Starting phenix.real_space_refine on Thu Mar 21 11:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5go9_9528/03_2024/5go9_9528.pdb" } resolution = 4.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 616 5.16 5 C 66960 2.51 5 N 17992 2.21 5 O 19496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2323": "NH1" <-> "NH2" Residue "A ARG 2519": "NH1" <-> "NH2" Residue "A ARG 3616": "NH1" <-> "NH2" Residue "A PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4148": "NH1" <-> "NH2" Residue "A ARG 4158": "NH1" <-> "NH2" Residue "A ARG 4498": "NH1" <-> "NH2" Residue "A ARG 4504": "NH1" <-> "NH2" Residue "A ARG 4791": "NH1" <-> "NH2" Residue "A ARG 4823": "NH1" <-> "NH2" Residue "A PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2323": "NH1" <-> "NH2" Residue "B ARG 2519": "NH1" <-> "NH2" Residue "B ARG 3616": "NH1" <-> "NH2" Residue "B PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4148": "NH1" <-> "NH2" Residue "B ARG 4158": "NH1" <-> "NH2" Residue "B ARG 4498": "NH1" <-> "NH2" Residue "B ARG 4504": "NH1" <-> "NH2" Residue "B ARG 4791": "NH1" <-> "NH2" Residue "B ARG 4823": "NH1" <-> "NH2" Residue "B PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2323": "NH1" <-> "NH2" Residue "C ARG 2519": "NH1" <-> "NH2" Residue "C ARG 3616": "NH1" <-> "NH2" Residue "C PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4148": "NH1" <-> "NH2" Residue "C ARG 4158": "NH1" <-> "NH2" Residue "C ARG 4498": "NH1" <-> "NH2" Residue "C ARG 4504": "NH1" <-> "NH2" Residue "C ARG 4791": "NH1" <-> "NH2" Residue "C ARG 4823": "NH1" <-> "NH2" Residue "C PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2323": "NH1" <-> "NH2" Residue "D ARG 2519": "NH1" <-> "NH2" Residue "D ARG 3616": "NH1" <-> "NH2" Residue "D PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4148": "NH1" <-> "NH2" Residue "D ARG 4158": "NH1" <-> "NH2" Residue "D ARG 4498": "NH1" <-> "NH2" Residue "D ARG 4504": "NH1" <-> "NH2" Residue "D ARG 4791": "NH1" <-> "NH2" Residue "D ARG 4823": "NH1" <-> "NH2" Residue "D PHE 4952": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 105068 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 26266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26266 Classifications: {'peptide': 3423} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 313} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1290 Unresolved non-hydrogen angles: 1651 Unresolved non-hydrogen dihedrals: 1071 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 17, 'GLU:plan': 30, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 709 Chain: "B" Number of atoms: 26266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26266 Classifications: {'peptide': 3423} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 313} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1290 Unresolved non-hydrogen angles: 1651 Unresolved non-hydrogen dihedrals: 1072 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 17, 'GLU:plan': 30, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 709 Chain: "C" Number of atoms: 26266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26266 Classifications: {'peptide': 3423} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 313} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1290 Unresolved non-hydrogen angles: 1651 Unresolved non-hydrogen dihedrals: 1071 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 17, 'GLU:plan': 30, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 709 Chain: "D" Number of atoms: 26266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26266 Classifications: {'peptide': 3423} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 313} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1290 Unresolved non-hydrogen angles: 1651 Unresolved non-hydrogen dihedrals: 1070 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 18, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 17, 'GLU:plan': 30, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 709 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25625 SG CYS A4889 199.297 200.055 85.121 1.00147.49 S ATOM 25650 SG CYS A4892 199.555 197.362 87.795 1.00 58.07 S ATOM 51891 SG CYS B4889 200.055 174.503 85.121 1.00147.49 S ATOM 51916 SG CYS B4892 197.362 174.245 87.795 1.00 58.07 S ATOM 78157 SG CYS C4889 174.503 173.745 85.121 1.00147.49 S ATOM 78182 SG CYS C4892 174.245 176.438 87.795 1.00 58.07 S ATOM A03EV SG CYS D4889 173.745 199.297 85.121 1.00147.49 S ATOM A03FK SG CYS D4892 176.438 199.555 87.795 1.00 58.07 S Time building chain proxies: 40.92, per 1000 atoms: 0.39 Number of scatterers: 105068 At special positions: 0 Unit cell: (374.85, 374.85, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 616 16.00 O 19496 8.00 N 17992 7.00 C 66960 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: 31.63 Conformation dependent library (CDL) restraints added in 14.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4892 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4914 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4889 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4892 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4914 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4889 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4892 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4914 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4889 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4892 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4914 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4889 " 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25736 Finding SS restraints... Secondary structure from input PDB file: 576 helices and 100 sheets defined 56.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.38 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 158 removed outlier: 3.836A pdb=" N CYS A 158 " --> pdb=" O GLY A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 158' Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 409 through 439 removed outlier: 4.301A pdb=" N VAL A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.752A pdb=" N PHE A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.669A pdb=" N HIS A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 525 through 540 Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.733A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 562 through 565 removed outlier: 3.894A pdb=" N LEU A 565 " --> pdb=" O LEU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.618A pdb=" N CYS A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.690A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.614A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.606A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.665A pdb=" N LEU A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 875 through 899 removed outlier: 3.842A pdb=" N ARG A 880 " --> pdb=" O PRO A 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 899 " --> pdb=" O MET A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 946 removed outlier: 4.231A pdb=" N MET A 935 " --> pdb=" O TYR A 931 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 4.011A pdb=" N PHE A 985 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 986 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 986' Processing helix chain 'A' and resid 989 through 1011 removed outlier: 3.561A pdb=" N ASP A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1059 removed outlier: 4.565A pdb=" N ASN A1046 " --> pdb=" O THR A1042 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1571 through 1576 removed outlier: 3.720A pdb=" N HIS A1575 " --> pdb=" O PHE A1571 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1576 " --> pdb=" O LYS A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1571 through 1576' Processing helix chain 'A' and resid 1647 through 1665 Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.824A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1691 removed outlier: 4.051A pdb=" N GLU A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A1691 " --> pdb=" O TYR A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1709 removed outlier: 3.554A pdb=" N ILE A1707 " --> pdb=" O TYR A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1722 removed outlier: 4.734A pdb=" N TYR A1714 " --> pdb=" O HIS A1710 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A1718 " --> pdb=" O TYR A1714 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1735 Processing helix chain 'A' and resid 1783 through 1804 removed outlier: 3.815A pdb=" N ALA A1789 " --> pdb=" O ASP A1785 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A1790 " --> pdb=" O ILE A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1831 Proline residue: A1820 - end of helix removed outlier: 3.770A pdb=" N MET A1831 " --> pdb=" O THR A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1847 Processing helix chain 'A' and resid 1900 through 1942 removed outlier: 3.539A pdb=" N LYS A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1914 " --> pdb=" O LEU A1910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A1932 " --> pdb=" O ALA A1928 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A1935 " --> pdb=" O ASP A1931 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A1939 " --> pdb=" O ALA A1935 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A1942 " --> pdb=" O GLN A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2013 removed outlier: 3.536A pdb=" N ILE A2010 " --> pdb=" O THR A2006 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2038 removed outlier: 3.675A pdb=" N ARG A2029 " --> pdb=" O THR A2025 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A2030 " --> pdb=" O ILE A2026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A2035 " --> pdb=" O LEU A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2074 removed outlier: 4.002A pdb=" N SER A2064 " --> pdb=" O GLN A2060 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A2068 " --> pdb=" O SER A2064 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A2070 " --> pdb=" O THR A2066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A2073 " --> pdb=" O ARG A2069 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A2074 " --> pdb=" O TRP A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2093 removed outlier: 3.982A pdb=" N VAL A2082 " --> pdb=" O ASP A2078 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A2087 " --> pdb=" O ARG A2083 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A2088 " --> pdb=" O ALA A2084 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A2093 " --> pdb=" O LEU A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2103 removed outlier: 3.896A pdb=" N ALA A2102 " --> pdb=" O GLY A2098 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A2103 " --> pdb=" O LEU A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2131 removed outlier: 3.656A pdb=" N THR A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A2127 " --> pdb=" O SER A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.903A pdb=" N MET A2143 " --> pdb=" O GLU A2139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A2144 " --> pdb=" O GLU A2140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A2145 " --> pdb=" O LYS A2141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A2152 " --> pdb=" O GLY A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2167 removed outlier: 3.961A pdb=" N MET A2163 " --> pdb=" O HIS A2159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2180 Processing helix chain 'A' and resid 2192 through 2207 removed outlier: 3.671A pdb=" N ASN A2196 " --> pdb=" O LYS A2192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A2197 " --> pdb=" O MET A2193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A2200 " --> pdb=" O ASN A2196 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A2205 " --> pdb=" O LEU A2201 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A2207 " --> pdb=" O TYR A2203 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2214 removed outlier: 3.989A pdb=" N ALA A2214 " --> pdb=" O GLN A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2217 No H-bonds generated for 'chain 'A' and resid 2215 through 2217' Processing helix chain 'A' and resid 2218 through 2226 removed outlier: 3.714A pdb=" N GLU A2224 " --> pdb=" O SER A2220 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2247 Processing helix chain 'A' and resid 2251 through 2258 Processing helix chain 'A' and resid 2259 through 2273 removed outlier: 3.981A pdb=" N LEU A2263 " --> pdb=" O ARG A2259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A2273 " --> pdb=" O TYR A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 4.136A pdb=" N TYR A2299 " --> pdb=" O GLU A2295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2328 removed outlier: 3.700A pdb=" N VAL A2320 " --> pdb=" O GLU A2316 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A2322 " --> pdb=" O ALA A2318 " (cutoff:3.500A) Processing helix chain 'A' and resid 2344 through 2349 removed outlier: 3.596A pdb=" N GLU A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2402 Processing helix chain 'A' and resid 2417 through 2425 removed outlier: 3.729A pdb=" N ARG A2421 " --> pdb=" O ALA A2417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A2423 " --> pdb=" O ARG A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2442 removed outlier: 3.567A pdb=" N SER A2438 " --> pdb=" O VAL A2434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A2439 " --> pdb=" O GLY A2435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A2440 " --> pdb=" O VAL A2436 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A2441 " --> pdb=" O ILE A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2477 removed outlier: 4.181A pdb=" N LYS A2466 " --> pdb=" O CYS A2462 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A2475 " --> pdb=" O LEU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2489 removed outlier: 3.770A pdb=" N LEU A2488 " --> pdb=" O PHE A2484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2489 " --> pdb=" O LEU A2485 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2499 Processing helix chain 'A' and resid 2500 through 2502 No H-bonds generated for 'chain 'A' and resid 2500 through 2502' Processing helix chain 'A' and resid 2512 through 2524 removed outlier: 4.046A pdb=" N ASN A2518 " --> pdb=" O ALA A2514 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A2519 " --> pdb=" O LEU A2515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A2521 " --> pdb=" O LEU A2517 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS A2522 " --> pdb=" O ASN A2518 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A2523 " --> pdb=" O ARG A2519 " (cutoff:3.500A) Processing helix chain 'A' and resid 2525 through 2529 removed outlier: 3.923A pdb=" N LEU A2529 " --> pdb=" O LEU A2526 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2552 removed outlier: 3.650A pdb=" N HIS A2541 " --> pdb=" O ALA A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2559 through 2576 removed outlier: 3.995A pdb=" N LYS A2564 " --> pdb=" O CYS A2560 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2601 removed outlier: 3.547A pdb=" N ARG A2592 " --> pdb=" O HIS A2588 " (cutoff:3.500A) Proline residue: A2598 - end of helix Processing helix chain 'A' and resid 2606 through 2627 removed outlier: 3.735A pdb=" N ARG A2617 " --> pdb=" O ASN A2613 