed outlier: 3.791A pdb=" N LEU B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'B' and resid 680 through 684 removed outlier: 4.151A pdb=" N PHE B 683 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP B 684 " --> pdb=" O GLU B 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 680 through 684' Processing helix chain 'B' and resid 689 through 698 removed outlier: 4.491A pdb=" N GLN B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 696 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 718 removed outlier: 3.753A pdb=" N VAL B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 removed outlier: 3.598A pdb=" N LYS B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 728 through 733' Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.671A pdb=" N LYS B 750 " --> pdb=" O ILE B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 768 removed outlier: 3.770A pdb=" N LEU B 767 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 778 removed outlier: 4.508A pdb=" N ILE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 778 " --> pdb=" O PRO B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 removed outlier: 5.770A pdb=" N LYS B 782 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 783 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 784 " --> pdb=" O LEU B 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 779 through 784' Processing helix chain 'B' and resid 792 through 803 removed outlier: 3.897A pdb=" N LEU B 799 " --> pdb=" O ILE B 795 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 800 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 801 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 802 " --> pdb=" O VAL B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 817 removed outlier: 3.878A pdb=" N VAL B 817 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 829 Processing helix chain 'B' and resid 836 through 847 removed outlier: 3.700A pdb=" N TRP B 842 " --> pdb=" O GLN B 838 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 847 " --> pdb=" O THR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 removed outlier: 4.214A pdb=" N THR B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 875 removed outlier: 3.751A pdb=" N ASN B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 875 " --> pdb=" O PHE B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 891 removed outlier: 3.856A pdb=" N GLU B 883 " --> pdb=" O GLY B 879 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 886 " --> pdb=" O ARG B 882 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 903 removed outlier: 4.006A pdb=" N VAL B 901 " --> pdb=" O TYR B 897 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN B 902 " --> pdb=" O LYS B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 940 removed outlier: 3.652A pdb=" N ASN B 940 " --> pdb=" O ASN B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 947 Processing helix chain 'B' and resid 968 through 981 removed outlier: 4.593A pdb=" N VAL B 972 " --> pdb=" O HIS B 968 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 973 " --> pdb=" O THR B 969 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 974 " --> pdb=" O MET B 970 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 979 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER B 981 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 998 removed outlier: 4.247A pdb=" N LEU B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 removed outlier: 3.809A pdb=" N VAL B1003 " --> pdb=" O ASN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1020 removed outlier: 4.185A pdb=" N GLN B1015 " --> pdb=" O PHE B1011 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B1020 " --> pdb=" O LEU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1030 Processing helix chain 'B' and resid 1031 through 1038 removed outlier: 3.900A pdb=" N VAL B1035 " --> pdb=" O MET B1031 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B1038 " --> pdb=" O ILE B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1053 removed outlier: 3.714A pdb=" N THR B1051 " --> pdb=" O SER B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1064 removed outlier: 3.896A pdb=" N GLY B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 removed outlier: 4.088A pdb=" N LEU B1069 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B1070 " --> pdb=" O PHE B1067 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1066 through 1070' Processing helix chain 'B' and resid 1071 through 1073 No H-bonds generated for 'chain 'B' and resid 1071 through 1073' Processing helix chain 'B' and resid 1074 through 1080 removed outlier: 3.674A pdb=" N ARG B1080 " --> pdb=" O PRO B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1101 removed outlier: 3.844A pdb=" N ILE B1094 " --> pdb=" O ARG B1090 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B1098 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B1099 " --> pdb=" O LYS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1123 Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.685A pdb=" N LEU B1142 " --> pdb=" O THR B1138 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1156 removed outlier: 3.995A pdb=" N ILE B1155 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B1156 " --> pdb=" O SER B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1152 through 1156' Processing helix chain 'B' and resid 1157 through 1166 removed outlier: 4.109A pdb=" N ARG B1161 " --> pdb=" O HIS B1157 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B1165 " --> pdb=" O ARG B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1174 Processing helix chain 'B' and resid 1175 through 1185 removed outlier: 3.904A pdb=" N SER B1179 " --> pdb=" O ASP B1175 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B1180 " --> pdb=" O THR B1176 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B1185 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1190 No H-bonds generated for 'chain 'B' and resid 1188 through 1190' Processing helix chain 'B' and resid 1191 through 1203 removed outlier: 4.297A pdb=" N VAL B1195 " --> pdb=" O PHE B1191 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN B1196 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL B1200 " --> pdb=" O ASN B1196 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG B1201 " --> pdb=" O LYS B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1219 removed outlier: 3.770A pdb=" N LEU B1212 " --> pdb=" O ARG B1208 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B1213 " --> pdb=" O TYR B1209 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS B1214 " --> pdb=" O ASP B1210 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE B1216 " --> pdb=" O LEU B1212 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B1217 " --> pdb=" O ILE B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1267 removed outlier: 3.635A pdb=" N LEU B1265 " --> pdb=" O THR B1262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B1266 " --> pdb=" O ILE B1263 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B1267 " --> pdb=" O ASN B1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1262 through 1267' Processing helix chain 'B' and resid 1276 through 1294 removed outlier: 4.035A pdb=" N LEU B1284 " --> pdb=" O TRP B1280 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B1285 " --> pdb=" O LEU B1281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B1292 " --> pdb=" O SER B1288 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B1293 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP B1294 " --> pdb=" O GLU B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1301 removed outlier: 3.647A pdb=" N LEU B1300 " --> pdb=" O SER B1297 " (cutoff:3.500A) Processing helix chain 'B' and resid 1303 through 1308 removed outlier: 3.827A pdb=" N GLN