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A2618 " --> pdb=" O HIS A2614 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A2624 " --> pdb=" O LYS A2620 " (cutoff:3.500A) Proline residue: A2625 - end of helix Processing helix chain 'A' and resid 2635 through 2651 Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2668 - end of helix removed outlier: 3.704A pdb=" N GLY A2675 " --> pdb=" O SER A2671 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2740 removed outlier: 3.782A pdb=" N GLU A2719 " --> pdb=" O PRO A2715 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A2721 " --> pdb=" O LYS A2717 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A2723 " --> pdb=" O GLU A2719 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A2724 " --> pdb=" O TYR A2720 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A2727 " --> pdb=" O ASN A2723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A2735 " --> pdb=" O ASP A2731 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A2736 " --> pdb=" O LYS A2732 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A2737 " --> pdb=" O TRP A2733 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A2740 " --> pdb=" O ASP A2736 " (cutoff:3.500A) Processing helix chain 'A' and resid 2749 through 2753 removed outlier: 4.083A pdb=" N LYS A2753 " --> pdb=" O ASP A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 3.895A pdb=" N ILE A2771 " --> pdb=" O LYS A2767 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A2772 " --> pdb=" O GLU A2768 " (cutoff:3.500A) Proline residue: A2775 - end of helix removed outlier: 3.500A pdb=" N THR A2782 " --> pdb=" O GLU A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2835 through 2862 removed outlier: 3.921A pdb=" N GLU A2860 " --> pdb=" O LYS A2856 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2878 Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.966A pdb=" N ASP A2886 " --> pdb=" O GLU A2882 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS A2889 " --> pdb=" O LYS A2885 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2894 " --> pdb=" O ALA A2890 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A2895 " --> pdb=" O GLN A2891 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A2896 " --> pdb=" O ASP A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2983 through 3004 Proline residue: A2990 - end of helix removed outlier: 3.928A pdb=" N GLY A2994 " --> pdb=" O PRO A2990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3027 removed outlier: 3.532A pdb=" N VAL A3014 " --> pdb=" O CYS A3010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A3017 " --> pdb=" O GLY A3013 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A3019 " --> pdb=" O LEU A3015 " (cutoff:3.500A) Processing helix chain 'A' and resid 3035 through 3051 Processing helix chain 'A' and resid 3062 through 3067 Processing helix chain 'A' and resid 3067 through 3080 Processing helix chain 'A' and resid 3101 through 3116 removed outlier: 3.512A pdb=" N HIS A3116 " --> pdb=" O HIS A3112 " (cutoff:3.500A) Processing helix chain 'A' and resid 3125 through 3143 removed outlier: 3.522A pdb=" N THR A3136 " --> pdb=" O TYR A3132 " (cutoff:3.500A) Processing helix chain 'A' and resid 3150 through 3165 removed outlier: 3.625A pdb=" N GLY A3165 " --> pdb=" O ALA A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3171 through 3180 removed outlier: 3.740A pdb=" N ASN A3180 " --> pdb=" O LEU A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3183 No H-bonds generated for 'chain 'A' and resid 3181 through 3183' Processing helix chain 'A' and resid 3614 through 3629 removed outlier: 4.071A pdb=" N GLU A3626 " --> pdb=" O LEU A3622 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A3627 " --> pdb=" O GLN A3623 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A3628 " --> pdb=" O GLY A3624 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3646 Processing helix chain 'A' and resid 3663 through 3677 removed outlier: 3.640A pdb=" N PHE A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3698 removed outlier: 3.717A pdb=" N ASP A3694 " --> pdb=" O MET A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3734 removed outlier: 3.945A pdb=" N LEU A3732 " --> pdb=" O GLN A3728 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3748 removed outlier: 3.767A pdb=" N MET A3740 " --> pdb=" O GLY A3736 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER A3746 " --> pdb=" O LEU A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3768 removed outlier: 3.575A pdb=" N THR A3759 " --> pdb=" O MET A3755 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A3765 " --> pdb=" O LYS A3761 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A3767 " --> pdb=" O GLY A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3771 through 3785 Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 4.301A pdb=" N PHE A3791 " --> pdb=" O ASP A3787 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3806 through 3813 removed outlier: 3.525A pdb=" N GLU A3810 " --> pdb=" O LEU A3806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A3811 " --> pdb=" O ASN A3807 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 3.675A pdb=" N ARG A3842 " --> pdb=" O CYS A3838 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3862 removed outlier: 3.533A pdb=" N ARG A3860 " --> pdb=" O GLN A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3870 through 3891 removed outlier: 3.552A pdb=" N SER A3874 " --> pdb=" O ASN A3870 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A3884 " --> pdb=" O LEU A3880 " (cutoff:3.500A) Processing helix chain 'A' and resid 3892 through 3897 removed outlier: 4.599A pdb=" N LYS A3896 " --> pdb=" O TYR A3892 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A3897 " --> pdb=" O TYR A3893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3892 through 3897' Processing helix chain 'A' and resid 3900 through 3924 removed outlier: 3.795A pdb=" N LYS A3909 " --> pdb=" O ARG A3905 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A3913 " --> pdb=" O LYS A3909 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A3919 " --> pdb=" O LYS A3915 " (cutoff:3.500A) Processing helix chain 'A' and resid 3929 through 3938 removed outlier: 3.523A pdb=" N HIS A3938 " --> pdb=" O GLN A3934 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3960 removed outlier: 3.557A pdb=" N ALA A3944 " --> pdb=" O ARG A3940 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS A3954 " --> pdb=" O HIS A3950 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A3957 " --> pdb=" O ALA A3953 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A3958 " --> pdb=" O HIS A3954 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3987 removed outlier: 3.581A pdb=" N VAL A3980 " --> pdb=" O GLN A3976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A3983 " --> pdb=" O MET A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 3.573A pdb=" N LEU A4004 " --> pdb=" O MET A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4029 removed outlier: 3.510A pdb=" N LYS A4016 " --> pdb=" O GLU A4012 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A4021 " --> pdb=" O PHE A4017 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A4023 " --> pdb=" O ASP A4019 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A4024 " --> pdb=" O MET A4020 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A4025 " --> pdb=" O PHE A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4045 through 4054 removed outlier: 3.740A pdb=" N ALA A4052 " --> pdb=" O ASP A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4057 No H-bonds generated for 'chain 'A' and resid 4055 through 4057' Processing helix chain 'A' and resid 4060 through 4071 Processing helix chain 'A' and resid 4081 through 4085 Processing helix chain 'A' and resid 4094 through 4110 Processing helix chain 'A' and resid 4113 through 4123 Processing helix chain 'A' and resid 4123 through 4131 removed outlier: 3.586A pdb=" N TYR A4129 " --> pdb=" O SER A4125 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4163 removed outlier: 3.539A pdb=" N TRP A4161 " --> pdb=" O SER A4157 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A4162 " --> pdb=" O ARG A4158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A4163 " --> pdb=" O THR A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4178 removed outlier: 3.722A pdb=" N ARG A4171 " --> pdb=" O LYS A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4184 through 4206 removed outlier: 3.944A pdb=" N GLU A4188 " --> pdb=" O LYS A4184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A4191 " --> pdb=" O MET A4187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A4192 " --> pdb=" O GLU A4188 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A4196 " --> pdb=" O ASN A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4487 through 4492 Processing helix chain 'A' and resid 4492 through 4499 removed outlier: 3.715A pdb=" N PHE A4496 " --> pdb=" O LEU A4492 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A4497 " --> pdb=" O LEU A4493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A4498 " --> pdb=" O ASN A4494 " (cutoff:3.500A) Processing helix chain 'A' and resid 4499 through 4519 removed outlier: 3.860A pdb=" N ALA A4507 " --> pdb=" O MET A4503 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4595 removed outlier: 3.552A pdb=" N ILE A4578 " --> pdb=" O ARG A4574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A4588 " --> pdb=" O SER A4584 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A4590 " --> pdb=" O PHE A4586 " (cutoff:3.500A) Processing helix chain 'A' and resid 4595 through 4613 Processing helix chain 'A' and resid 4626 through 4631 removed outlier: 3.501A pdb=" N GLN A4630 " --> pdb=" O ASP A4626 " (cutoff:3.500A) Processing helix chain 'A' and resid 4632 through 4638 removed outlier: 3.649A pdb=" N VAL A4635 " --> pdb=" O ASP A4632 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A4636 " --> pdb=" O ARG A4633 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4646 removed outlier: 3.990A pdb=" N TRP A4646 " --> pdb=" O ASN A4643 " (cutoff:3.500A) Processing helix chain 'A' and resid 4647 through 4648 No H-bonds generated for 'chain 'A' and resid 4647 through 4648' Processing helix chain 'A' and resid 4649 through 4663 removed outlier: 6.618A pdb=" N GLU A4660 " --> pdb=" O ASP A4656 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE A4661 " --> pdb=" O LYS A4657 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A4662 " --> pdb=" O TYR A4658 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4672 removed outlier: 3.674A pdb=" N SER A4668 " --> pdb=" O ARG A4664 " (cutoff:3.500A) Processing helix chain 'A' and resid 4697 through 4702 removed outlier: 4.355A pdb=" N ILE A4702 " --> pdb=" O VAL A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 removed outlier: 3.688A pdb=" N THR A4716 " --> pdb=" O GLY A4712 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4736 removed outlier: 3.696A pdb=" N MET A4729 " --> pdb=" O TRP A4725 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS A4734 " --> pdb=" O SER A4730 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A4735 " --> pdb=" O VAL A4731 " (cutoff:3.500A) Processing helix chain 'A' and resid 4738 through 4749 removed outlier: 3.685A pdb=" N HIS A4743 " --> pdb=" O PHE A4740 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A4744 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A4745 " --> pdb=" O ALA A4742 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4763 removed outlier: 4.008A pdb=" N THR A4756 " --> pdb=" O LYS A4752 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A4757 " --> pdb=" O THR A4753 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A4761 " --> pdb=" O ILE A4757 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A4762 " --> pdb=" O LEU A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4764 through 4790 removed outlier: 3.523A pdb=" N VAL A4769 " --> pdb=" O GLY A4765 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A4770 " --> pdb=" O LYS A4766 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A4787 " --> pdb=" O THR A4783 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A4788 " --> pdb=" O VAL A4784 " (cutoff:3.500A) Processing helix chain 'A' and resid 4791 through 4794 removed outlier: 3.611A pdb=" N TYR A4794 " --> pdb=" O ARG A4791 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4791 through 4794' Processing helix chain 'A' and resid 4809 through 4820 Processing helix chain 'A' and resid 4840 through 4855 removed outlier: 3.552A pdb=" N THR A4850 " --> pdb=" O ILE A4846 " (cutoff:3.500A) Processing helix chain 'A' and resid 4857 through 4888 removed outlier: 3.546A pdb=" N ALA A4861 " --> pdb=" O VAL A4857 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A4867 " --> pdb=" O ILE A4863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A4877 " --> pdb=" O GLU A4873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A4882 " --> pdb=" O GLN A4878 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A4886 " --> pdb=" O LYS A4882 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 3.834A pdb=" N THR A4901 " --> pdb=" O TYR A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4904 through 4912 removed outlier: 3.781A pdb=" N THR A4908 " --> pdb=" O HIS A4904 " (cutoff:3.500A) Processing helix chain 'A' and resid 4916 through 4928 Processing helix chain 'A' and resid 4935 through 4948 Processing helix chain 'A' and resid 4958 through 4963 removed outlier: 3.647A pdb=" N TYR A4963 " --> pdb=" O PHE A4959 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 158 removed outlier: 3.836A pdb=" N CYS B 158 " --> pdb=" O GLY B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 409 through 439 removed outlier: 4.301A pdb=" N VAL B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.752A pdb=" N PHE B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.669A pdb=" N HIS B 506 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.733A pdb=" N CYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 562 through 565 removed outlier: 3.894A pdb=" N LEU B 565 " --> pdb=" O LEU B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 565' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.618A pdb=" N CYS B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.690A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.614A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.606A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.665A pdb=" N LEU B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 875 through 899 removed outlier: 3.842A pdb=" N ARG B 880 " --> pdb=" O PRO B 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 881 " --> pdb=" O HIS B 877 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 892 " --> pdb=" O ASN B 888 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 899 " --> pdb=" O MET B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 946 removed outlier: 4.231A pdb=" N MET B 935 " --> pdb=" O TYR B 931 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 940 " --> pdb=" O SER B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 986 removed outlier: 4.011A pdb=" N PHE B 985 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 986 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 986' Processing helix chain 'B' and resid 989 through 1011 removed outlier: 3.561A pdb=" N ASP B 997 " --> pdb=" O GLU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1059 removed outlier: 4.565A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1571 through 1576 removed outlier: 3.720A pdb=" N HIS B1575 " --> pdb=" O PHE B1571 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B1576 " --> pdb=" O LYS B1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1571 through 1576' Processing helix chain 'B' and resid 1647 through 1665 Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.824A pdb=" N ALA B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) Processing helix chain 'B' and resid 1682 through 1691 removed outlier: 4.051A pdb=" N GLU B1690 " --> pdb=" O LEU B1686 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B1691 " --> pdb=" O TYR B1687 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1709 removed outlier: 3.554A pdb=" N ILE B1707 " --> pdb=" O TYR B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1722 removed outlier: 4.734A pdb=" N TYR B1714 " --> pdb=" O HIS B1710 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B1718 " --> pdb=" O TYR B1714 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1735 Processing helix chain 'B' and resid 1783 through 1804 removed outlier: 3.815A pdb=" N ALA B1789 " --> pdb=" O ASP B1785 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B1790 " --> pdb=" O ILE B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1831 Proline residue: B1820 - end of helix removed outlier: 3.770A pdb=" N MET B1831 " --> pdb=" O THR B1827 " (cutoff:3.500A) Processing helix chain 'B' and resid 1837 through 1847 Processing helix chain 'B' and resid 1900 through 1942 removed outlier: 3.539A pdb=" N LYS B1904 " --> pdb=" O PRO B1900 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B1914 " --> pdb=" O LEU B1910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B1932 " --> pdb=" O ALA B1928 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B1935 " --> pdb=" O ASP B1931 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B1939 " --> pdb=" O ALA B1935 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B1942 " --> pdb=" O GLN B1938 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2013 removed outlier: 3.536A pdb=" N ILE B2010 " --> pdb=" O THR B2006 " (cutoff:3.500A) Processing helix chain 'B' and resid 2025 through 2038 removed outlier: 3.675A pdb=" N ARG B2029 " --> pdb=" O THR B2025 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B2030 " --> pdb=" O ILE B2026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B2035 " --> pdb=" O LEU B2031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2059 through 2074 removed outlier: 4.002A pdb=" N SER B2064 " --> pdb=" O GLN B2060 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B2068 " --> pdb=" O SER B2064 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B2070 " --> pdb=" O THR B2066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B2073 " --> pdb=" O ARG B2069 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B2074 " --> pdb=" O TRP B2070 " (cutoff:3.500A) Processing helix chain 'B' and resid 2078 through 2093 removed outlier: 3.982A pdb=" N VAL B2082 " --> pdb=" O ASP B2078 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B2087 " --> pdb=" O ARG B2083 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B2088 " --> pdb=" O ALA B2084 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B2093 " --> pdb=" O LEU B2089 " (cutoff:3.500A) Processing helix chain 'B' and resid 2096 through 2103 removed outlier: 3.896A pdb=" N ALA B2102 " --> pdb=" O GLY B2098 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B2103 " --> pdb=" O LEU B2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2131 removed outlier: 3.656A pdb=" N THR B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B2127 " --> pdb=" O SER B2123 " (cutoff:3.500A) Processing helix chain 'B' and resid 2139 through 2153 removed outlier: 3.903A pdb=" N MET B2143 " --> pdb=" O GLU B2139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B2144 " --> pdb=" O GLU B2140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B2145 " --> pdb=" O LYS B2141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B2152 " --> pdb=" O GLY B2148 " (cutoff:3.500A) Processing helix chain 'B' and resid 2159 through 2167 removed outlier: 3.961A pdb=" N MET B2163 " --> pdb=" O HIS B2159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B2164 " --> pdb=" O PRO B2160 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2180 Processing helix chain 'B' and resid 2192 through 2207 removed outlier: 3.671A pdb=" N ASN B2196 " --> pdb=" O LYS B2192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B2197 " --> pdb=" O MET B2193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B2200 " --> pdb=" O ASN B2196 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B2205 " --> pdb=" O LEU B2201 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B2207 " --> pdb=" O TYR B2203 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2214 removed outlier: 3.989A pdb=" N ALA B2214 " --> pdb=" O GLN B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2215 through 2217 No H-bonds generated for 'chain 'B' and resid 2215 through 2217' Processing helix chain 'B' and resid 2218 through 2226 removed outlier: 3.714A pdb=" N GLU B2224 " --> pdb=" O SER B2220 " (cutoff:3.500A) Processing helix chain 'B' and resid 2240 through 2247 Processing helix chain 'B' and resid 2251 through 2258 Processing helix chain 'B' and resid 2259 through 2273 removed outlier: 3.981A pdb=" N LEU B2263 " --> pdb=" O ARG B2259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B2273 " --> pdb=" O TYR B2269 " (cutoff:3.500A) Processing helix chain 'B' and resid 2295 through 2308 removed outlier: 4.136A pdb=" N TYR B2299 " --> pdb=" O GLU B2295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) Processing helix chain 'B' and resid 2314 through 2328 removed outlier: 3.700A pdb=" N VAL B2320 " --> pdb=" O GLU B2316 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B2322 " --> pdb=" O ALA B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2344 through 2349 removed outlier: 3.596A pdb=" N GLU B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2402 Processing helix chain 'B' and resid 2417 through 2425 removed outlier: 3.729A pdb=" N ARG B2421 " --> pdb=" O ALA B2417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B2423 " --> pdb=" O ARG B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2432 through 2442 removed outlier: 3.567A pdb=" N SER B2438 " --> pdb=" O VAL B2434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B2439 " --> pdb=" O GLY B2435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B2440 " --> pdb=" O VAL B2436 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B2441 " --> pdb=" O ILE B2437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2462 through 2477 removed outlier: 4.181A pdb=" N LYS B2466 " --> pdb=" O CYS B2462 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B2475 " --> pdb=" O LEU B2471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2482 through 2489 removed outlier: 3.770A pdb=" N LEU B2488 " --> pdb=" O PHE B2484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B2489 " --> pdb=" O LEU B2485 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2499 Processing helix chain 'B' and resid 2500 through 2502 No H-bonds generated for 'chain 'B' and resid 2500 through 2502' Processing helix chain 'B' and resid 2512 through 2524 removed outlier: 4.046A pdb=" N ASN B2518 " --> pdb=" O ALA B2514 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B2519 " --> pdb=" O LEU B2515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B2521 " --> pdb=" O LEU B2517 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B2522 " --> pdb=" O ASN B2518 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B2523 " --> pdb=" O ARG B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2529 removed outlier: 3.923A pdb=" N LEU B2529 " --> pdb=" O LEU B2526 " (cutoff:3.500A) Processing helix chain 'B' and resid 2535 through 2552 removed outlier: 3.650A pdb=" N HIS B2541 " --> pdb=" O ALA B2537 " (cutoff:3.500A) Processing helix chain 'B' and resid 2559 through 2576 removed outlier: 3.995A pdb=" N LYS B2564 " --> pdb=" O CYS B2560 " (cutoff:3.500A) Processing helix chain 'B' and resid 2583 through 2601 removed outlier: 3.547A pdb=" N ARG B2592 " --> pdb=" O HIS B2588 " (cutoff:3.500A) Proline residue: B2598 - end of helix Processing helix chain 'B' and resid 2606 through 2627 removed outlier: 3.735A pdb=" N ARG B2617 " --> pdb=" O ASN B2613 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B2618 " --> pdb=" O HIS B2614 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B2624 " --> pdb=" O LYS B2620 " (cutoff:3.500A) Proline residue: B2625 - end of helix Processing helix chain 'B' and resid 2635 through 2651 Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2668 - end of helix removed outlier: 3.704A pdb=" N GLY B2675 " --> pdb=" O SER B2671 " (cutoff:3.500A) Processing helix chain 'B' and resid 2715 through 2740 removed outlier: 3.782A pdb=" N GLU B2719 " --> pdb=" O PRO B2715 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B2721 " --> pdb=" O LYS B2717 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B2723 " --> pdb=" O GLU B2719 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B2724 " --> pdb=" O TYR B2720 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B2727 " --> pdb=" O ASN B2723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B2735 " --> pdb=" O ASP B2731 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B2736 " --> pdb=" O LYS B2732 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B2737 " --> pdb=" O TRP B2733 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B2740 " --> pdb=" O ASP B2736 " (cutoff:3.500A) Processing helix chain 'B' and resid 2749 through 2753 removed outlier: 4.083A pdb=" N LYS B2753 " --> pdb=" O ASP B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 3.895A pdb=" N ILE B2771 " --> pdb=" O LYS B2767 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR B2772 " --> pdb=" O GLU B2768 " (cutoff:3.500A) Proline residue: B2775 - end of helix removed outlier: 3.500A pdb=" N THR B2782 " --> pdb=" O GLU B2778 " (cutoff:3.500A) Processing helix chain 'B' and resid 2835 through 2862 removed outlier: 3.921A pdb=" N GLU B2860 " --> pdb=" O LYS B2856 " (cutoff:3.500A) Processing helix chain 'B' and resid 2874 through 2878 Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.966A pdb=" N ASP B2886 " --> pdb=" O GLU B2882 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B2889 " --> pdb=" O LYS B2885 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B2894 " --> pdb=" O ALA B2890 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B2895 " --> pdb=" O GLN B2891 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B2896 " --> pdb=" O ASP B2892 " (cutoff:3.500A) Processing helix chain 'B' and resid 2983 through 3004 Proline residue: B2990 - end of helix removed outlier: 3.928A pdb=" N GLY B2994 " --> pdb=" O PRO B2990 " (cutoff:3.500A) Processing helix chain 'B' and resid 3010 through 3027 removed outlier: 3.532A pdb=" N VAL B3014 " --> pdb=" O CYS B3010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B3017 " --> pdb=" O GLY B3013 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B3019 " --> pdb=" O LEU B3015 " (cutoff:3.500A) Processing helix chain 'B' and resid 3035 through 3051 Processing helix chain 'B' and resid 3062 through 3067 Processing helix chain 'B' and resid 3067 through 3080 Processing helix chain 'B' and resid 3101 through 3116 removed outlier: 3.512A pdb=" N HIS B3116 " --> pdb=" O HIS B3112 " (cutoff:3.500A) Processing helix chain 'B' and resid 3125 through 3143 removed outlier: 3.522A pdb=" N THR B3136 " --> pdb=" O TYR B3132 " (cutoff:3.500A) Processing helix chain 'B' and resid 3150 through 3165 removed outlier: 3.625A pdb=" N GLY B3165 " --> pdb=" O ALA B3161 " (cutoff:3.500A) Processing helix chain 'B' and resid 3171 through 3180 removed outlier: 3.740A pdb=" N ASN B3180 " --> pdb=" O LEU B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3181 through 3183 No H-bonds generated for 'chain 'B' and resid 3181 through 3183' Processing helix chain 'B' and resid 3614 through 3629 removed outlier: 4.071A pdb=" N GLU B3626 " --> pdb=" O LEU B3622 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS B3627 " --> pdb=" O GLN B3623 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER B3628 " --> pdb=" O GLY B3624 " (cutoff:3.500A) Processing helix chain 'B' and resid 3637 through 3646 Processing helix chain 'B' and resid 3663 through 3677 removed outlier: 3.640A pdb=" N PHE B3672 " --> pdb=" O LEU B3668 " (cutoff:3.500A) Processing helix chain 'B' and resid 3686 through 3698 removed outlier: 3.717A pdb=" N ASP B3694 " --> pdb=" O MET B3690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3734 removed outlier: 3.945A pdb=" N LEU B3732 " --> pdb=" O GLN B3728 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) Processing helix chain 'B' and resid 3736 through 3748 removed outlier: 3.767A pdb=" N MET B3740 " --> pdb=" O GLY B3736 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B3746 " --> pdb=" O LEU B3742 " (cutoff:3.500A) Processing helix chain 'B' and resid 3753 through 3768 removed outlier: 3.575A pdb=" N THR B3759 " --> pdb=" O MET B3755 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B3765 " --> pdb=" O LYS B3761 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B3767 " --> pdb=" O GLY B3763 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3785 Processing helix chain 'B' and resid 3787 through 3800 removed outlier: 4.301A pdb=" N PHE B3791 " --> pdb=" O ASP B3787 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B3800 " --> pdb=" O GLY B3796 " (cutoff:3.500A) Processing helix chain 'B' and resid 3806 through 3813 removed outlier: 3.525A pdb=" N GLU B3810 " --> pdb=" O LEU B3806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B3811 " --> pdb=" O ASN B3807 " (cutoff:3.500A) Processing helix chain 'B' and resid 3834 through 3847 removed outlier: 3.675A pdb=" N ARG B3842 " --> pdb=" O CYS B3838 " (cutoff:3.500A) Processing helix chain 'B' and resid 3852 through 3862 removed outlier: 3.533A pdb=" N ARG B3860 " --> pdb=" O GLN B3856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3870 through 3891 removed outlier: 3.552A pdb=" N SER B3874 " --> pdb=" O ASN B3870 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B3884 " --> pdb=" O LEU B3880 " (cutoff:3.500A) Processing helix chain 'B' and resid 3892 through 3897 removed outlier: 4.599A pdb=" N LYS B3896 " --> pdb=" O TYR B3892 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B3897 " --> pdb=" O TYR B3893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3892 through 3897' Processing helix chain 'B' and resid 3900 through 3924 removed outlier: 3.795A pdb=" N LYS B3909 " --> pdb=" O ARG B3905 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B3913 " --> pdb=" O LYS B3909 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B3919 " --> pdb=" O LYS B3915 " (cutoff:3.500A) Processing helix chain 'B' and resid 3929 through 3938 removed outlier: 3.523A pdb=" N HIS B3938 " --> pdb=" O GLN B3934 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3960 removed outlier: 3.557A pdb=" N ALA B3944 " --> pdb=" O ARG B3940 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B3954 " --> pdb=" O HIS B3950 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B3957 " --> pdb=" O