B1308 " --> pdb=" O TRP B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1316 removed outlier: 3.529A pdb=" N MET B1313 " --> pdb=" O TYR B1310 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B1314 " --> pdb=" O ASN B1311 " (cutoff:3.500A) Processing helix chain 'B' and resid 1319 through 1327 removed outlier: 4.122A pdb=" N VAL B1323 " --> pdb=" O ASN B1319 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B1324 " --> pdb=" O ALA B1320 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B1325 " --> pdb=" O ALA B1321 " (cutoff:3.500A) Processing helix chain 'B' and resid 1333 through 1343 Processing helix chain 'B' and resid 1350 through 1360 Processing helix chain 'B' and resid 1373 through 1377 removed outlier: 3.699A pdb=" N ASP B1376 " --> pdb=" O PRO B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1390 removed outlier: 3.775A pdb=" N ARG B1386 " --> pdb=" O LEU B1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1405 Processing helix chain 'B' and resid 1425 through 1430 removed outlier: 3.888A pdb=" N ALA B1429 " --> pdb=" O GLN B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1453 removed outlier: 3.783A pdb=" N GLU B1451 " --> pdb=" O ALA B1447 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B1452 " --> pdb=" O THR B1448 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1453 " --> pdb=" O TRP B1449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1447 through 1453' Processing helix chain 'B' and resid 1459 through 1468 Processing helix chain 'B' and resid 1473 through 1481 Processing helix chain 'B' and resid 1481 through 1486 removed outlier: 3.915A pdb=" N GLU B1485 " --> pdb=" O MET B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1498 removed outlier: 4.225A pdb=" N LEU B1493 " --> pdb=" O GLU B1489 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS B1494 " --> pdb=" O TRP B1490 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1522 removed outlier: 4.259A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1520 " --> pdb=" O ALA B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1534 removed outlier: 3.655A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS B1534 " --> pdb=" O GLU B1530 " (cutoff:3.500A) Processing helix chain 'B' and resid 1544 through 1554 removed outlier: 4.408A pdb=" N ALA B1548 " --> pdb=" O ALA B1544 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B1549 " --> pdb=" O PHE B1545 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B1553 " --> pdb=" O VAL B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1566 removed outlier: 3.702A pdb=" N GLN B1562 " --> pdb=" O SER B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1567 through 1570 removed outlier: 3.873A pdb=" N LEU B1570 " --> pdb=" O ALA B1567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1567 through 1570' Processing helix chain 'B' and resid 1572 through 1577 removed outlier: 4.206A pdb=" N THR B1576 " --> pdb=" O ASP B1572 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B1577 " --> pdb=" O ALA B1573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1572 through 1577' Processing helix chain 'B' and resid 1586 through 1597 removed outlier: 3.826A pdb=" N VAL B1591 " --> pdb=" O TYR B1587 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER B1592 " --> pdb=" O GLY B1588 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B1594 " --> pdb=" O MET B1590 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1619 removed outlier: 3.673A pdb=" N ARG B1616 " --> pdb=" O ARG B1612 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B1619 " --> pdb=" O ILE B1615 " (cutoff:3.500A) Processing helix chain 'B' and resid 1622 through 1626 removed outlier: 3.521A pdb=" N GLY B1625 " --> pdb=" O ARG B1622 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1637 removed outlier: 4.164A pdb=" N ASP B1632 " --> pdb=" O ILE B1629 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLN B1634 " --> pdb=" O GLU B1631 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B1635 " --> pdb=" O ASP B1632 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1642 removed outlier: 3.559A pdb=" N SER B1641 " --> pdb=" O MET B1638 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B1642 " --> pdb=" O VAL B1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1638 through 1642' Processing helix chain 'B' and resid 1645 through 1649 Processing helix chain 'B' and resid 1652 through 1662 removed outlier: 3.660A pdb=" N TYR B1656 " --> pdb=" O THR B1652 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B1662 " --> pdb=" O SER B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 removed outlier: 3.803A pdb=" N LEU B1673 " --> pdb=" O ALA B1669 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1707 removed outlier: 3.817A pdb=" N THR B1697 " --> pdb=" O HIS B1693 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B1706 " --> pdb=" O LYS B1702 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B1707 " --> pdb=" O ASN B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1712 through 1725 removed outlier: 3.594A pdb=" N GLN B1718 " --> pdb=" O PHE B1714 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1731 Processing helix chain 'B' and resid 1736 through 1751 removed outlier: 3.732A pdb=" N LYS B1740 " --> pdb=" O ASP B1736 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B1749 " --> pdb=" O LYS B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1752 through 1755 removed outlier: 3.592A pdb=" N GLY B1755 " --> pdb=" O LEU B1752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1752 through 1755' Processing helix chain 'B' and resid 1757 through 1762 removed outlier: 4.038A pdb=" N LEU B1761 " --> pdb=" O TRP B1757 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1781 removed outlier: 3.628A pdb=" N LEU B1773 " --> pdb=" O ILE B1769 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B1774 " --> pdb=" O PRO B1770 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B1779 " --> pdb=" O TYR B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1790 removed outlier: 3.535A pdb=" N ALA B1789 " --> pdb=" O TRP B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1791 through 1812 removed outlier: 3.701A pdb=" N ALA B1800 " --> pdb=" O MET B1796 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B1801 " --> pdb=" O ASN B1797 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B1802 " --> pdb=" O PHE B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1869 through 1878 removed outlier: 3.605A pdb=" N THR B1876 " --> pdb=" O ASP B1872 " (cutoff:3.500A) Processing helix chain 'B' and resid 1885 through 1893 removed outlier: 4.334A pdb=" N PHE B1889 " --> pdb=" O VAL B1885 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B1890 " --> pdb=" O GLN B1886 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B1891 " --> pdb=" O GLY B1887 " (cutoff:3.500A) Processing helix chain 'B' and resid 1898 through 1903 removed outlier: 4.288A pdb=" N ASP B1902 " --> pdb=" O ASN B1898 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1903 " --> pdb=" O ASN B1899 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1898 through 1903' Processing helix chain 'B' and resid 1904 through 1914 removed outlier: 4.302A pdb=" N LEU B1909 " --> pdb=" O ARG B1905 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP B1910 " --> pdb=" O VAL B1906 " (cutoff:3.500A) Processing helix chain 'B' and resid 1916 through 1923 Processing helix chain 'B' and resid 1923 through 1928 removed outlier: 3.513A pdb=" N LYS B1928 " --> pdb=" O VAL B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1965 removed outlier: 4.015A pdb=" N THR B1962 " --> pdb=" O HIS B1958 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B1963 " --> pdb=" O GLN B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1971 removed outlier: 3.897A pdb=" N ALA B1971 " --> pdb=" O HIS B1968 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1968 through 1971' Processing helix chain 'B' and resid 1972 through 1977 removed outlier: 3.661A pdb=" N LEU B1976 " --> pdb=" O LEU B1972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1998 removed outlier: 4.572A pdb=" N HIS B1988 " --> pdb=" O THR B1984 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN B1989 " --> pdb=" O THR B1985 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA B1990 " --> pdb=" O ALA B1986 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B1991 " --> pdb=" O ARG B1987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2001 No H-bonds generated for 'chain 'B' and resid 1999 through 2001' Processing helix chain 'B' and resid 2005 through 2021 removed outlier: 3.588A pdb=" N MET B2011 " --> pdb=" O GLN B2007 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2041 removed outlier: 4.070A pdb=" N MET B2026 " --> pdb=" O LEU B2022 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP B2027 " --> pdb=" O TRP B2023 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS B2028 " --> pdb=" O HIS B2024 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B2034 " --> pdb=" O GLY B2030 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B2038 " --> pdb=" O ALA B2034 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2056 Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2064 through 2074 Processing helix chain 'B' and resid 2077 through 2087 removed outlier: 4.219A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B2083 " --> pdb=" O MET B2079 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B2084 " --> pdb=" O GLU B2080 " (cutoff:3.500A) Processing helix chain 'B' and resid 2097 through 2113 removed outlier: 3.749A pdb=" N ARG B2109 " --> pdb=" O TYR B2105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B2110 " --> pdb=" O HIS B2106 " (cutoff:3.500A) Processing helix chain 'B' and resid 2122 through 2127 removed outlier: 3.945A pdb=" N VAL B2126 " --> pdb=" O GLU B2122 " (cutoff:3.500A) Processing helix chain 'B' and resid 2128 through 2131 Processing helix chain 'B' and resid 2200 through 2209 removed outlier: 4.017A pdb=" N LEU B2204 " --> pdb=" O GLN B2200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B2205 " --> pdb=" O LEU B2201 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN B2206 " --> pdb=" O PHE B2202 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2217 removed outlier: 3.719A pdb=" N ARG B2217 " --> pdb=" O PRO B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2254 removed outlier: 3.667A pdb=" N ARG B2251 " --> pdb=" O HIS B2247 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B2252 " --> pdb=" O ALA B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2265 through 2272 Processing helix chain 'B' and resid 2287 through 2291 removed outlier: 3.761A pdb=" N ALA B2290 " --> pdb=" O PHE B2287 " (cutoff:3.500A) Processing helix chain 'B' and resid 2298 through 2303 removed outlier: 3.728A pdb=" N LEU B2302 " --> pdb=" O ASP B2298 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B2303 " --> pdb=" O LEU B2299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2298 through 2303' Processing helix chain 'B' and resid 2310 through 2323 removed outlier: 3.637A pdb=" N ASP B2315 " --> pdb=" O GLU B2311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B2321 " --> pdb=" O ARG B2317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B2323 " --> pdb=" O ASN B2319 " (cutoff:3.500A) Processing helix chain 'B' and resid 2329 through 2335 Processing helix chain 'B' and resid 2340 through 2342 No H-bonds generated for 'chain 'B' and resid 2340 through 2342' Processing helix chain 'B' and resid 2380 through 2386 Processing helix chain 'B' and resid 2396 through 2409 removed outlier: 3.788A pdb=" N THR B2402 " --> pdb=" O ILE B2398 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B2403 " --> pdb=" O THR B2399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B2404 " --> pdb=" O CYS B2400 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B2405 " --> pdb=" O HIS B2401 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B2406 " --> pdb=" O THR B2402 " (cutoff:3.500A) Processing helix chain 'B' and resid 2410 through 2415 Processing helix chain 'B' and resid 2417 through 2422 removed outlier: 4.118A pdb=" N PHE B2421 " --> pdb=" O VAL B2417 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B2422 " --> pdb=" O LEU B2418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2417 through 2422' Processing helix chain 'B' and resid 2427 through 2431 removed outlier: 4.040A pdb=" N ARG B2430 " --> pdb=" O LEU B2427 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2510 removed outlier: 3.697A pdb=" N ILE B2498 " --> pdb=" O ASN B2494 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B2499 " --> pdb=" O LYS B2495 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B2501 " --> pdb=" O ALA B2497 " (cutoff:3.500A) Processing helix chain 'B' and resid 2520 through 2528 removed outlier: 3.563A pdb=" N LEU B2528 " --> pdb=" O GLN B2524 " (cutoff:3.500A) Processing helix chain 'B' and resid 2529 through 2534 removed outlier: 3.853A pdb=" N SER B2534 " --> pdb=" O LYS B2530 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 211 Proline residue: E 199 - end of helix Processing helix chain 'E' and resid 216 through 234 Processing helix chain 'E' and resid 240 through 250 Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.942A pdb=" N HIS E 261 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 265 " --> pdb=" O HIS E 261 " (cutoff:3.500A) Proline residue: E 266 - end of helix Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 282 through 292 removed outlier: 3.849A pdb=" N GLY E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE E 288 " --> pdb=" O SER E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 Processing helix chain 'E' and resid 298 through 316 Proline residue: E 304 - end of helix removed outlier: 3.516A pdb=" N VAL E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 327 through 337 removed outlier: 3.899A pdb=" N ILE E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.972A pdb=" N ILE E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 350 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 354 " --> pdb=" O LEU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 374 removed outlier: 3.989A pdb=" N VAL E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU E 372 " --> pdb=" O PHE E 368 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 373 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 374' Processing helix chain 'E' and resid 378 through 399 removed outlier: 4.351A pdb=" N ARG E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Proline residue: E 385 - end of helix Processing helix chain 'E' and resid 405 through 409 removed outlier: 3.782A pdb=" N LEU E 408 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL E 409 " --> pdb=" O GLU E 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 409' Processing helix chain 'E' and resid 410 through 418 removed outlier: 4.124A pdb=" N SER E 415 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 removed outlier: 4.064A pdb=" N ALA E 423 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 424 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 420 through 424' Processing helix chain 'E' and resid 430 through 448 Proline residue: E 439 - end of helix removed outlier: 4.234A pdb=" N CYS E 448 " --> pdb=" O HIS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 469 Proline residue: E 462 - end of helix Processing helix chain 'E' and resid 473 through 476 removed outlier: 3.796A pdb=" N LEU E 476 " --> pdb=" O LEU E 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 