ALA B3953 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS B3958 " --> pdb=" O HIS B3954 " (cutoff:3.500A) Processing helix chain 'B' and resid 3965 through 3987 removed outlier: 3.581A pdb=" N VAL B3980 " --> pdb=" O GLN B3976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B3983 " --> pdb=" O MET B3979 " (cutoff:3.500A) Processing helix chain 'B' and resid 3994 through 4007 removed outlier: 3.573A pdb=" N LEU B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) Processing helix chain 'B' and resid 4010 through 4029 removed outlier: 3.510A pdb=" N LYS B4016 " --> pdb=" O GLU B4012 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B4021 " --> pdb=" O PHE B4017 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B4023 " --> pdb=" O ASP B4019 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU B4024 " --> pdb=" O MET B4020 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B4025 " --> pdb=" O PHE B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4045 through 4054 removed outlier: 3.740A pdb=" N ALA B4052 " --> pdb=" O ASP B4048 " (cutoff:3.500A) Processing helix chain 'B' and resid 4055 through 4057 No H-bonds generated for 'chain 'B' and resid 4055 through 4057' Processing helix chain 'B' and resid 4060 through 4071 Processing helix chain 'B' and resid 4081 through 4085 Processing helix chain 'B' and resid 4094 through 4110 Processing helix chain 'B' and resid 4113 through 4123 Processing helix chain 'B' and resid 4123 through 4131 removed outlier: 3.586A pdb=" N TYR B4129 " --> pdb=" O SER B4125 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4163 removed outlier: 3.539A pdb=" N TRP B4161 " --> pdb=" O SER B4157 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B4162 " --> pdb=" O ARG B4158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B4163 " --> pdb=" O THR B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4165 through 4178 removed outlier: 3.722A pdb=" N ARG B4171 " --> pdb=" O LYS B4167 " (cutoff:3.500A) Processing helix chain 'B' and resid 4184 through 4206 removed outlier: 3.944A pdb=" N GLU B4188 " --> pdb=" O LYS B4184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B4191 " --> pdb=" O MET B4187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B4192 " --> pdb=" O GLU B4188 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B4196 " --> pdb=" O ASN B4192 " (cutoff:3.500A) Processing helix chain 'B' and resid 4487 through 4492 Processing helix chain 'B' and resid 4492 through 4499 removed outlier: 3.715A pdb=" N PHE B4496 " --> pdb=" O LEU B4492 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B4497 " --> pdb=" O LEU B4493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B4498 " --> pdb=" O ASN B4494 " (cutoff:3.500A) Processing helix chain 'B' and resid 4499 through 4519 removed outlier: 3.860A pdb=" N ALA B4507 " --> pdb=" O MET B4503 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4595 removed outlier: 3.552A pdb=" N ILE B4578 " --> pdb=" O ARG B4574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B4588 " --> pdb=" O SER B4584 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B4590 " --> pdb=" O PHE B4586 " (cutoff:3.500A) Processing helix chain 'B' and resid 4595 through 4613 Processing helix chain 'B' and resid 4626 through 4631 removed outlier: 3.501A pdb=" N GLN B4630 " --> pdb=" O ASP B4626 " (cutoff:3.500A) Processing helix chain 'B' and resid 4632 through 4638 removed outlier: 3.649A pdb=" N VAL B4635 " --> pdb=" O ASP B4632 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B4636 " --> pdb=" O ARG B4633 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4646 removed outlier: 3.990A pdb=" N TRP B4646 " --> pdb=" O ASN B4643 " (cutoff:3.500A) Processing helix chain 'B' and resid 4647 through 4648 No H-bonds generated for 'chain 'B' and resid 4647 through 4648' Processing helix chain 'B' and resid 4649 through 4663 removed outlier: 6.618A pdb=" N GLU B4660 " --> pdb=" O ASP B4656 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B4661 " --> pdb=" O LYS B4657 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B4662 " --> pdb=" O TYR B4658 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4672 removed outlier: 3.674A pdb=" N SER B4668 " --> pdb=" O ARG B4664 " (cutoff:3.500A) Processing helix chain 'B' and resid 4697 through 4702 removed outlier: 4.355A pdb=" N ILE B4702 " --> pdb=" O VAL B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 removed outlier: 3.688A pdb=" N THR B4716 " --> pdb=" O GLY B4712 " (cutoff:3.500A) Processing helix chain 'B' and resid 4717 through 4736 removed outlier: 3.696A pdb=" N MET B4729 " --> pdb=" O TRP B4725 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B4734 " --> pdb=" O SER B4730 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR B4735 " --> pdb=" O VAL B4731 " (cutoff:3.500A) Processing helix chain 'B' and resid 4738 through 4749 removed outlier: 3.685A pdb=" N HIS B4743 " --> pdb=" O PHE B4740 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B4744 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B4745 " --> pdb=" O ALA B4742 " (cutoff:3.500A) Processing helix chain 'B' and resid 4751 through 4763 removed outlier: 4.008A pdb=" N THR B4756 " --> pdb=" O LYS B4752 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B4757 " --> pdb=" O THR B4753 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B4761 " --> pdb=" O ILE B4757 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B4762 " --> pdb=" O LEU B4758 " (cutoff:3.500A) Processing helix chain 'B' and resid 4764 through 4790 removed outlier: 3.523A pdb=" N VAL B4769 " --> pdb=" O GLY B4765 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B4770 " --> pdb=" O LYS B4766 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B4787 " --> pdb=" O THR B4783 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B4788 " --> pdb=" O VAL B4784 " (cutoff:3.500A) Processing helix chain 'B' and resid 4791 through 4794 removed outlier: 3.611A pdb=" N TYR B4794 " --> pdb=" O ARG B4791 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4791 through 4794' Processing helix chain 'B' and resid 4809 through 4820 Processing helix chain 'B' and resid 4840 through 4855 removed outlier: 3.552A pdb=" N THR B4850 " --> pdb=" O ILE B4846 " (cutoff:3.500A) Processing helix chain 'B' and resid 4857 through 4888 removed outlier: 3.546A pdb=" N ALA B4861 " --> pdb=" O VAL B4857 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B4867 " --> pdb=" O ILE B4863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B4877 " --> pdb=" O GLU B4873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B4882 " --> pdb=" O GLN B4878 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU B4886 " --> pdb=" O LYS B4882 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 3.834A pdb=" N THR B4901 " --> pdb=" O TYR B4898 " (cutoff:3.500A) Processing helix chain 'B' and resid 4904 through 4912 removed outlier: 3.781A pdb=" N THR B4908 " --> pdb=" O HIS B4904 " (cutoff:3.500A) Processing helix chain 'B' and resid 4916 through 4928 Processing helix chain 'B' and resid 4935 through 4948 Processing helix chain 'B' and resid 4958 through 4963 removed outlier: 3.647A pdb=" N TYR B4963 " --> pdb=" O PHE B4959 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 158 removed outlier: 3.836A pdb=" N CYS C 158 " --> pdb=" O GLY C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 409 through 439 removed outlier: 4.301A pdb=" N VAL C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 428 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 435 " --> pdb=" O ARG C 431 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.752A pdb=" N PHE C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 removed outlier: 3.669A pdb=" N HIS C 506 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.733A pdb=" N CYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 554 through 561 Processing helix chain 'C' and resid 562 through 565 removed outlier: 3.894A pdb=" N LEU C 565 " --> pdb=" O LEU C 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 565' Processing helix chain 'C' and resid 567 through 582 removed outlier: 3.618A pdb=" N CYS C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 removed outlier: 3.690A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.614A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.606A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.665A pdb=" N LEU C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 636 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.842A pdb=" N ARG C 880 " --> pdb=" O PRO C 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE C 881 " --> pdb=" O HIS C 877 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 899 " --> pdb=" O MET C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 946 removed outlier: 4.231A pdb=" N MET C 935 " --> pdb=" O TYR C 931 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 940 " --> pdb=" O SER C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 986 removed outlier: 4.011A pdb=" N PHE C 985 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 986 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 986' Processing helix chain 'C' and resid 989 through 1011 removed outlier: 3.561A pdb=" N ASP C 997 " --> pdb=" O GLU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1059 removed outlier: 4.565A pdb=" N ASN C1046 " --> pdb=" O THR C1042 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C1050 " --> pdb=" O ASN C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1571 through 1576 removed outlier: 3.720A pdb=" N HIS C1575 " --> pdb=" O PHE C1571 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C1576 " --> pdb=" O LYS C1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1571 through 1576' Processing helix chain 'C' and resid 1647 through 1665 Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.824A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) Processing helix chain 'C' and resid 1682 through 1691 removed outlier: 4.051A pdb=" N GLU C1690 " --> pdb=" O LEU C1686 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C1691 " --> pdb=" O TYR C1687 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1709 removed outlier: 3.554A pdb=" N ILE C1707 " --> pdb=" O TYR C1703 " (cutoff:3.500A) Processing helix chain 'C' and resid 1710 through 1722 removed outlier: 4.734A pdb=" N TYR C1714 " --> pdb=" O HIS C1710 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C1718 " --> pdb=" O TYR C1714 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1735 Processing helix chain 'C' and resid 1783 through 1804 removed outlier: 3.815A pdb=" N ALA C1789 " --> pdb=" O ASP C1785 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C1790 " --> pdb=" O ILE C1786 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1831 Proline residue: C1820 - end of helix removed outlier: 3.770A pdb=" N MET C1831 " --> pdb=" O THR C1827 " (cutoff:3.500A) Processing helix chain 'C' and resid 1837 through 1847 Processing helix chain 'C' and resid 1900 through 1942 removed outlier: 3.539A pdb=" N LYS C1904 " --> pdb=" O PRO C1900 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C1914 " --> pdb=" O LEU C1910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C1932 " --> pdb=" O ALA C1928 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C1935 " --> pdb=" O ASP C1931 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C1939 " --> pdb=" O ALA C1935 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C1942 " --> pdb=" O GLN C1938 " (cutoff:3.500A) Processing helix chain 'C' and resid 2000 through 2013 removed outlier: 3.536A pdb=" N ILE C2010 " --> pdb=" O THR C2006 " (cutoff:3.500A) Processing helix chain 'C' and resid 2025 through 2038 removed outlier: 3.675A pdb=" N ARG C2029 " --> pdb=" O THR C2025 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C2030 " --> pdb=" O ILE C2026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C2035 " --> pdb=" O LEU C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2059 through 2074 removed outlier: 4.002A pdb=" N SER C2064 " --> pdb=" O GLN C2060 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C2068 " --> pdb=" O SER C2064 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP C2070 " --> pdb=" O THR C2066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C2073 " --> pdb=" O ARG C2069 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C2074 " --> pdb=" O TRP C2070 " (cutoff:3.500A) Processing helix chain 'C' and resid 2078 through 2093 removed outlier: 3.982A pdb=" N VAL C2082 " --> pdb=" O ASP C2078 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C2087 " --> pdb=" O ARG C2083 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C2088 " --> pdb=" O ALA C2084 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C2093 " --> pdb=" O LEU C2089 " (cutoff:3.500A) Processing helix chain 'C' and resid 2096 through 2103 removed outlier: 3.896A pdb=" N ALA C2102 " --> pdb=" O GLY C2098 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C2103 " --> pdb=" O LEU C2099 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2131 removed outlier: 3.656A pdb=" N THR C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C2127 " --> pdb=" O SER C2123 " (cutoff:3.500A) Processing helix chain 'C' and resid 2139 through 2153 removed outlier: 3.903A pdb=" N MET C2143 " --> pdb=" O GLU C2139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C2144 " --> pdb=" O GLU C2140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C2145 " --> pdb=" O LYS C2141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C2152 " --> pdb=" O GLY C2148 " (cutoff:3.500A) Processing helix chain 'C' and resid 2159 through 2167 removed outlier: 3.961A pdb=" N MET C2163 " --> pdb=" O HIS C2159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C2164 " --> pdb=" O PRO C2160 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2180 Processing helix chain 'C' and resid 2192 through 2207 removed outlier: 3.671A pdb=" N ASN C2196 " --> pdb=" O LYS C2192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C2197 " --> pdb=" O MET C2193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C2200 " --> pdb=" O ASN C2196 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C2205 " --> pdb=" O LEU C2201 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C2207 " --> pdb=" O TYR C2203 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2214 removed outlier: 3.989A pdb=" N ALA C2214 " --> pdb=" O GLN C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2215 through 2217 No H-bonds generated for 'chain 'C' and resid 2215 through 2217' Processing helix chain 'C' and resid 2218 through 2226 removed outlier: 3.714A pdb=" N GLU C2224 " --> pdb=" O SER C2220 " (cutoff:3.500A) Processing helix chain 'C' and resid 2240 through 2247 Processing helix chain 'C' and resid 2251 through 2258 Processing helix chain 'C' and resid 2259 through 2273 removed outlier: 3.981A pdb=" N LEU C2263 " --> pdb=" O ARG C2259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C2273 " --> pdb=" O TYR C2269 " (cutoff:3.500A) Processing helix chain 'C' and resid 2295 through 2308 removed outlier: 4.136A pdb=" N TYR C2299 " --> pdb=" O GLU C2295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2328 removed outlier: 3.700A pdb=" N VAL C2320 " --> pdb=" O GLU C2316 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C2322 " --> pdb=" O ALA C2318 " (cutoff:3.500A) Processing helix chain 'C' and resid 2344 through 2349 removed outlier: 3.596A pdb=" N GLU C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) Processing helix chain 'C' and resid 2387 through 2402 Processing helix chain 'C' and resid 2417 through 2425 removed outlier: 3.729A pdb=" N ARG C2421 " --> pdb=" O ALA C2417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C2423 " --> pdb=" O ARG C2419 " (cutoff:3.500A) Processing helix chain 'C' and resid 2432 through 2442 removed outlier: 3.567A pdb=" N SER C2438 " --> pdb=" O VAL C2434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C2439 " --> pdb=" O GLY C2435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C2440 " --> pdb=" O VAL C2436 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C2441 " --> pdb=" O ILE C2437 " (cutoff:3.500A) Processing helix chain 'C' and resid 2462 through 2477 removed outlier: 4.181A pdb=" N LYS C2466 " --> pdb=" O CYS C2462 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C2467 " --> pdb=" O PRO C2463 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C2475 " --> pdb=" O LEU C2471 " (cutoff:3.500A) Processing helix chain 'C' and resid 2482 through 2489 removed outlier: 3.770A pdb=" N LEU C2488 " --> pdb=" O PHE C2484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C2489 " --> pdb=" O LEU C2485 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2499 Processing helix chain 'C' and resid 2500 through 2502 No H-bonds generated for 'chain 'C' and resid 2500 through 2502' Processing helix chain 'C' and resid 2512 through 2524 removed outlier: 4.046A pdb=" N ASN C2518 " --> pdb=" O ALA C2514 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C2519 " --> pdb=" O LEU C2515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C2521 " --> pdb=" O LEU C2517 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS C2522 " --> pdb=" O ASN C2518 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C2523 " --> pdb=" O ARG C2519 " (cutoff:3.500A) Processing helix chain 'C' and resid 2525 through 2529 removed outlier: 3.923A pdb=" N LEU C2529 " --> pdb=" O LEU C2526 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2552 removed outlier: 3.650A pdb=" N HIS C2541 " --> pdb=" O ALA C2537 " (cutoff:3.500A) Processing helix chain 'C' and resid 2559 through 2576 removed outlier: 3.995A pdb=" N LYS C2564 " --> pdb=" O CYS C2560 " (cutoff:3.500A) Processing helix chain 'C' and resid 2583 through 2601 removed outlier: 3.547A pdb=" N ARG C2592 " --> pdb=" O HIS C2588 " (cutoff:3.500A) Proline residue: C2598 - end of helix Processing helix chain 'C' and resid 2606 through 2627 removed outlier: 3.735A pdb=" N ARG C2617 " --> pdb=" O ASN C2613 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS C2618 " --> pdb=" O HIS C2614 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C2624 " --> pdb=" O LYS C2620 " (cutoff:3.500A) Proline residue: C2625 - end of helix Processing helix chain 'C' and resid 2635 through 2651 Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2668 - end of helix removed outlier: 3.704A pdb=" N GLY C2675 " --> pdb=" O SER C2671 " (cutoff:3.500A) Processing helix chain 'C' and resid 2715 through 2740 removed outlier: 3.782A pdb=" N GLU C2719 " --> pdb=" O PRO C2715 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C2721 " --> pdb=" O LYS C2717 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C2723 " --> pdb=" O GLU C2719 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C2724 " --> pdb=" O TYR C2720 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C2727 " --> pdb=" O ASN C2723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C2735 " --> pdb=" O ASP C2731 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C2736 " --> pdb=" O LYS C2732 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C2737 " --> pdb=" O TRP C2733 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C2740 " --> pdb=" O ASP C2736 " (cutoff:3.500A) Processing helix chain 'C' and resid 2749 through 2753 removed outlier: 4.083A pdb=" N LYS C2753 " --> pdb=" O ASP C2750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 3.895A pdb=" N ILE C2771 " --> pdb=" O LYS C2767 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C2772 " --> pdb=" O GLU C2768 " (cutoff:3.500A) Proline residue: C2775 - end of helix removed outlier: 3.500A pdb=" N THR C2782 " --> pdb=" O GLU C2778 " (cutoff:3.500A) Processing helix chain 'C' and resid 2835 through 2862 removed outlier: 3.921A pdb=" N GLU C2860 " --> pdb=" O LYS C2856 " (cutoff:3.500A) Processing helix chain 'C' and resid 2874 through 2878 Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.966A pdb=" N ASP C2886 " --> pdb=" O GLU C2882 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS C2889 " --> pdb=" O LYS C2885 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C2894 " --> pdb=" O ALA C2890 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C2895 " --> pdb=" O GLN C2891 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C2896 " --> pdb=" O ASP C2892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2983 through 3004 Proline residue: C2990 - end of helix removed outlier: 3.928A pdb=" N GLY C2994 " --> pdb=" O PRO C2990 " (cutoff:3.500A) Processing helix chain 'C' and resid 3010 through 3027 removed outlier: 3.532A pdb=" N VAL C3014 " --> pdb=" O CYS C3010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C3017 " --> pdb=" O GLY C3013 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C3019 " --> pdb=" O LEU C3015 " (cutoff:3.500A) Processing helix chain 'C' and resid 3035 through 3051 Processing helix chain 'C' and resid 3062 through 3067 Processing helix chain 'C' and resid 3067 through 3080 Processing helix chain 'C' and resid 3101 through 3116 removed outlier: 3.512A pdb=" N HIS C3116 " --> pdb=" O HIS C3112 " (cutoff:3.500A) Processing helix chain 'C' and resid 3125 through 3143 removed outlier: 3.522A pdb=" N THR C3136 " --> pdb=" O TYR C3132 " (cutoff:3.500A) Processing helix chain 'C' and resid 3150 through 3165 removed outlier: 3.625A pdb=" N GLY C3165 " --> pdb=" O ALA C3161 " (cutoff:3.500A) Processing helix chain 'C' and resid 3171 through 3180 removed outlier: 3.740A pdb=" N ASN C3180 " --> pdb=" O LEU C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3181 through 3183 No H-bonds generated for 'chain 'C' and resid 3181 through 3183' Processing helix chain 'C' and resid 3614 through 3629 removed outlier: 4.071A pdb=" N GLU C3626 " --> pdb=" O LEU C3622 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS C3627 " --> pdb=" O GLN C3623 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C3628 " --> pdb=" O GLY C3624 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3646 Processing helix chain 'C' and resid 3663 through 3677 removed outlier: 3.640A pdb=" N PHE C3672 " --> pdb=" O LEU C3668 " (cutoff:3.500A) Processing helix chain 'C' and resid 3686 through 3698 removed outlier: 3.717A pdb=" N ASP C3694 " --> pdb=" O MET C3690 " (cutoff:3.500A) Processing helix chain 'C' and resid 3715 through 3734 removed outlier: 3.945A pdb=" N LEU C3732 " --> pdb=" O GLN C3728 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) Processing helix chain 'C' and resid 3736 through 3748 removed outlier: 3.767A pdb=" N MET C3740 " --> pdb=" O GLY C3736 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER C3746 " --> pdb=" O LEU C3742 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3768 removed outlier: 3.575A pdb=" N THR C3759 " --> pdb=" O MET C3755 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C3765 " --> pdb=" O LYS C3761 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C3767 " --> pdb=" O GLY C3763 " (cutoff:3.500A) Processing helix chain 'C' and resid 3771 through 3785 Processing helix chain 'C' and resid 3787 through 3800 removed outlier: 4.301A pdb=" N PHE C3791 " --> pdb=" O ASP C3787 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C3800 " --> pdb=" O GLY C3796 " (cutoff:3.500A) Processing helix chain 'C' and resid 3806 through 3813 removed outlier: 3.525A pdb=" N GLU C3810 " --> pdb=" O LEU C3806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C3811 " --> pdb=" O ASN C3807 " (cutoff:3.500A) Processing helix chain 'C' and resid 3834 through 3847 removed outlier: 3.675A pdb=" N ARG C3842 " --> pdb=" O CYS C3838 " (cutoff:3.500A) Processing helix chain 'C' and resid 3852 through 3862 removed outlier: 3.533A pdb=" N ARG C3860 " --> pdb=" O GLN C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3870 through 3891 removed outlier: 3.552A pdb=" N SER C3874 " --> pdb=" O ASN C3870 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C3884 " --> pdb=" O LEU C3880 " (cutoff:3.500A) Processing helix chain 'C' and resid 3892 through 3897 removed outlier: 4.599A pdb=" N LYS C3896 " --> pdb=" O TYR C3892 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C3897 " --> pdb=" O TYR C3893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3892 through 3897' Processing helix chain 'C' and resid 3900 through 3924 removed outlier: 3.795A pdb=" N LYS C3909 " --> pdb=" O ARG C3905 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C3913 " --> pdb=" O LYS C3909 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C3919 " --> pdb=" O LYS C3915 " (cutoff:3.500A) Processing helix chain 'C' and resid 3929 through 3938 removed outlier: 3.523A pdb=" N HIS C3938 " --> pdb=" O GLN C3934 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3960 removed outlier: 3.557A pdb=" N ALA C3944 " --> pdb=" O ARG C3940 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C3954 " --> pdb=" O HIS C3950 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C3957 " --> pdb=" O ALA C3953 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS C3958 " --> pdb=" O HIS C3954 " (cutoff:3.500A) Processing helix chain 'C' and resid 3965 through 3987 removed outlier: 3.581A pdb=" N VAL C3980 " --> pdb=" O GLN C3976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C3983 " --> pdb=" O MET C3979 " (cutoff:3.500A) Processing helix chain 'C' and resid 3994 through 4007 removed outlier: 3.573A pdb=" N LEU C4004 " --> pdb=" O MET C4000 " (cutoff:3.500A) Processing helix chain 'C' and resid 4010 through 4029 removed outlier: 3.510A pdb=" N LYS C4016 " --> pdb=" O GLU C4012 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C4021 " --> pdb=" O PHE C4017 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C4023 " --> pdb=" O ASP C4019 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU C4024 " --> pdb=" O MET C4020 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C4025 " --> pdb=" O PHE C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4045 through 4054 removed outlier: 3.740A pdb=" N ALA C4052 " --> pdb=" O ASP C4048 " (cutoff:3.500A) Processing helix chain 'C' and resid 4055 through 4057 No H-bonds generated for 'chain 'C' and resid 4055 through 4057' Processing helix chain 'C' and resid 4060 through 4071 Processing helix chain 'C' and resid 4081 through 4085 Processing helix chain 'C' and resid 4094 through 4110 Processing helix chain 'C' and resid 4113 through 4123 Processing helix chain 'C' and resid 4123 through 4131 removed outlier: 3.586A pdb=" N TYR C4129 " --> pdb=" O SER C4125 " (cutoff:3.500A) Processing helix chain 'C' and resid 4154 through 4163 removed outlier: 3.539A pdb=" N TRP C4161 " --> pdb=" O SER C4157 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C4162 " --> pdb=" O ARG C4158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C4163 " --> pdb=" O THR C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4165 through 4178 removed outlier: 3.722A pdb=" N ARG C4171 " --> pdb=" O LYS C4167 " (cutoff:3.500A) Processing helix chain 'C' and resid 4184 through 4206 removed outlier: 3.944A pdb=" N GLU C4188 " --> pdb=" O LYS C4184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C4191 " --> pdb=" O MET C4187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C4192 " --> pdb=" O GLU C4188 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C4196 " --> pdb=" O ASN C4192 " (cutoff:3.500A) Processing helix chain 'C' and resid 4487 through 4492 Processing helix chain 'C' and resid 4492 through 4499 removed outlier: 3.715A pdb=" N PHE C4496 " --> pdb=" O LEU C4492 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C4497 " --> pdb=" O LEU C4493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C4498 " --> pdb=" O ASN C4494 " (cutoff:3.500A) Processing helix chain 'C' and resid 4499 through 4519 removed outlier: 3.860A pdb=" N ALA C4507 " --> pdb=" O MET C4503 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4595 removed outlier: 3.552A pdb=" N ILE C4578 " --> pdb=" O ARG C4574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C4588 " --> pdb=" O SER C4584 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C4590 " --> pdb=" O PHE C4586 " (cutoff:3.500A) Processing helix chain 'C' and resid 4595 through 4613 Processing helix chain 'C' and resid 4626 through 4631 removed outlier: 3.501A pdb=" N GLN C4630 " --> pdb=" O ASP C4626 " (cutoff:3.500A) Processing helix chain 'C' and resid 4632 through 4638 removed outlier: 3.649A pdb=" N VAL C4635 " --> pdb=" O ASP C4632 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C4636 " --> pdb=" O ARG C4633 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4646 removed outlier: 3.990A pdb=" N TRP C4646 " --> pdb=" O ASN C4643 " (cutoff:3.500A) Processing helix chain 'C' and resid 4647 through 4648 No H-bonds generated for 'chain 'C' and resid 4647 through 4648' Processing helix chain 'C' and resid 4649 through 4663 removed outlier: 6.618A pdb=" N GLU C4660 " --> pdb=" O ASP C4656 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE C4661 " --> pdb=" O LYS C4657 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C4662 " --> pdb=" O TYR C4658 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4672 removed outlier: 3.674A pdb=" N SER C4668 " --> pdb=" O ARG C4664 " (cutoff:3.500A) Processing helix chain 'C' and resid 4697 through 4702 removed outlier: 4.355A pdb=" N ILE C4702 " --> pdb=" O VAL C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 removed outlier: 3.688A pdb=" N THR C4716 " --> pdb=" O GLY C4712 " (cutoff:3.500A) Processing helix chain 'C' and resid 4717 through 4736 removed outlier: 3.696A pdb=" N MET C4729 " --> pdb=" O TRP C4725 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS C4734 " --> pdb=" O SER C4730 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C4735 " --> pdb=" O VAL C4731 " (cutoff:3.500A) Processing helix chain 'C' and resid 4738 through 4749 removed outlier: 3.685A pdb=" N HIS C4743 " --> pdb=" O PHE C4740 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C4744 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C4745 " --> pdb=" O ALA C4742 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4763 removed outlier: 4.008A pdb=" N THR C4756 " --> pdb=" O LYS C4752 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C4757 " --> pdb=" O THR C4753 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C4761 " --> pdb=" O ILE C4757 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C4762 " --> pdb=" O LEU C4758 " (cutoff:3.500A) Processing helix chain 'C' and resid 4764 through 4790 removed outlier: 3.523A pdb=" N VAL C4769 " --> pdb=" O GLY C4765 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C4770 " --> pdb=" O LYS C4766 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C4787 " --> pdb=" O THR C4783 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C4788 " --> pdb=" O VAL C4784 " (cutoff:3.500A) Processing helix chain 'C' and resid 4791 