476' Processing helix chain 'E' and resid 477 through 483 removed outlier: 3.723A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 507 removed outlier: 4.282A pdb=" N ILE E 502 " --> pdb=" O ILE E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 536 removed outlier: 3.688A pdb=" N ILE E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 549 Processing helix chain 'E' and resid 551 through 557 removed outlier: 3.640A pdb=" N LYS E 556 " --> pdb=" O GLY E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 578 removed outlier: 3.708A pdb=" N PHE E 573 " --> pdb=" O GLN E 569 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 574 " --> pdb=" O LEU E 570 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG E 575 " --> pdb=" O HIS E 571 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 576 " --> pdb=" O ARG E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 592 Processing helix chain 'E' and resid 594 through 609 removed outlier: 3.738A pdb=" N LYS E 599 " --> pdb=" O PHE E 595 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR E 609 " --> pdb=" O GLY E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 613 removed outlier: 4.281A pdb=" N LEU E 613 " --> pdb=" O GLU E 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 610 through 613' Processing helix chain 'E' and resid 622 through 632 removed outlier: 3.861A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 640 removed outlier: 3.796A pdb=" N GLY E 639 " --> pdb=" O ALA E 636 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET E 640 " --> pdb=" O SER E 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 636 through 640' Processing helix chain 'E' and resid 652 through 665 removed outlier: 3.613A pdb=" N ILE E 663 " --> pdb=" O TYR E 659 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY E 664 " --> pdb=" O PHE E 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 681 Processing helix chain 'E' and resid 693 through 705 Processing helix chain 'E' and resid 731 through 744 removed outlier: 4.084A pdb=" N HIS E 735 " --> pdb=" O TYR E 731 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 736 " --> pdb=" O ALA E 732 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 744 " --> pdb=" O LEU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 764 removed outlier: 3.510A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 764 " --> pdb=" O HIS E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 772 removed outlier: 3.666A pdb=" N ALA E 770 " --> pdb=" O ILE E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 811 removed outlier: 3.730A pdb=" N LEU E 805 " --> pdb=" O GLY E 801 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU E 806 " --> pdb=" O LEU E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 removed outlier: 3.995A pdb=" N GLU E 820 " --> pdb=" O SER E 816 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG E 821 " --> pdb=" O TYR E 817 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL E 824 " --> pdb=" O GLU E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 843 Processing helix chain 'E' and resid 847 through 861 Proline residue: E 857 - end of helix Processing helix chain 'E' and resid 867 through 872 removed outlier: 3.952A pdb=" N LEU E 871 " --> pdb=" O ASN E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 885 Processing helix chain 'E' and resid 890 through 896 removed outlier: 3.532A pdb=" N HIS E 894 " --> pdb=" O LYS E 890 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 896 " --> pdb=" O GLY E 892 " (cutoff:3.500A) Processing helix chain 'E' and resid 896 through 907 removed outlier: 3.875A pdb=" N ILE E 901 " --> pdb=" O GLU E 897 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE E 902 " --> pdb=" O VAL E 898 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS E 906 " --> pdb=" O ILE E 902 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG E 907 " --> pdb=" O THR E 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 930 removed outlier: 4.318A pdb=" N ASP E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 930 " --> pdb=" O SER E 926 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 958 Proline residue: E 950 - end of helix Processing helix chain 'E' and resid 959 through 975 Processing helix chain 'E' and resid 985 through 994 removed outlier: 3.663A pdb=" N ASP E 991 " --> pdb=" O CYS E 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 992 " --> pdb=" O HIS E 988 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 994 " --> pdb=" O TRP E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1018 removed outlier: 3.649A pdb=" N ASP E1007 " --> pdb=" O VAL E1003 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL E1008 " --> pdb=" O VAL E1004 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN E1010 " --> pdb=" O ASP E1006 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU E1011 " --> pdb=" O ASP E1007 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS E1012 " --> pdb=" O VAL E1008 " (cutoff:3.500A) Processing helix chain 'E' and resid 1611 through 1626 Processing helix chain 'E' and resid 1631 through 1648 Processing helix chain 'E' and resid 1681 through 1695 Processing helix chain 'F' and resid 193 through 211 Proline residue: F 199 - end of helix Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 250 Processing helix chain 'F' and resid 257 through 268 removed outlier: 3.942A pdb=" N HIS F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 265 " --> pdb=" O HIS F 261 " (cutoff:3.500A) Proline residue: F 266 - end of helix Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.849A pdb=" N GLY F 287 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE F 288 " --> pdb=" O SER F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 Processing helix chain 'F' and resid 298 through 316 Proline residue: F 304 - end of helix removed outlier: 3.516A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'F' and resid 327 through 337 removed outlier: 3.899A pdb=" N ILE F 334 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 354 removed outlier: 3.971A pdb=" N ILE F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 350 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 374 removed outlier: 3.989A pdb=" N VAL F 369 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU F 372 " --> pdb=" O PHE F 368 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 365 through 374' Processing helix chain 'F' and resid 378 through 399 removed outlier: 4.351A pdb=" N ARG F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Proline residue: F 385 - end of helix Processing helix chain 'F' and resid 405 through 409 removed outlier: 3.782A pdb=" N LEU F 408 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 409 " --> pdb=" O GLU F 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 405 through 409' Processing helix chain 'F' and resid 410 through 418 removed outlier: 4.123A pdb=" N SER F 415 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.064A pdb=" N ALA F 423 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 424 " --> pdb=" O VAL F 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 420 through 424' Processing helix chain 'F' and resid 430 through 448 Proline residue: F 439 - end of helix removed outlier: 4.235A pdb=" N CYS F 448 " --> pdb=" O HIS F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 469 Proline residue: F 462 - end of helix Processing helix chain 'F' and resid 473 through 476 removed outlier: 3.796A pdb=" N LEU F 476 " --> pdb=" O LEU F 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 473 through 476' Processing helix chain 'F' and resid 477 through 483 removed outlier: 3.724A pdb=" N GLU F 481 " --> pdb=" O LYS F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 507 removed outlier: 4.283A pdb=" N ILE F 502 " --> pdb=" O ILE F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 536 removed outlier: 3.688A pdb=" N ILE F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 549 Processing helix chain 'F' and resid 551 through 557 removed outlier: 3.640A pdb=" N LYS F 556 " --> pdb=" O GLY F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 578 removed outlier: 3.708A pdb=" N PHE F 573 " --> pdb=" O GLN F 569 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL F 574 " --> pdb=" O LEU F 570 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 Processing helix chain 'F' and resid 594 through 609 removed outlier: 3.738A pdb=" N LYS F 599 " --> pdb=" O PHE F 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN F 600 " --> pdb=" O ALA F 596 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR F 609 " --> pdb=" O GLY F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 613 removed outlier: 4.281A pdb=" N LEU F 613 " --> pdb=" O GLU F 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 610 through 613' Processing helix chain 'F' and resid 622 through 632 removed outlier: 3.862A pdb=" N LEU F 626 " --> pdb=" O TYR F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 640 removed outlier: 3.796A pdb=" N GLY F 639 " --> pdb=" O ALA F 636 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET F 640 " --> pdb=" O SER F 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 636 through 640' Processing helix chain 'F' and resid 652 through 665 removed outlier: 3.613A pdb=" N ILE F 663 " --> pdb=" O TYR F 659 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY F 664 " --> pdb=" O PHE F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 681 Processing helix chain 'F' and resid 693 through 705 Processing helix chain 'F' and resid 731 through 744 removed outlier: 4.084A pdb=" N HIS F 735 " --> pdb=" O TYR F 731 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU F 736 " --> pdb=" O ALA F 732 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 764 removed outlier: 3.510A pdb=" N THR F 757 " --> pdb=" O GLU F 753 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 764 " --> pdb=" O HIS F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 772 removed outlier: 3.665A pdb=" N ALA F 770 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 801 through 811 removed outlier: 3.730A pdb=" N LEU F 805 " --> pdb=" O GLY F 801 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 removed outlier: 3.995A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG F 821 " --> pdb=" O TYR F 817 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 824 " --> pdb=" O GLU F 820 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 843 Processing helix chain 'F' and resid 847 through 861 Proline residue: F 857 - end of helix Processing helix chain 'F' and resid 867 through 872 removed outlier: 3.953A pdb=" N LEU F 871 " --> pdb=" O ASN F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 885 Processing helix chain 'F' and resid 890 through 896 removed outlier: 3.532A pdb=" N HIS F 894 " --> pdb=" O LYS F 890 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 896 " --> pdb=" O GLY F 892 " (cutoff:3.500A) Processing helix chain 'F' and resid 896 through 907 removed outlier: 3.876A pdb=" N ILE F 901 " --> pdb=" O GLU F 897 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE F 902 " --> pdb=" O VAL F 898 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS F 906 " --> pdb=" O ILE F 902 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG F 907 " --> pdb=" O THR F 903 " (cutoff:3.500A) Processing helix chain 'F' and resid 911 through 930 removed outlier: 4.317A pdb=" N ASP F 915 " --> pdb=" O THR F 911 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 930 " --> pdb=" O SER F 926 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 958 Proline residue: F 950 - end of helix Processing helix chain 'F' and resid 959 through 975 Processing helix chain 'F' and resid 985 through 994 removed outlier: 3.664A pdb=" N ASP F 991 " --> pdb=" O CYS F 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA F 992 " --> pdb=" O HIS F 988 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 994 " --> pdb=" O TRP F 990 " (cutoff:3.500A) Processing helix chain 'F' and resid 1002 through 1018 removed outlier: 3.649A pdb=" N ASP F1007 " --> pdb=" O VAL F1003 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F1008 " --> pdb=" O VAL F1004 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F1010 " --> pdb=" O ASP F1006 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU F1011 " --> pdb=" O ASP F1007 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS F1012 " --> pdb=" O VAL F1008 " (cutoff:3.500A) Processing helix chain 'F' and resid 1611 through 1626 Processing helix chain 'F' and resid 1631 through 1648 Processing helix chain 'F' and resid 1681 through 1695 Processing helix chain 'G' and resid 9 through 20 removed outlier: 4.287A pdb=" N UNK G 13 " --> pdb=" O UNK G 9 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK G 14 " --> pdb=" O UNK G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.642A pdb=" N UNK G 57 " --> pdb=" O UNK G 53 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N UNK G 58 " --> pdb=" O UNK G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.748A pdb=" N UNK G 76 " --> pdb=" O UNK G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 104 removed outlier: 4.397A pdb=" N UNK G 93 " --> pdb=" O UNK G 89 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK G 102 " --> pdb=" O UNK G 98 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N UNK G 104 " --> pdb=" O UNK G 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 removed outlier: 4.287A pdb=" N UNK H 13 " --> pdb=" O UNK H 9 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK H 14 " --> pdb=" O UNK H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.642A pdb=" N UNK H 57 " --> pdb=" O UNK H 53 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N UNK H 58 " --> pdb=" O UNK H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.748A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 104 removed outlier: 3.539A pdb=" N UNK H 102 " --> pdb=" O UNK H 98 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N UNK H 104 " --> pdb=" O UNK H 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2170 through 2175 removed outlier: 3.652A pdb=" N PHE A2182 " --> pdb=" O LEU A2174 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A2187 " --> pdb=" O GLY A2235 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A2235 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2243 through 2244 Processing sheet with id=AA3, first strand: chain 'B' and resid 2170 through 2175 removed outlier: 3.652A pdb=" N PHE B2182 " --> pdb=" O LEU B2174 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B2187 " --> pdb=" O GLY B2235 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B2235 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2243 through 2244 Processing sheet with id=AA5, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.062A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.663A pdb=" N ILE C 57 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 93 removed outlier: 4.026A pdb=" N SER C 90 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 100 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 removed outlier: 6.558A pdb=" N GLY C 146 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 134 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU C 136 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU C 142 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.166A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 223 through 228 removed outlier: 3.750A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 243 through 245 Processing sheet with id=AB3, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB4, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.062A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 50 removed outlier: 3.663A pdb=" N ILE D 57 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 93 removed outlier: 4.026A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET D 100 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 131 through 136 removed outlier: 6.557A pdb=" N GLY D 146 " --> pdb=" O ASN D 132 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL D 134 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE D 144 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU D 136 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU D 142 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 184 through 188 removed outlier: 6.166A pdb=" N CYS D 194 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS D 215 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 196 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 223 through 228 removed outlier: 3.749A pdb=" N GLN D 225 " --> pdb=" O CYS D 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 243 through 245 Processing sheet with id=AC2, first strand: chain 'D' and resid 294 through 295 1768 hydrogen bonds defined for protein. 5118 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: 22.70 Time building geometry restraints manager: 19.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 16896 1.35 - 1.46: 10433 1.46 - 1.58: 22201 1.58 - 1.70: 0 1.70 - 1.81: 430 Bond restraints: 49960 Sorted by residual: bond pdb=" C MET A 727 " pdb=" N PRO A 728 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.24e-02 6.50e+03 1.13e+01 bond pdb=" C MET B 727 " pdb=" N PRO B 728 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.24e-02 6.50e+03 1.12e+01 bond pdb=" C THR A 631 " pdb=" N PRO A 632 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.33e+00 bond pdb=" N LEU E 430 " pdb=" CA LEU E 430 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" C THR B 631 " pdb=" N PRO B 632 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.23e+00 ... (remaining 49955 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 1272 106.53 - 113.40: 27174 113.40 - 120.27: 18867 120.27 - 127.14: 20221 127.14 - 134.01: 512 Bond angle restraints: 68046 Sorted by residual: angle pdb=" C GLU F 429 " pdb=" N LEU F 430 " pdb=" CA LEU F 430 " ideal model delta sigma weight residual 121.70 133.87 -12.17 1.80e+00 3.09e-01 4.57e+01 angle pdb=" C GLU E 429 " pdb=" N LEU E 430 " pdb=" CA LEU E 430 " ideal model delta sigma weight residual 121.70 133.85 -12.15 1.80e+00 3.09e-01 4.56e+01 angle pdb=" C LEU F 212 " pdb=" N LYS F 213 " pdb=" CA LYS F 213 " ideal model delta sigma weight residual 121.70 133.51 -11.81 1.80e+00 3.09e-01 4.30e+01 angle pdb=" C LEU E 212 " pdb=" N LYS E 213 " pdb=" CA LYS E 213 " ideal model delta sigma weight residual 121.70 133.48 -11.78 1.80e+00 3.09e-01 4.28e+01 angle pdb=" N ILE A1027 " pdb=" CA ILE A1027 " pdb=" C ILE A1027 " ideal model delta sigma weight residual 113.20 106.96 6.24 9.60e-01 1.09e+00 4.23e+01 ... (remaining 68041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 28681 15.09 - 30.18: 992 30.18 - 45.27: 309 45.27 - 60.37: 40 60.37 - 75.46: 32 Dihedral angle restraints: 30054 sinusoidal: 9850 harmonic: 20204 Sorted by residual: dihedral pdb=" CA PRO A 120 " pdb=" C PRO A 120 " pdb=" N VAL A 121 " pdb=" CA VAL A 121 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO B 120 " pdb=" C PRO B 120 " pdb=" N VAL B 121 " pdb=" CA VAL B 121 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ARG B 960 " pdb=" C ARG B 960 " pdb=" N ASP B 961 " pdb=" CA ASP B 961 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 30051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6947 0.063 - 0.126: 1044 0.126 - 0.189: 73 0.189 - 0.252: 10 0.252 - 0.315: 4 Chirality restraints: 8078 Sorted by residual: chirality pdb=" CB VAL A 854 " pdb=" CA VAL A 854 " pdb=" CG1 VAL A 854 " pdb=" CG2 VAL A 854 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL B 854 " pdb=" CA VAL B 854 " pdb=" CG1 VAL B 854 " pdb=" CG2 VAL B 854 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU B 856 " pdb=" N GLU B 856 " pdb=" C GLU B 856 " pdb=" CB GLU B 856 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 8075 not shown) Planarity restraints: 8896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 791 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO B 792 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 792 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 792 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 791 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO A 792 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 792 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 792 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 856 " -0.047 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 857 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 857 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 857 " -0.039 5.00e-02 4.00e+02 ... (remaining 8893 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 13920 2.80 - 3.33: 39723 3.33 - 3.85: 75229 3.85 - 4.38: 81638 4.38 - 4.90: 138917 Nonbonded interactions: 349427 Sorted by model distance: nonbonded pdb=" O PHE A1888 " pdb=" OG SER A1891 " model vdw 2.281 2.440 nonbonded pdb=" O PHE B1888 " pdb=" OG SER B1891 " model vdw 2.282 2.440 nonbonded pdb=" O GLU B2363 " pdb=" OG1 THR B2367 " model vdw 2.285 2.440 nonbonded pdb=" O GLU A2363 " pdb=" OG1 THR A2367 " model vdw 2.286 2.440 nonbonded pdb=" O LEU A 894 " pdb=" OH TYR A1587 " model vdw 2.298 2.440 ... (remaining 349422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.050 Extract box with map and model: 16.210 Check model and map are aligned: 0.710 Set scattering table: 0.410 Process input model: 126.990 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 0.051 49960 Z= 0.199 Angle : 0.771 12.166 68046 Z= 0.407 Chirality : 0.045 0.315 8078 Planarity : 0.006 0.114 8896 Dihedral : 9.658 75.457 16850 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.25 % 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: -5.28 (0.07), residues: 6556 helix: -3.85 (0.05), residues: 3062 sheet: -1.58 (0.33), residues: 232 loop : -3.29 (0.09), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1786 HIS 0.014 0.001 HIS A1744 PHE 0.019 0.001 PHE B1751 TYR 0.015 0.001 TYR B 861 ARG 0.017 0.000 ARG B 859 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13112 Ramachandran restraints generated. 6556 Oldfield, 0 Emsley, 6556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13112 Ramachandran restraints generated. 6556 Oldfield, 0 Emsley, 6556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8230 (mttp) REVERT: A 488 MET cc_start: 0.5099 (mmp) cc_final: 0.4683 (tpp) REVERT: A 671 ILE cc_start: 0.8838 (mt) cc_final: 0.8372 (mt) REVERT: A 732 LYS cc_start: 0.9089 (pttp) cc_final: 0.8885 (pttp) REVERT: A 795 ILE cc_start: 0.8553 (mt) cc_final: 0.8335 (tt) REVERT: A 799 LEU cc_start: 0.9027 (mm) cc_final: 0.8368 (tt) REVERT: A 822 ILE cc_start: 0.9280 (mt) cc_final: 0.8933 (pt) REVERT: A 839 VAL cc_start: 0.9154 (m) cc_final: 0.8948 (p) REVERT: A 841 LEU cc_start: 0.9166 (mm) cc_final: 0.8762 (tt) REVERT: A 887 VAL cc_start: 0.8517 (t) cc_final: 0.8278 (p) REVERT: A 978 ILE cc_start: 0.9175 (mt) cc_final: 0.8962 (mm) REVERT: A 1010 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7989 (tp30) REVERT: A 1053 ILE cc_start: 0.9339 (pt) cc_final: 0.9031 (pt) REVERT: A 1109 ASP cc_start: 0.9235 (p0) cc_final: 0.8452 (p0) REVERT: A 1110 TYR cc_start: 0.8611 (m-80) cc_final: 0.8192 (m-80) REVERT: A 1137 GLU cc_start: 0.9326 (pm20) cc_final: 0.8874 (pm20) REVERT: A 1175 ASP cc_start: 0.9122 (m-30) cc_final: 0.8786 (p0) REVERT: A 1311 ASN cc_start: 0.8595 (m-40) cc_final: 0.8158 (p0) REVERT: A 1427 GLU cc_start: 0.8770 (pm20) cc_final: 0.8257 (pt0) REVERT: A 1481 MET cc_start: 0.9154 (mtp) cc_final: 0.8814 (ptp) REVERT: A 1512 MET cc_start: 0.8334 (tpp) cc_final: 0.8127 (ttt) REVERT: A 1539 ASP cc_start: 0.9265 (t70) cc_final: 0.8836 (p0) REVERT: A 1592 SER cc_start: 0.9379 (m) cc_final: 0.9131 (p) REVERT: A 1650 MET cc_start: 0.7801 (mmt) cc_final: 0.7418 (mpp) REVERT: A 1904 LEU cc_start: 0.9505 (mt) cc_final: 0.9163 (pt) REVERT: A 1905 ARG cc_start: 0.8924 (mmp80) cc_final: 0.8619 (mmm160) REVERT: A 2156 ILE cc_start: 0.7704 (tp) cc_final: 0.7502 (tp) REVERT: A 2194 GLN cc_start: 0.9051 (mt0) cc_final: 0.8643 (tm-30) REVERT: A 2215 SER cc_start: 0.8555 (m) cc_final: 0.7806 (p) REVERT: A 2249 LEU cc_start: 0.9334 (mm) cc_final: 0.8936 (mm) REVERT: A 2252 ASP cc_start: 0.9293 (m-30) cc_final: 0.8891 (p0) REVERT: A 2262 ASN cc_start: 0.7400 (m-40) cc_final: 0.6904 (t0) REVERT: A 2263 ILE cc_start: 0.7840 (tp) cc_final: 0.7516 (tt) REVERT: A 2404 MET cc_start: 0.9142 (tpp) cc_final: 0.8876 (ttm) REVERT: A 2415 MET cc_start: 0.8539 (mmm) cc_final: 0.8214 (mmm) outliers start: 1 outliers final: 1 residues processed: 439 average time/residue: 0.3385 time to fit residues: 213.1834 Evaluate side-chains 252 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.031 Evaluate side-chains 39 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: C 15 LEU cc_start: 0.9445 (tp) cc_final: 0.9239 (mt) REVERT: C 255 MET cc_start: 0.8189 (ttp) cc_final: 0.7911 (ptp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1624 time to fit residues: 7.5461 Evaluate side-chains 15 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.303 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.415 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0396 time to fit residues: 1.3317 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.453 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0237 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 580 optimal weight: 9.9990 chunk 521 optimal weight: 10.0000 chunk 289 optimal weight: 0.0170 chunk 178 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 278 optimal weight: 0.0870 chunk 539 optimal weight: 0.8980 chunk 208 optimal weight: 0.1980 chunk 327 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 624 optimal weight: 20.0000 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 HIS B 193 ASN B 743 HIS B 763 ASN B 899 HIS B 962 GLN B1206 HIS ** B1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1420 ASN B1634 GLN B1687 HIS ** B1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1782 HIS B1937 GLN B1997 ASN B2001 HIS B2194 GLN B2219 ASN B2277 HIS Total number of N/Q/H flips: 17 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN D 311 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 49960 Z= 0.129 Angle : 0.532 10.156 68046 Z= 0.268 Chirality : 0.040 0.189 8078 Planarity : 0.005 0.116 8896 Dihedral : 3.814 25.652 7300 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.09), residues: 6556 helix: -2.32 (0.07), residues: 3202 sheet: -1.56 (0.32), residues: 268 loop : -2.84 (0.10), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1910 HIS 0.007 0.001 HIS A1958 PHE 0.039 0.001 PHE A1363 TYR 0.038 0.001 TYR A2396 ARG 0.011 0.000 ARG B1154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.023 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: B 617 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7134 (mm-30) REVERT: B 697 PHE cc_start: 0.8711 (m-80) cc_final: 0.8242 (m-80) REVERT: B 755 ARG cc_start: 0.8246 (tpt170) cc_final: 0.7878 (mmp-170) REVERT: B 777 LYS cc_start: 0.9513 (mppt) cc_final: 0.9026 (pttt) REVERT: B 799 LEU cc_start: 0.9219 (mm) cc_final: 0.8693 (tt) REVERT: B 805 LEU cc_start: 0.8704 (mt) cc_final: 0.8418 (mt) REVERT: B 841 LEU cc_start: 0.9448 (mm) cc_final: 0.8878 (tt) REVERT: B 843 THR cc_start: 0.8245 (m) cc_final: 0.7429 (m) REVERT: B 1068 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8977 (pttt) REVERT: B 1109 ASP cc_start: 0.9189 (p0) cc_final: 0.8344 (p0) REVERT: B 1292 LEU cc_start: 0.7565 (mt) cc_final: 0.7136 (tt) REVERT: B 1382 LEU cc_start: 0.8598 (pt) cc_final: 0.8257 (mt) REVERT: B 1481 MET cc_start: 0.9041 (mtp) cc_final: 0.8573 (ptp) REVERT: B 1591 VAL cc_start: 0.9403 (p) cc_final: 0.9146 (m) REVERT: B 1592 SER cc_start: 0.9511 (m) cc_final: 0.9225 (p) REVERT: B 1595 MET cc_start: 0.9210 (ttt) cc_final: 0.8872 (mtp) REVERT: B 1638 MET cc_start: 0.7289 (ttt) cc_final: 0.6450 (tpt) REVERT: B 1650 MET cc_start: 0.7713 (mmt) cc_final: 0.7281 (mpp) REVERT: B 2011 MET cc_start: 0.9169 (tmm) cc_final: 0.8728 (ppp) REVERT: B 2249 LEU cc_start: 0.9142 (mm) cc_final: 0.8783 (mm) REVERT: B 2252 ASP cc_start: 0.9135 (m-30) cc_final: 0.8713 (p0) REVERT: B 2358 PHE cc_start: 0.8988 (m-10) cc_final: 0.8707 (m-10) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3071 time to fit residues: 140.3727 Evaluate side-chains 221 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.727 Evaluate side-chains 23 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.308 Fit side-chains REVERT: D 15 LEU cc_start: 0.9562 (tp) cc_final: 0.9360 (mm) REVERT: D 87 ASN cc_start: 0.6458 (t0) cc_final: 0.6082 (p0) REVERT: D 185 MET cc_start: 0.9262 (tpt) cc_final: 0.9030 (tpp) REVERT: D 255 MET cc_start: 0.8065 (ttp) cc_final: 0.7632 (pmm) REVERT: D 273 MET cc_start: 0.7275 (mtt) cc_final: 0.6766 (ptp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1367 time to fit residues: 4.0582 Evaluate side-chains 15 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.300 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0404 time to fit residues: 1.4722 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.456 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0265 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 347 optimal weight: 0.9990 chunk 193 optimal weight: 0.0870 chunk 519 optimal weight: 30.0000 chunk 425 optimal weight: 0.4980 chunk 172 optimal weight: 0.5980 chunk 625 optimal weight: 5.9990 chunk 676 optimal weight: 0.0770 chunk 557 optimal weight: 0.9980 chunk 620 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 502 optimal weight: 40.0000 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS B1554 GLN ** B1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2502 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 49960 Z= 0.243 Angle : 0.856 29.489 68046 Z= 0.419 Chirality : 0.051 0.502 8078 Planarity : 0.009 0.202 8896 Dihedral : 4.169 30.474 7300 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.33 % Allowed : 2.58 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.09), residues: 6556 helix: -1.99 (0.08), residues: 3186 sheet: -1.50 (0.31), residues: 288 loop : -2.81 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 199 HIS 0.061 0.003 HIS B 262 PHE 0.086 0.005 PHE B 183 TYR 0.077 0.003 TYR A 144 ARG 0.062 0.002 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 270 time to evaluate : 2.079 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: B 150 LYS cc_start: 0.8798 (tmtt) cc_final: 0.8467 (mttp) REVERT: B 488 MET cc_start: 0.3656 (tpt) cc_final: 0.3419 (tpp) REVERT: B 697 PHE cc_start: 0.8668 (m-80) cc_final: 0.8272 (m-80) REVERT: B 777 LYS cc_start: 0.9516 (mppt) cc_final: 0.9105 (pttt) REVERT: B 799 LEU cc_start: 0.9328 (mm) cc_final: 0.8792 (tt) REVERT: B 805 LEU cc_start: 0.8761 (mt) cc_final: 0.8454 (mt) REVERT: B 841 LEU cc_start: 0.9445 (mm) cc_final: 0.8875 (tt) REVERT: B 843 THR cc_start: 0.8271 (m) cc_final: 0.7559 (m) REVERT: B 887 VAL cc_start: 0.8645 (t) cc_final: 0.8253 (t) REVERT: B 970 MET cc_start: 0.8663 (ptm) cc_final: 0.8200 (mpp) REVERT: B 1031 MET cc_start: 0.8438 (tmm) cc_final: 0.8199 (tmm) REVERT: B 1038 MET cc_start: 0.7233 (tmm) cc_final: 0.6642 (tmm) REVERT: B 1068 LYS cc_start: 0.9343 (mmtm) cc_final: 0.8966 (pttt) REVERT: B 1109 ASP cc_start: 0.8631 (p0) cc_final: 0.8270 (p0) REVERT: B 1110 TYR cc_start: 0.7906 (m-80) cc_final: 0.7188 (m-10) REVERT: B 1382 LEU cc_start: 0.8668 (pt) cc_final: 0.8358 (mt) REVERT: B 1481 MET cc_start: 0.8920 (mtp) cc_final: 0.8560 (ptm) REVERT: B 1591 VAL cc_start: 0.9420 (p) cc_final: 0.9167 (m) REVERT: B 1592 SER cc_start: 0.9519 (m) cc_final: 0.9231 (p) REVERT: B 1595 MET cc_start: 0.9193 (ttt) cc_final: 0.8878 (mtp) REVERT: B 1638 MET cc_start: 0.7342 (ttt) cc_final: 0.6496 (tpt) REVERT: B 1650 MET cc_start: 0.7576 (mmt) cc_final: 0.7259 (mpp) REVERT: B 2216 LEU cc_start: 0.8795 (mm) cc_final: 0.8564 (mt) REVERT: B 2249 LEU cc_start: 0.9129 (mm) cc_final: 0.8755 (mm) REVERT: B 2252 ASP cc_start: 0.9159 (m-30) cc_final: 0.8675 (p0) REVERT: B 2358 PHE cc_start: 0.8978 (m-10) cc_final: 0.8749 (m-80) outliers start: 7 outliers final: 2 residues processed: 272 average time/residue: 0.2851 time to fit residues: 119.1609 Evaluate side-chains 213 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.888 Evaluate side-chains 21 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.265 Fit side-chains REVERT: D 15 LEU cc_start: 0.9558 (tp) cc_final: 0.9292 (mp) REVERT: D 185 MET cc_start: 0.9301 (tpt) cc_final: 0.9046 (tpp) REVERT: D 255 MET cc_start: 0.8098 (ttp) cc_final: 0.7707 (ptp) REVERT: D 273 MET cc_start: 0.7331 (mtt) cc_final: 0.6775 (ptp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0916 time to fit residues: 2.7393 Evaluate side-chains 14 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.265 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.445 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0400 time to fit residues: 1.4087 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.544 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0268 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 688 random chunks: chunk 618 optimal weight: 1.9990 chunk 470 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 298 optimal weight: 0.0000 chunk 420 optimal weight: 0.9980 chunk 628 optimal weight: 20.0000 chunk 665 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 595 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 HIS B 829 GLN ** B1202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1968 HIS B1997 ASN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 49960 Z= 0.243 Angle : 0.856 29.489 68046 Z= 0.419 Chirality : 0.051 0.502 8078 Planarity : 0.009 0.202 8896 Dihedral : 4.169 30.474 7300 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.05 % Allowed : 0.00 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.09), residues: 6556 helix: -1.99 (0.08), residues: 3186 sheet: -1.50 (0.31), residues: 288 loop : -2.81 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 199 HIS 0.061 0.003 HIS B 262 PHE 0.086 0.005 PHE A 183 TYR 0.077 0.003 TYR B 144 ARG 0.062 0.002 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8778 Ramachandran restraints generated. 4389 Oldfield, 0 Emsley, 4389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 2.037 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: B 150 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8468 (mttp) REVERT: B 488 MET cc_start: 0.3657 (tpt) cc_final: 0.3394 (tpp) REVERT: B 697 PHE cc_start: 0.8705 (m-80) cc_final: 0.8296 (m-80) REVERT: B 777 LYS cc_start: 0.9519 (mppt) cc_final: 0.9105 (pttt) REVERT: B 799 LEU cc_start: 0.9326 (mm) cc_final: 0.8793 (tt) REVERT: B 805 LEU cc_start: 0.8759 (mt) cc_final: 0.8452 (mt) REVERT: B 841 LEU cc_start: 0.9462 (mm) cc_final: 0.8875 (tt) REVERT: B 843 THR cc_start: 0.8157 (m) cc_final: 0.7420 (m) REVERT: B 887 VAL cc_start: 0.8648 (t) cc_final: 0.8253 (t) REVERT: B 970 MET cc_start: 0.8670 (ptm) cc_final: 0.8189 (mpp) REVERT: B 1031 MET cc_start: 0.8443 (tmm) cc_final: 0.8199 (tmm) REVERT: B 1038 MET cc_start: 0.7227 (tmm) cc_final: 0.6647 (tmm) REVERT: B 1068 LYS cc_start: 0.9340 (mmtm) cc_final: 0.8963 (pttt) REVERT: B 1109 ASP cc_start: 0.8634 (p0) cc_final: 0.8263 (p0) REVERT: B 1110 TYR cc_start: 0.7918 (m-80) cc_final: 0.7204 (m-10) REVERT: B 1300 LEU cc_start: 0.9184 (tp) cc_final: 0.8984 (tp) REVERT: B 1382 LEU cc_start: 0.8655 (pt) cc_final: 0.8355 (mt) REVERT: B 1481 MET cc_start: 0.8817 (mtp) cc_final: 0.8574 (ptm) REVERT: B 1591 VAL cc_start: 0.9425 (p) cc_final: 0.9166 (m) REVERT: B 1592 SER cc_start: 0.9515 (m) cc_final: 0.9231 (p) REVERT: B 1595 MET cc_start: 0.9196 (ttt) cc_final: 0.8876 (mtp) REVERT: B 1638 MET cc_start: 0.7343 (ttt) cc_final: 0.6496 (tpt) REVERT: B 1650 MET cc_start: 0.7574 (mmt) cc_final: 0.7261 (mpp) REVERT: B 2047 MET cc_start: 0.5965 (ptm) cc_final: 0.5729 (ptm) REVERT: B 2216 LEU cc_start: 0.8789 (mm) cc_final: 0.8567 (mt) REVERT: B 2249 LEU cc_start: 0.9119 (mm) cc_final: 0.8763 (mm) REVERT: B 2252 ASP cc_start: 0.9160 (m-30) cc_final: 0.8675 (p0) REVERT: B 2358 PHE cc_start: 0.9010 (m-10) cc_final: 0.8750 (m-80) outliers start: 1 outliers final: 1 residues processed: 253 average time/residue: 0.2796 time to fit residues: 110.5368 Evaluate side-chains 211 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.007 Evaluate side-chains 20 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.313 Fit side-chains REVERT: D 15 LEU cc_start: 0.9557 (tp) cc_final: 0.9292 (mp) REVERT: D 185 MET cc_start: 0.9300 (tpt) cc_final: 0.9046 (tpp) REVERT: D 255 MET cc_start: 0.8094 (ttp) cc_final: 0.7707 (ptp) REVERT: D 273 MET cc_start: 0.7321 (mtt) cc_final: 0.6775 (ptp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1038 time to fit residues: 2.9744 Evaluate side-chains 14 residues out of total 269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.315 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0414 time to fit residues: 1.5315 Evaluate side-chains 10 residues out of total 740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.537 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0282 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0707 > 50: distance: 2 - 3: 11.849 distance: 2 - 5: 8.403 distance: 3 - 4: 17.159 distance: 3 - 12: 20.428 distance: 4 - 28: 40.748 distance: 5 - 6: 6.778 distance: 6 - 8: 5.161 distance: 7 - 9: 3.329 distance: 8 - 10: 10.408 distance: 9 - 11: 9.723 distance: 10 - 11: 14.206 distance: 12 - 13: 15.131 distance: 13 - 14: 3.257 distance: 13 - 16: 3.468 distance: 14 - 15: 7.629 distance: 14 - 21: 9.767 distance: 17 - 18: 3.146 distance: 18 - 19: 9.731 distance: 19 - 20: 9.008 distance: 21 - 22: 7.307 distance: 22 - 23: 5.627 distance: 22 - 25: 4.175 distance: 23 - 24: 5.774 distance: 23 - 28: 37.418 distance: 25 - 27: 6.929 distance: 28 - 29: 59.071 distance: 29 - 30: 26.262 distance: 29 - 32: 30.669 distance: 30 - 31: 23.252 distance: 30 - 40: 4.863 distance: 32 - 33: 15.875 distance: 33 - 34: 15.194 distance: 33 - 35: 10.761 distance: 34 - 36: 4.638 distance: 35 - 37: 3.604 distance: 36 - 38: 6.994 distance: 37 - 38: 10.714 distance: 38 - 39: 14.510 distance: 40 - 41: 8.897 distance: 41 - 42: 18.616 distance: 41 - 44: 15.929 distance: 42 - 43: 15.925 distance: 42 - 48: 40.622 distance: 44 - 45: 15.377 distance: 45 - 47: 13.719 distance: 48 - 49: 33.723 distance: 48 - 54: 35.403 distance: 49 - 50: 9.305 distance: 49 - 52: 16.490 distance: 50 - 51: 8.144 distance: 50 - 55: 15.053 distance: 52 - 53: 18.266 distance: 53 - 54: 18.398 distance: 55 - 56: 7.502 distance: 57 - 58: 6.167 distance: 57 - 66: 3.825 distance: 60 - 61: 6.461 distance: 61 - 62: 23.616 distance: 62 - 63: 45.747 distance: 63 - 64: 42.930 distance: 63 - 65: 34.908 distance: 66 - 67: 15.378 distance: 67 - 68: 16.240 distance: 67 - 70: 6.255 distance: 68 - 69: 7.662 distance: 68 - 73: 11.457 distance: 70 - 72: 3.329 distance: 73 - 74: 4.149