through 4794 removed outlier: 3.611A pdb=" N TYR C4794 " --> pdb=" O ARG C4791 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4791 through 4794' Processing helix chain 'C' and resid 4809 through 4820 Processing helix chain 'C' and resid 4840 through 4855 removed outlier: 3.552A pdb=" N THR C4850 " --> pdb=" O ILE C4846 " (cutoff:3.500A) Processing helix chain 'C' and resid 4857 through 4888 removed outlier: 3.546A pdb=" N ALA C4861 " --> pdb=" O VAL C4857 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C4867 " --> pdb=" O ILE C4863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C4877 " --> pdb=" O GLU C4873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C4882 " --> pdb=" O GLN C4878 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU C4886 " --> pdb=" O LYS C4882 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 3.834A pdb=" N THR C4901 " --> pdb=" O TYR C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4904 through 4912 removed outlier: 3.781A pdb=" N THR C4908 " --> pdb=" O HIS C4904 " (cutoff:3.500A) Processing helix chain 'C' and resid 4916 through 4928 Processing helix chain 'C' and resid 4935 through 4948 Processing helix chain 'C' and resid 4958 through 4963 removed outlier: 3.647A pdb=" N TYR C4963 " --> pdb=" O PHE C4959 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 158 removed outlier: 3.836A pdb=" N CYS D 158 " --> pdb=" O GLY D 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 158' Processing helix chain 'D' and resid 270 through 273 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 409 through 439 removed outlier: 4.301A pdb=" N VAL D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 428 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 435 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.752A pdb=" N PHE D 489 " --> pdb=" O ARG D 485 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 506 removed outlier: 3.669A pdb=" N HIS D 506 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 524 No H-bonds generated for 'chain 'D' and resid 522 through 524' Processing helix chain 'D' and resid 525 through 540 Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.733A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 554 through 561 Processing helix chain 'D' and resid 562 through 565 removed outlier: 3.894A pdb=" N LEU D 565 " --> pdb=" O LEU D 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 562 through 565' Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.618A pdb=" N CYS D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 removed outlier: 3.690A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.614A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.606A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.665A pdb=" N LEU D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 636 " --> pdb=" O ILE D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 Processing helix chain 'D' and resid 875 through 899 removed outlier: 3.842A pdb=" N ARG D 880 " --> pdb=" O PRO D 876 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE D 881 " --> pdb=" O HIS D 877 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 897 " --> pdb=" O TRP D 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 899 " --> pdb=" O MET D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 946 removed outlier: 4.231A pdb=" N MET D 935 " --> pdb=" O TYR D 931 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 940 " --> pdb=" O SER D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 986 removed outlier: 4.011A pdb=" N PHE D 985 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 986 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 986' Processing helix chain 'D' and resid 989 through 1011 removed outlier: 3.561A pdb=" N ASP D 997 " --> pdb=" O GLU D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 4.565A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D1050 " --> pdb=" O ASN D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1571 through 1576 removed outlier: 3.720A pdb=" N HIS D1575 " --> pdb=" O PHE D1571 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D1576 " --> pdb=" O LYS D1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1571 through 1576' Processing helix chain 'D' and resid 1647 through 1665 Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.824A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) Processing helix chain 'D' and resid 1682 through 1691 removed outlier: 4.051A pdb=" N GLU D1690 " --> pdb=" O LEU D1686 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN D1691 " --> pdb=" O TYR D1687 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1709 removed outlier: 3.554A pdb=" N ILE D1707 " --> pdb=" O TYR D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1710 through 1722 removed outlier: 4.734A pdb=" N TYR D1714 " --> pdb=" O HIS D1710 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D1718 " --> pdb=" O TYR D1714 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1735 Processing helix chain 'D' and resid 1783 through 1804 removed outlier: 3.815A pdb=" N ALA D1789 " --> pdb=" O ASP D1785 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D1790 " --> pdb=" O ILE D1786 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1831 Proline residue: D1820 - end of helix removed outlier: 3.770A pdb=" N MET D1831 " --> pdb=" O THR D1827 " (cutoff:3.500A) Processing helix chain 'D' and resid 1837 through 1847 Processing helix chain 'D' and resid 1900 through 1942 removed outlier: 3.539A pdb=" N LYS D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D1914 " --> pdb=" O LEU D1910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D1932 " --> pdb=" O ALA D1928 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D1935 " --> pdb=" O ASP D1931 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D1939 " --> pdb=" O ALA D1935 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D1942 " --> pdb=" O GLN D1938 " (cutoff:3.500A) Processing helix chain 'D' and resid 2000 through 2013 removed outlier: 3.536A pdb=" N ILE D2010 " --> pdb=" O THR D2006 " (cutoff:3.500A) Processing helix chain 'D' and resid 2025 through 2038 removed outlier: 3.675A pdb=" N ARG D2029 " --> pdb=" O THR D2025 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D2030 " --> pdb=" O ILE D2026 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D2035 " --> pdb=" O LEU D2031 " (cutoff:3.500A) Processing helix chain 'D' and resid 2059 through 2074 removed outlier: 4.002A pdb=" N SER D2064 " --> pdb=" O GLN D2060 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL D2068 " --> pdb=" O SER D2064 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D2070 " --> pdb=" O THR D2066 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D2073 " --> pdb=" O ARG D2069 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D2074 " --> pdb=" O TRP D2070 " (cutoff:3.500A) Processing helix chain 'D' and resid 2078 through 2093 removed outlier: 3.982A pdb=" N VAL D2082 " --> pdb=" O ASP D2078 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D2087 " --> pdb=" O ARG D2083 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D2088 " --> pdb=" O ALA D2084 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR D2093 " --> pdb=" O LEU D2089 " (cutoff:3.500A) Processing helix chain 'D' and resid 2096 through 2103 removed outlier: 3.896A pdb=" N ALA D2102 " --> pdb=" O GLY D2098 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D2103 " --> pdb=" O LEU D2099 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2131 removed outlier: 3.656A pdb=" N THR D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D2127 " --> pdb=" O SER D2123 " (cutoff:3.500A) Processing helix chain 'D' and resid 2139 through 2153 removed outlier: 3.903A pdb=" N MET D2143 " --> pdb=" O GLU D2139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D2144 " --> pdb=" O GLU D2140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D2145 " --> pdb=" O LYS D2141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D2152 " --> pdb=" O GLY D2148 " (cutoff:3.500A) Processing helix chain 'D' and resid 2159 through 2167 removed outlier: 3.961A pdb=" N MET D2163 " --> pdb=" O HIS D2159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D2164 " --> pdb=" O PRO D2160 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2180 Processing helix chain 'D' and resid 2192 through 2207 removed outlier: 3.671A pdb=" N ASN D2196 " --> pdb=" O LYS D2192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D2197 " --> pdb=" O MET D2193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D2200 " --> pdb=" O ASN D2196 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D2205 " --> pdb=" O LEU D2201 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D2207 " --> pdb=" O TYR D2203 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2214 removed outlier: 3.989A pdb=" N ALA D2214 " --> pdb=" O GLN D2210 " (cutoff:3.500A) Processing helix chain 'D' and resid 2215 through 2217 No H-bonds generated for 'chain 'D' and resid 2215 through 2217' Processing helix chain 'D' and resid 2218 through 2226 removed outlier: 3.714A pdb=" N GLU D2224 " --> pdb=" O SER D2220 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2247 Processing helix chain 'D' and resid 2251 through 2258 Processing helix chain 'D' and resid 2259 through 2273 removed outlier: 3.981A pdb=" N LEU D2263 " --> pdb=" O ARG D2259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS D2273 " --> pdb=" O TYR D2269 " (cutoff:3.500A) Processing helix chain 'D' and resid 2295 through 2308 removed outlier: 4.136A pdb=" N TYR D2299 " --> pdb=" O GLU D2295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2328 removed outlier: 3.700A pdb=" N VAL D2320 " --> pdb=" O GLU D2316 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D2322 " --> pdb=" O ALA D2318 " (cutoff:3.500A) Processing helix chain 'D' and resid 2344 through 2349 removed outlier: 3.596A pdb=" N GLU D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) Processing helix chain 'D' and resid 2387 through 2402 Processing helix chain 'D' and resid 2417 through 2425 removed outlier: 3.729A pdb=" N ARG D2421 " --> pdb=" O ALA D2417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D2423 " --> pdb=" O ARG D2419 " (cutoff:3.500A) Processing helix chain 'D' and resid 2432 through 2442 removed outlier: 3.567A pdb=" N SER D2438 " --> pdb=" O VAL D2434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D2439 " --> pdb=" O GLY D2435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D2440 " --> pdb=" O VAL D2436 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D2441 " --> pdb=" O ILE D2437 " (cutoff:3.500A) Processing helix chain 'D' and resid 2462 through 2477 removed outlier: 4.181A pdb=" N LYS D2466 " --> pdb=" O CYS D2462 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D2467 " --> pdb=" O PRO D2463 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D2475 " --> pdb=" O LEU D2471 " (cutoff:3.500A) Processing helix chain 'D' and resid 2482 through 2489 removed outlier: 3.770A pdb=" N LEU D2488 " --> pdb=" O PHE D2484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU D2489 " --> pdb=" O LEU D2485 " (cutoff:3.500A) Processing helix chain 'D' and resid 2493 through 2499 Processing helix chain 'D' and resid 2500 through 2502 No H-bonds generated for 'chain 'D' and resid 2500 through 2502' Processing helix chain 'D' and resid 2512 through 2524 removed outlier: 4.046A pdb=" N ASN D2518 " --> pdb=" O ALA D2514 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D2519 " --> pdb=" O LEU D2515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D2521 " --> pdb=" O LEU D2517 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS D2522 " --> pdb=" O ASN D2518 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D2523 " --> pdb=" O ARG D2519 " (cutoff:3.500A) Processing helix chain 'D' and resid 2525 through 2529 removed outlier: 3.923A pdb=" N LEU D2529 " --> pdb=" O LEU D2526 " (cutoff:3.500A) Processing helix chain 'D' and resid 2535 through 2552 removed outlier: 3.650A pdb=" N HIS D2541 " --> pdb=" O ALA D2537 " (cutoff:3.500A) Processing helix chain 'D' and resid 2559 through 2576 removed outlier: 3.995A pdb=" N LYS D2564 " --> pdb=" O CYS D2560 " (cutoff:3.500A) Processing helix chain 'D' and resid 2583 through 2601 removed outlier: 3.547A pdb=" N ARG D2592 " --> pdb=" O HIS D2588 " (cutoff:3.500A) Proline residue: D2598 - end of helix Processing helix chain 'D' and resid 2606 through 2627 removed outlier: 3.735A pdb=" N ARG D2617 " --> pdb=" O ASN D2613 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS D2618 " --> pdb=" O HIS D2614 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D2624 " --> pdb=" O LYS D2620 " (cutoff:3.500A) Proline residue: D2625 - end of helix Processing helix chain 'D' and resid 2635 through 2651 Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2668 - end of helix removed outlier: 3.704A pdb=" N GLY D2675 " --> pdb=" O SER D2671 " (cutoff:3.500A) Processing helix chain 'D' and resid 2715 through 2740 removed outlier: 3.782A pdb=" N GLU D2719 " --> pdb=" O PRO D2715 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D2721 " --> pdb=" O LYS D2717 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D2723 " --> pdb=" O GLU D2719 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D2724 " --> pdb=" O TYR D2720 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D2727 " --> pdb=" O ASN D2723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D2735 " --> pdb=" O ASP D2731 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP D2736 " --> pdb=" O LYS D2732 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D2737 " --> pdb=" O TRP D2733 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN D2740 " --> pdb=" O ASP D2736 " (cutoff:3.500A) Processing helix chain 'D' and resid 2749 through 2753 removed outlier: 4.083A pdb=" N LYS D2753 " --> pdb=" O ASP D2750 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 3.895A pdb=" N ILE D2771 " --> pdb=" O LYS D2767 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR D2772 " --> pdb=" O GLU D2768 " (cutoff:3.500A) Proline residue: D2775 - end of helix removed outlier: 3.500A pdb=" N THR D2782 " --> pdb=" O GLU D2778 " (cutoff:3.500A) Processing helix chain 'D' and resid 2835 through 2862 removed outlier: 3.921A pdb=" N GLU D2860 " --> pdb=" O LYS D2856 " (cutoff:3.500A) Processing helix chain 'D' and resid 2874 through 2878 Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.966A pdb=" N ASP D2886 " --> pdb=" O GLU D2882 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS D2889 " --> pdb=" O LYS D2885 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D2894 " --> pdb=" O ALA D2890 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D2895 " --> pdb=" O GLN D2891 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D2896 " --> pdb=" O ASP D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2983 through 3004 Proline residue: D2990 - end of helix removed outlier: 3.928A pdb=" N GLY D2994 " --> pdb=" O PRO D2990 " (cutoff:3.500A) Processing helix chain 'D' and resid 3010 through 3027 removed outlier: 3.532A pdb=" N VAL D3014 " --> pdb=" O CYS D3010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D3017 " --> pdb=" O GLY D3013 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D3019 " --> pdb=" O LEU D3015 " (cutoff:3.500A) Processing helix chain 'D' and resid 3035 through 3051 Processing helix chain 'D' and resid 3062 through 3067 Processing helix chain 'D' and resid 3067 through 3080 Processing helix chain 'D' and resid 3101 through 3116 removed outlier: 3.512A pdb=" N HIS D3116 " --> pdb=" O HIS D3112 " (cutoff:3.500A) Processing helix chain 'D' and resid 3125 through 3143 removed outlier: 3.522A pdb=" N THR D3136 " --> pdb=" O TYR D3132 " (cutoff:3.500A) Processing helix chain 'D' and resid 3150 through 3165 removed outlier: 3.625A pdb=" N GLY D3165 " --> pdb=" O ALA D3161 " (cutoff:3.500A) Processing helix chain 'D' and resid 3171 through 3180 removed outlier: 3.740A pdb=" N ASN D3180 " --> pdb=" O LEU D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3181 through 3183 No H-bonds generated for 'chain 'D' and resid 3181 through 3183' Processing helix chain 'D' and resid 3614 through 3629 removed outlier: 4.071A pdb=" N GLU D3626 " --> pdb=" O LEU D3622 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS D3627 " --> pdb=" O GLN D3623 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D3628 " --> pdb=" O GLY D3624 " (cutoff:3.500A) Processing helix chain 'D' and resid 3637 through 3646 Processing helix chain 'D' and resid 3663 through 3677 removed outlier: 3.640A pdb=" N PHE D3672 " --> pdb=" O LEU D3668 " (cutoff:3.500A) Processing helix chain 'D' and resid 3686 through 3698 removed outlier: 3.717A pdb=" N ASP D3694 " --> pdb=" O MET D3690 " (cutoff:3.500A) Processing helix chain 'D' and resid 3715 through 3734 removed outlier: 3.945A pdb=" N LEU D3732 " --> pdb=" O GLN D3728 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) Processing helix chain 'D' and resid 3736 through 3748 removed outlier: 3.767A pdb=" N MET D3740 " --> pdb=" O GLY D3736 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER D3746 " --> pdb=" O LEU D3742 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3768 removed outlier: 3.575A pdb=" N THR D3759 " --> pdb=" O MET D3755 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D3765 " --> pdb=" O LYS D3761 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D3767 " --> pdb=" O GLY D3763 " (cutoff:3.500A) Processing helix chain 'D' and resid 3771 through 3785 Processing helix chain 'D' and resid 3787 through 3800 removed outlier: 4.301A pdb=" N PHE D3791 " --> pdb=" O ASP D3787 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D3800 " --> pdb=" O GLY D3796 " (cutoff:3.500A) Processing helix chain 'D' and resid 3806 through 3813 removed outlier: 3.525A pdb=" N GLU D3810 " --> pdb=" O LEU D3806 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D3811 " --> pdb=" O ASN D3807 " (cutoff:3.500A) Processing helix chain 'D' and resid 3834 through 3847 removed outlier: 3.675A pdb=" N ARG D3842 " --> pdb=" O CYS D3838 " (cutoff:3.500A) Processing helix chain 'D' and resid 3852 through 3862 removed outlier: 3.533A pdb=" N ARG D3860 " --> pdb=" O GLN D3856 " (cutoff:3.500A) Processing helix chain 'D' and resid 3870 through 3891 removed outlier: 3.552A pdb=" N SER D3874 " --> pdb=" O ASN D3870 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D3884 " --> pdb=" O LEU D3880 " (cutoff:3.500A) Processing helix chain 'D' and resid 3892 through 3897 removed outlier: 4.599A pdb=" N LYS D3896 " --> pdb=" O TYR D3892 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP D3897 " --> pdb=" O TYR D3893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3892 through 3897' Processing helix chain 'D' and resid 3900 through 3924 removed outlier: 3.795A pdb=" N LYS D3909 " --> pdb=" O ARG D3905 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D3913 " --> pdb=" O LYS D3909 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D3919 " --> pdb=" O LYS D3915 " (cutoff:3.500A) Processing helix chain 'D' and resid 3929 through 3938 removed outlier: 3.523A pdb=" N HIS D3938 " --> pdb=" O GLN D3934 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3960 removed outlier: 3.557A pdb=" N ALA D3944 " --> pdb=" O ARG D3940 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D3954 " --> pdb=" O HIS D3950 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D3957 " --> pdb=" O ALA D3953 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS D3958 " --> pdb=" O HIS D3954 " (cutoff:3.500A) Processing helix chain 'D' and resid 3965 through 3987 removed outlier: 3.581A pdb=" N VAL D3980 " --> pdb=" O GLN D3976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D3983 " --> pdb=" O MET D3979 " (cutoff:3.500A) Processing helix chain 'D' and resid 3994 through 4007 removed outlier: 3.573A pdb=" N LEU D4004 " --> pdb=" O MET D4000 " (cutoff:3.500A) Processing helix chain 'D' and resid 4010 through 4029 removed outlier: 3.510A pdb=" N LYS D4016 " --> pdb=" O GLU D4012 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D4021 " --> pdb=" O PHE D4017 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D4023 " --> pdb=" O ASP D4019 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU D4024 " --> pdb=" O MET D4020 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D4025 " --> pdb=" O PHE D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4045 through 4054 removed outlier: 3.740A pdb=" N ALA D4052 " --> pdb=" O ASP D4048 " (cutoff:3.500A) Processing helix chain 'D' and resid 4055 through 4057 No H-bonds generated for 'chain 'D' and resid 4055 through 4057' Processing helix chain 'D' and resid 4060 through 4071 Processing helix chain 'D' and resid 4081 through 4085 Processing helix chain 'D' and resid 4094 through 4110 Processing helix chain 'D' and resid 4113 through 4123 Processing helix chain 'D' and resid 4123 through 4131 removed outlier: 3.586A pdb=" N TYR D4129 " --> pdb=" O SER D4125 " (cutoff:3.500A) Processing helix chain 'D' and resid 4154 through 4163 removed outlier: 3.539A pdb=" N TRP D4161 " --> pdb=" O SER D4157 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D4162 " --> pdb=" O ARG D4158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D4163 " --> pdb=" O THR D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4165 through 4178 removed outlier: 3.722A pdb=" N ARG D4171 " --> pdb=" O LYS D4167 " (cutoff:3.500A) Processing helix chain 'D' and resid 4184 through 4206 removed outlier: 3.944A pdb=" N GLU D4188 " --> pdb=" O LYS D4184 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D4191 " --> pdb=" O MET D4187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN D4192 " --> pdb=" O GLU D4188 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP D4196 " --> pdb=" O ASN D4192 " (cutoff:3.500A) Processing helix chain 'D' and resid 4487 through 4492 Processing helix chain 'D' and resid 4492 through 4499 removed outlier: 3.715A pdb=" N PHE D4496 " --> pdb=" O LEU D4492 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D4497 " --> pdb=" O LEU D4493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D4498 " --> pdb=" O ASN D4494 " (cutoff:3.500A) Processing helix chain 'D' and resid 4499 through 4519 removed outlier: 3.860A pdb=" N ALA D4507 " --> pdb=" O MET D4503 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4595 removed outlier: 3.552A pdb=" N ILE D4578 " --> pdb=" O ARG D4574 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE D4588 " --> pdb=" O SER D4584 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D4590 " --> pdb=" O PHE D4586 " (cutoff:3.500A) Processing helix chain 'D' and resid 4595 through 4613 Processing helix chain 'D' and resid 4626 through 4631 removed outlier: 3.501A pdb=" N GLN D4630 " --> pdb=" O ASP D4626 " (cutoff:3.500A) Processing helix chain 'D' and resid 4632 through 4638 removed outlier: 3.649A pdb=" N VAL D4635 " --> pdb=" O ASP D4632 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D4636 " --> pdb=" O ARG D4633 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4646 removed outlier: 3.990A pdb=" N TRP D4646 " --> pdb=" O ASN D4643 " (cutoff:3.500A) Processing helix chain 'D' and resid 4647 through 4648 No H-bonds generated for 'chain 'D' and resid 4647 through 4648' Processing helix chain 'D' and resid 4649 through 4663 removed outlier: 6.618A pdb=" N GLU D4660 " --> pdb=" O ASP D4656 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE D4661 " --> pdb=" O LYS D4657 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D4662 " --> pdb=" O TYR D4658 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4672 removed outlier: 3.674A pdb=" N SER D4668 " --> pdb=" O ARG D4664 " (cutoff:3.500A) Processing helix chain 'D' and resid 4697 through 4702 removed outlier: 4.355A pdb=" N ILE D4702 " --> pdb=" O VAL D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 removed outlier: 3.688A pdb=" N THR D4716 " --> pdb=" O GLY D4712 " (cutoff:3.500A) Processing helix chain 'D' and resid 4717 through 4736 removed outlier: 3.696A pdb=" N MET D4729 " --> pdb=" O TRP D4725 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS D4734 " --> pdb=" O SER D4730 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D4735 " --> pdb=" O VAL D4731 " (cutoff:3.500A) Processing helix chain 'D' and resid 4738 through 4749 removed outlier: 3.685A pdb=" N HIS D4743 " --> pdb=" O PHE D4740 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D4744 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D4745 " --> pdb=" O ALA D4742 " (cutoff:3.500A) Processing helix chain 'D' and resid 4751 through 4763 removed outlier: 4.008A pdb=" N THR D4756 " --> pdb=" O LYS D4752 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE D4757 " --> pdb=" O THR D4753 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL D4761 " --> pdb=" O ILE D4757 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D4762 " --> pdb=" O LEU D4758 " (cutoff:3.500A) Processing helix chain 'D' and resid 4764 through 4790 removed outlier: 3.523A pdb=" N VAL D4769 " --> pdb=" O GLY D4765 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D4770 " --> pdb=" O LYS D4766 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D4787 " --> pdb=" O THR D4783 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D4788 " --> pdb=" O VAL D4784 " (cutoff:3.500A) Processing helix chain 'D' and resid 4791 through 4794 removed outlier: 3.611A pdb=" N TYR D4794 " --> pdb=" O ARG D4791 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4791 through 4794' Processing helix chain 'D' and resid 4809 through 4820 Processing helix chain 'D' and resid 4840 through 4855 removed outlier: 3.552A pdb=" N THR D4850 " --> pdb=" O ILE D4846 " (cutoff:3.500A) Processing helix chain 'D' and resid 4857 through 4888 removed outlier: 3.546A pdb=" N ALA D4861 " --> pdb=" O VAL D4857 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D4867 " --> pdb=" O ILE D4863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D4877 " --> pdb=" O GLU D4873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D4882 " --> pdb=" O GLN D4878 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU D4886 " --> pdb=" O LYS D4882 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 3.834A pdb=" N THR D4901 " --> pdb=" O TYR D4898 " (cutoff:3.500A) Processing helix chain 'D' and resid 4904 through 4912 removed outlier: 3.781A pdb=" N THR D4908 " --> pdb=" O HIS D4904 " (cutoff:3.500A) Processing helix chain 'D' and resid 4916 through 4928 Processing helix chain 'D' and resid 4935 through 4948 Processing helix chain 'D' and resid 4958 through 4963 removed outlier: 3.647A pdb=" N TYR D4963 " --> pdb=" O PHE D4959 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.508A pdb=" N ARG A 122 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.532A pdb=" N GLU A 31 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 136 removed outlier: 3.931A pdb=" N ASP A 146 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A 203 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA7, first strand: chain 'A' and resid 244 through 246 removed outlier: 3.666A pdb=" N ARG A 389 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 645 through 650 removed outlier: 3.874A pdb=" N GLN A 645 " --> pdb=" O HIS A1631 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A1629 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 769 through 770 removed outlier: 6.447A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB3, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB4, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB5, first strand: chain 'A' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY A 852 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A1216 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A1104 " --> pdb=" O ASN A1216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY A 852 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A1216 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A1104 " --> pdb=" O ASN A1216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1172 " --> pdb=" O ASP A1167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A1175 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A1190 " --> pdb=" O PHE A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 903 through 904 removed outlier: 6.174A pdb=" N GLN A 903 " --> pdb=" O HIS A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1149 through 1150 removed outlier: 3.996A pdb=" N ARG A1114 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1257 through 1259 removed outlier: 3.831A pdb=" N LEU A1595 " --> pdb=" O PHE A1301 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A1301 " --> pdb=" O LEU A1595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1426 through 1427 Processing sheet with id=AC2, first strand: chain 'A' and resid 1504 through 1505 Processing sheet with id=AC3, first strand: chain 'A' and resid 1726 through 1727 Processing sheet with id=AC4, first strand: chain 'A' and resid 2789 through 2791 removed outlier: 4.056A pdb=" N SER A2905 " --> pdb=" O ARG A2789 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A2791 " --> pdb=" O ALA A2903 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 4043 through 4044 Processing sheet with id=AC6, first strand: chain 'A' and resid 4134 through 4136 Processing sheet with id=AC7, first strand: chain 'A' and resid 4521 through 4522 Processing sheet with id=AC8, first strand: chain 'B' and resid 121 through 123 removed outlier: 3.508A pdb=" N ARG B 122 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.532A pdb=" N GLU B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AD2, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AD3, first strand: chain 'B' and resid 129 through 136 removed outlier: 3.931A pdb=" N ASP B 146 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 147 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 203 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AD5, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.666A pdb=" N ARG B 389 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AD7, first strand: chain 'B' and resid 645 through 650 removed outlier: 3.874A pdb=" N GLN B 645 " --> pdb=" O HIS B1631 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B1629 " --> pdb=" O ARG B 647 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 769 through 770 removed outlier: 6.447A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 723 through 725 Processing sheet with id=AE1, first strand: chain 'B' and resid 723 through 725 Processing sheet with id=AE2, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE3, first strand: chain 'B' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY B 852 " --> pdb=" O GLN B1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B1216 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY B 852 " --> pdb=" O GLN B1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B1216 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B1172 " --> pdb=" O ASP B1167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B1175 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B1190 " --> pdb=" O PHE B1175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 903 through 904 removed outlier: 6.174A pdb=" N GLN B 903 " --> pdb=" O HIS B 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 1149 through 1150 removed outlier: 3.996A pdb=" N ARG B1114 " --> pdb=" O SER B1206 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1257 through 1259 removed outlier: 3.831A pdb=" N LEU B1595 " --> pdb=" O PHE B1301 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE B1301 " --> pdb=" O LEU B1595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1426 through 1427 Processing sheet with id=AE9, first strand: chain 'B' and resid 1504 through 1505 Processing sheet with id=AF1, first strand: chain 'B' and resid 1726 through 1727 Processing sheet with id=AF2, first strand: chain 'B' and resid 2789 through 2791 removed outlier: 4.056A pdb=" N SER B2905 " --> pdb=" O ARG B2789 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B2791 " --> pdb=" O ALA B2903 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 4043 through 4044 Processing sheet with id=AF4, first strand: chain 'B' and resid 4134 through 4136 Processing sheet with id=AF5, first strand: chain 'B' and resid 4521 through 4522 Processing sheet with id=AF6, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.508A pdb=" N ARG C 122 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 26 through 28 removed outlier: 3.532A pdb=" N GLU C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 35 through 38 Processing sheet with id=AF9, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AG1, first strand: chain 'C' and resid 129 through 136 removed outlier: 3.931A pdb=" N ASP C 146 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL C 147 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 203 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AG3, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.666A pdb=" N ARG C 389 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AG5, first strand: chain 'C' and resid 645 through 650 removed outlier: 3.874A pdb=" N GLN C 645 " --> pdb=" O HIS C1631 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C1629 " --> pdb=" O ARG C 647 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 769 through 770 removed outlier: 6.447A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 723 through 725 Processing sheet with id=AG8, first strand: chain 'C' and resid 723 through 725 Processing sheet with id=AG9, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AH1, first strand: chain 'C' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY C 852 " --> pdb=" O GLN C1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN C1216 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C1104 " --> pdb=" O ASN C1216 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY C 852 " --> pdb=" O GLN C1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN C1216 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C1104 " --> pdb=" O ASN C1216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1172 " --> pdb=" O ASP C1167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE C1175 " --> pdb=" O LEU C1190 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU C1190 " --> pdb=" O PHE C1175 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 903 through 904 removed outlier: 6.174A pdb=" N GLN C 903 " --> pdb=" O HIS C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'C' and resid 1149 through 1150 removed outlier: 3.996A pdb=" N ARG C1114 " --> pdb=" O SER C1206 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1257 through 1259 removed outlier: 3.831A pdb=" N LEU C1595 " --> pdb=" O PHE C1301 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE C1301 " --> pdb=" O LEU C1595 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1426 through 1427 Processing sheet with id=AH7, first strand: chain 'C' and resid 1504 through 1505 Processing sheet with id=AH8, first strand: chain 'C' and resid 1726 through 1727 Processing sheet with id=AH9, first strand: chain 'C' and resid 2789 through 2791 removed outlier: 4.056A pdb=" N SER C2905 " --> pdb=" O ARG C2789 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C2791 " --> pdb=" O ALA C2903 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 4043 through 4044 Processing sheet with id=AI2, first strand: chain 'C' and resid 4134 through 4136 Processing sheet with id=AI3, first strand: chain 'C' and resid 4521 through 4522 Processing sheet with id=AI4, first strand: chain 'D' and resid 121 through 123 removed outlier: 3.508A pdb=" N ARG D 122 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 26 through 28 removed outlier: 3.532A pdb=" N GLU D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 35 through 38 Processing sheet with id=AI7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AI8, first strand: chain 'D' and resid 129 through 136 removed outlier: 3.931A pdb=" N ASP D 146 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 233 through 234 Processing sheet with id=AJ1, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.666A pdb=" N ARG D 389 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 305 through 308 Processing sheet with id=AJ3, first strand: chain 'D' and resid 645 through 650 removed outlier: 3.874A pdb=" N GLN D 645 " --> pdb=" O HIS D1631 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D1629 " --> pdb=" O ARG D 647 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 769 through 770 removed outlier: 6.447A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 723 through 725 Processing sheet with id=AJ6, first strand: chain 'D' and resid 723 through 725 Processing sheet with id=AJ7, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AJ8, first strand: chain 'D' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY D 852 " --> pdb=" O GLN D1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D1216 " --> pdb=" O GLU D1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 841 through 842 removed outlier: 3.855A pdb=" N GLY D 852 " --> pdb=" O GLN D1211 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D1216 " --> pdb=" O GLU D1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D1172 " --> pdb=" O ASP D1167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE D1175 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU D1190 " --> pdb=" O PHE D1175 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 903 through 904 removed outlier: 6.174A pdb=" N GLN D 903 " --> pdb=" O HIS D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'D' and resid 1149 through 1150 removed outlier: 3.996A pdb=" N ARG D1114 " --> pdb=" O SER D1206 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 1257 through 1259 removed outlier: 3.831A pdb=" N LEU D1595 " --> pdb=" O PHE D1301 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE D1301 " --> pdb=" O LEU D1595 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 1426 through 1427 Processing sheet with id=AK5, first strand: chain 'D' and resid 1504 through 1505 Processing sheet with id=AK6, first strand: chain 'D' and resid 1726 through 1727 Processing sheet with id=AK7, first strand: chain 'D' and resid 2789 through 2791 removed outlier: 4.056A pdb=" N SER D2905 " --> pdb=" O ARG D2789 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D2791 " --> pdb=" O ALA D2903 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 4043 through 4044 Processing sheet with id=AK9, first strand: chain 'D' and resid 4134 through 4136 Processing sheet with id=AL1, first strand: chain 'D' and resid 4521 through 4522 5120 hydrogen bonds defined for protein. 14592 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: 82.65 Time building geometry restraints manager: 34.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.27: 17336 1.27 - 1.43: 30072 1.43 - 1.59: 58564 1.59 - 1.76: 112 1.76 - 1.92: 920 Bond restraints: 107004 Sorted by residual: bond pdb=" CA PRO B4954 " pdb=" C PRO B4954 " ideal model delta sigma weight residual 1.522 1.410 0.112 9.90e-03 1.02e+04 1.28e+02 bond pdb=" CA PRO C4954 " pdb=" C PRO C4954 " ideal model delta sigma weight residual 1.522 1.410 0.112 9.90e-03 1.02e+04 1.28e+02 bond pdb=" CA PRO A4954 " pdb=" C PRO A4954 " ideal model delta sigma weight residual 1.522 1.410 0.112 9.90e-03 1.02e+04 1.28e+02 bond pdb=" CA PRO D4954 " pdb=" C PRO D4954 " ideal model delta sigma weight residual 1.522 1.410 0.112 9.90e-03 1.02e+04 1.28e+02 bond pdb=" CA ALA A4955 " pdb=" C ALA A4955 " ideal model delta sigma weight residual 1.526 1.409 0.118 1.07e-02 8.73e+03 1.21e+02 ... (remaining 106999 not shown) Histogram of bond angle deviations from ideal: 88.53 - 98.13: 88 98.13 - 107.72: 6416 107.72 - 117.32: 71708 117.32 - 126.92: 64972 126.92 - 136.52: 1412 Bond angle restraints: 144596 Sorted by residual: angle pdb=" C GLU C1847 " pdb=" N PRO C1848 " pdb=" CA PRO C1848 " ideal model delta sigma weight residual 119.84 135.89 -16.05 1.25e+00 6.40e-01 1.65e+02 angle pdb=" C GLU A1847 " pdb=" N PRO A1848 " pdb=" CA PRO A1848 " ideal model delta sigma weight residual 119.84 135.89 -16.05 1.25e+00 6.40e-01 1.65e+02 angle pdb=" C GLU D1847 " pdb=" N PRO D1848 " pdb=" CA PRO D1848 " ideal model delta sigma weight residual 119.84 135.89 -16.05 1.25e+00 6.40e-01 1.65e+02 angle pdb=" C GLU B1847 " pdb=" N PRO B1848 " pdb=" CA PRO B1848 " ideal model delta sigma weight residual 119.84 135.89 -16.05 1.25e+00 6.40e-01 1.65e+02 angle pdb=" C VAL D1579 " pdb=" N PRO D1580 " pdb=" CA PRO D1580 " ideal model delta sigma weight residual 119.84 108.06 11.78 1.25e+00 6.40e-01 8.88e+01 ... (remaining 144591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.11: 62044 26.11 - 52.22: 1612 52.22 - 78.33: 116 78.33 - 104.44: 8 104.44 - 130.55: 8 Dihedral angle restraints: 63788 sinusoidal: 24176 harmonic: 39612 Sorted by residual: dihedral pdb=" CA GLY B 852 " pdb=" C GLY B 852 " pdb=" N PRO B 853 " pdb=" CA PRO B 853 " ideal model delta harmonic sigma weight residual -180.00 -49.45 -130.55 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLY A 852 " pdb=" C GLY A 852 " pdb=" N PRO A 853 " pdb=" CA PRO A 853 " ideal model delta harmonic sigma weight residual -180.00 -49.45 -130.55 0 5.00e+00 4.00e-02 6.82e+02 dihedral pdb=" CA GLY C 852 " pdb=" C GLY C 852 " pdb=" N PRO C 853 " pdb=" CA PRO C 853 " ideal model delta harmonic sigma weight residual -180.00 -49.45 -130.55 0 5.00e+00 4.00e-02 6.82e+02 ... (remaining 63785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 13724 0.151 - 0.302: 2288 0.302 - 0.453: 284 0.453 - 0.603: 16 0.603 - 0.754: 12 Chirality restraints: 16324 Sorted by residual: chirality pdb=" CA PHE B4739 " pdb=" N PHE B4739 " pdb=" C PHE B4739 " pdb=" CB PHE B4739 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA PHE C4739 " pdb=" N PHE C4739 " pdb=" C PHE C4739 " pdb=" CB PHE C4739 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA PHE D4739 " pdb=" N PHE D4739 " pdb=" C PHE D4739 " pdb=" CB PHE D4739 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 16321 not shown) Planarity restraints: 18540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C4950 " 0.033 2.00e-02 2.50e+03 4.67e-02 5.45e+01 pdb=" CG TRP C4950 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP C4950 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP C4950 " -0.107 2.00e-02 2.50e+03 pdb=" NE1 TRP C4950 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP C4950 " -0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP C4950 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C4950 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP C4950 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP C4950 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D4950 " -0.033 2.00e-02 2.50e+03 4.67e-02 5.45e+01 pdb=" CG TRP D4950 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP D4950 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D4950 " 0.107 2.00e-02 2.50e+03 pdb=" NE1 TRP D4950 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP D4950 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP D4950 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D4950 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP D4950 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP D4950 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A4950 " -0.033 2.00e-02 2.50e+03 4.67e-02 5.45e+01 pdb=" CG TRP A4950 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A4950 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A4950 " 0.107 2.00e-02 2.50e+03 pdb=" NE1 TRP A4950 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP A4950 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP A4950 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4950 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4950 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A4950 " -0.035 2.00e-02 2.50e+03 ... (remaining 18537 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 9612 2.73 - 3.27: 103736 3.27 - 3.81: 172088 3.81 - 4.36: 222000 4.36 - 4.90: 343048 Nonbonded interactions: 850484 Sorted by model distance: nonbonded pdb=" OG SER B3802 " pdb=" O ASP B3833 " model vdw 2.185 2.440 nonbonded pdb=" OG SER A3802 " pdb=" O ASP A3833 " model vdw 2.185 2.440 nonbonded pdb=" OG SER D3802 " pdb=" O ASP D3833 " model vdw 2.185 2.440 nonbonded pdb=" OG SER C3802 " pdb=" O ASP C3833 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR A4617 " pdb=" O GLY A4629 " model vdw 2.201 2.440 ... (remaining 850479 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.160 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: 0.110 Extract box with map and model: 32.570 Check model and map are aligned: 1.200 Set scattering table: 0.740 Process input model: 277.180 Find NCS groups from input model: 5.880 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 328.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.020 0.170 107004 Z= 1.266 Angle : 1.788 21.094 144596 Z= 1.054 Chirality : 0.113 0.754 16324 Planarity : 0.009 0.113 18540 Dihedral : 12.275 130.551 38052 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.67 % Favored : 90.70 % Rotamer: Outliers : 0.88 % Allowed : 4.25 % Favored : 94.86 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.31 % Twisted General : 0.71 % 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: -4.90 (0.05), residues: 13156 helix: -3.31 (0.04), residues: 6816 sheet: -2.78 (0.15), residues: 932 loop : -3.05 (0.07), residues: 5408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.011 TRP B4950 HIS 0.025 0.006 HIS A4914 PHE 0.085 0.010 PHE C4952 TYR 0.081 0.011 TYR D4945 ARG 0.034 0.003 ARG D2327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26312 Ramachandran restraints generated. 13156 Oldfield, 0 Emsley, 13156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2746 residues out of total 12064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 2644 time to evaluate : 9.595 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 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 303, in __init__ self.caller(self.optimize_sidechains) 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 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable