Starting phenix.real_space_refine on Thu Mar 21 10:34:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5goa_9529/03_2024/5goa_9529.pdb" } resolution = 4.2 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= 0.006 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 66964 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 TYR 2107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2323": "NH1" <-> "NH2" Residue "A ARG 2519": "NH1" <-> "NH2" Residue "A ARG 3614": "NH1" <-> "NH2" Residue "A ARG 3616": "NH1" <-> "NH2" Residue "A PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4148": "NH1" <-> "NH2" Residue "A ARG 4158": "NH1" <-> "NH2" Residue "A GLU 4168": "OE1" <-> "OE2" Residue "A ARG 4171": "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 TYR 2107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2323": "NH1" <-> "NH2" Residue "B ARG 2519": "NH1" <-> "NH2" Residue "B ARG 3614": "NH1" <-> "NH2" Residue "B ARG 3616": "NH1" <-> "NH2" Residue "B PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4148": "NH1" <-> "NH2" Residue "B ARG 4158": "NH1" <-> "NH2" Residue "B ARG 4171": "NH1" <-> "NH2" Residue "B ARG 4498": "NH1" <-> "NH2" Residue "B ARG 4504": "NH1" <-> "NH2" Residue "B TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 2107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2323": "NH1" <-> "NH2" Residue "C ARG 2519": "NH1" <-> "NH2" Residue "C ARG 3614": "NH1" <-> "NH2" Residue "C ARG 3616": "NH1" <-> "NH2" Residue "C PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4148": "NH1" <-> "NH2" Residue "C ARG 4158": "NH1" <-> "NH2" Residue "C GLU 4168": "OE1" <-> "OE2" Residue "C ARG 4171": "NH1" <-> "NH2" Residue "C ARG 4498": "NH1" <-> "NH2" Residue "C ARG 4504": "NH1" <-> "NH2" Residue "C TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 2107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2323": "NH1" <-> "NH2" Residue "D ARG 2519": "NH1" <-> "NH2" Residue "D ARG 3614": "NH1" <-> "NH2" Residue "D ARG 3616": "NH1" <-> "NH2" Residue "D PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4148": "NH1" <-> "NH2" Residue "D ARG 4158": "NH1" <-> "NH2" Residue "D ARG 4171": "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: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 105072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 26267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26267 Classifications: {'peptide': 3423} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1649 Unresolved non-hydrogen dihedrals: 1070 Unresolved non-hydrogen chiralities: 115 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: 26267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26267 Classifications: {'peptide': 3423} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1649 Unresolved non-hydrogen dihedrals: 1073 Unresolved non-hydrogen chiralities: 115 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: 26267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26267 Classifications: {'peptide': 3423} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1649 Unresolved non-hydrogen dihedrals: 1072 Unresolved non-hydrogen chiralities: 115 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: 26267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3423, 26267 Classifications: {'peptide': 3423} Incomplete info: {'truncation_to_alanine': 314} Link IDs: {'PTRANS': 117, 'TRANS': 3305} Chain breaks: 66 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1649 Unresolved non-hydrogen dihedrals: 1070 Unresolved non-hydrogen chiralities: 115 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 204.085 174.735 83.852 1.00204.95 S ATOM 25650 SG CYS A4892 202.405 175.340 86.857 1.00186.45 S ATOM 51892 SG CYS B4889 174.733 171.845 83.850 1.00196.22 S ATOM 51917 SG CYS B4892 175.327 173.539 86.849 1.00191.26 S ATOM 78159 SG CYS C4889 171.841 201.189 83.851 1.00190.39 S ATOM 78184 SG CYS C4892 173.524 200.591 86.849 1.00182.00 S ATOM A03EY SG CYS D4889 201.188 204.074 83.852 1.00193.84 S ATOM A03FN SG CYS D4892 200.581 202.402 86.852 1.00182.18 S Time building chain proxies: 39.13, per 1000 atoms: 0.37 Number of scatterers: 105072 At special positions: 0 Unit cell: (376.95, 376.95, 203.7, 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 66964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.71 Conformation dependent library (CDL) restraints added in 13.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4914 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4892 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4889 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4914 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4892 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4889 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4914 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4892 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4889 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4914 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4892 " 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: 25744 Finding SS restraints... Secondary structure from input PDB file: 548 helices and 107 sheets defined 55.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.85 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.597A pdb=" N ILE A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 65 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 65' Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.605A pdb=" N GLN A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 270 through 273 removed outlier: 3.707A pdb=" N SER A 273 " --> pdb=" O HIS A 270 " (cutoff:3.500A) No H-bonds generated for '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: 3.597A pdb=" N ALA A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.555A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.625A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 525 through 540 removed outlier: 3.538A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.949A pdb=" N CYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 549 " --> pdb=" O ARG A 545 " (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: 4.116A 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: 3.542A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.639A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.604A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.789A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.613A pdb=" N CYS A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.610A pdb=" N ALA A 825 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 899 removed outlier: 3.969A pdb=" N ARG A 880 " --> pdb=" O PRO A 876 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 891 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 899 " --> pdb=" O MET A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 946 removed outlier: 4.613A pdb=" N MET A 935 " --> pdb=" O TYR A 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1039 through 1060 removed outlier: 3.536A pdb=" N LYS A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A1045 " --> pdb=" O ARG A1041 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A1046 " --> pdb=" O THR A1042 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1057 " --> pdb=" O ALA A1053 " (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: 3.548A pdb=" N HIS A1575 " --> pdb=" O PHE A1571 " (cutoff:3.500A) removed outlier: 3.524A 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 removed outlier: 3.725A pdb=" N HIS A1654 " --> pdb=" O LEU A1650 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1681 removed outlier: 3.649A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 3.669A pdb=" N LEU A1685 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1710 removed outlier: 3.515A pdb=" N HIS A1710 " --> pdb=" O LEU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 3.916A pdb=" N MET A1720 " --> pdb=" O THR A1716 " (cutoff:3.500A) removed outlier: 4.008A 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: 3.813A pdb=" N ALA A1789 " --> pdb=" O ASP A1785 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A1790 " --> pdb=" O ILE A1786 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1831 Proline residue: A1820 - end of helix removed outlier: 3.797A 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: 3.777A pdb=" N TYR A1913 " --> pdb=" O LEU A1909 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1914 " --> pdb=" O LEU A1910 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A1932 " --> pdb=" O ALA A1928 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A1935 " --> pdb=" O ASP A1931 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A1939 " --> pdb=" O ALA A1935 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A1940 " --> pdb=" O LYS A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2009 Processing helix chain 'A' and resid 2025 through 2039 removed outlier: 3.590A pdb=" N ARG A2029 " --> pdb=" O THR A2025 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A2030 " --> pdb=" O ILE A2026 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A2035 " --> pdb=" O LEU A2031 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR A2039 " --> pdb=" O GLU A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2074 removed outlier: 3.796A pdb=" N MET A2067 " --> pdb=" O ILE A2063 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A2073 " --> pdb=" O ARG A2069 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A2074 " --> pdb=" O TRP A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2094 removed outlier: 3.943A pdb=" N VAL A2082 " --> pdb=" O ASP A2078 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A2087 " --> pdb=" O ARG A2083 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A2088 " --> pdb=" O ALA A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2096 through 2103 removed outlier: 3.624A pdb=" N ALA A2102 " --> pdb=" O GLY A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2131 removed outlier: 3.817A pdb=" N THR A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A2119 " --> pdb=" O GLU A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.964A pdb=" N MET A2143 " --> pdb=" O GLU A2139 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A2144 " --> pdb=" O GLU A2140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A2152 " --> pdb=" O GLY A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2167 removed outlier: 3.781A pdb=" N MET A2163 " --> pdb=" O HIS A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2180 Processing helix chain 'A' and resid 2192 through 2206 removed outlier: 3.748A pdb=" N ASN A2196 " --> pdb=" O LYS A2192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A2197 " --> pdb=" O MET A2193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A2205 " --> pdb=" O LEU A2201 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A2206 " --> pdb=" O CYS A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2217 removed outlier: 3.758A pdb=" N ALA A2214 " --> pdb=" O GLN A2210 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A2215 " --> pdb=" O ASN A2211 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A2217 " --> pdb=" O LYS A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2226 removed outlier: 3.725A pdb=" N GLU A2224 " --> pdb=" O SER A2220 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2247 removed outlier: 3.509A pdb=" N ALA A2244 " --> pdb=" O PRO A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2251 through 2258 Processing helix chain 'A' and resid 2259 through 2273 removed outlier: 3.856A pdb=" N LEU A2263 " --> pdb=" O ARG A2259 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A2266 " --> pdb=" O ASP A2262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A2269 " --> pdb=" O LYS A2265 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A2273 " --> pdb=" O TYR A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 4.130A pdb=" N TYR A2299 " --> pdb=" O GLU A2295 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2326 removed outlier: 3.651A pdb=" N VAL A2320 " --> pdb=" O GLU A2316 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A2322 " --> pdb=" O ALA A2318 " (cutoff:3.500A) Processing helix chain 'A' and resid 2344 through 2354 removed outlier: 3.637A pdb=" N MET A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A2351 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A2352 " --> pdb=" O MET A2348 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A2353 " --> pdb=" O GLU A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2402 removed outlier: 3.686A pdb=" N TYR A2393 " --> pdb=" O ILE A2389 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A2394 " --> pdb=" O MET A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2418 through 2426 Processing helix chain 'A' and resid 2432 through 2440 removed outlier: 3.605A pdb=" N VAL A2436 " --> pdb=" O ASP A2432 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A2437 " --> pdb=" O LEU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2477 removed outlier: 4.304A pdb=" N LYS A2466 " --> pdb=" O CYS A2462 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A2467 " --> pdb=" O PRO A2463 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2488 removed outlier: 3.633A pdb=" N LEU A2488 " --> pdb=" O PHE A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2499 Processing helix chain 'A' and resid 2500 through 2503 removed outlier: 4.368A pdb=" N LEU A2503 " --> pdb=" O ALA A2500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2500 through 2503' Processing helix chain 'A' and resid 2512 through 2524 removed outlier: 4.000A pdb=" N ASN A2518 " --> pdb=" O ALA A2514 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A2519 " --> pdb=" O LEU A2515 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS A2522 " --> pdb=" O ASN A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2525 through 2529 removed outlier: 3.663A pdb=" N LEU A2529 " --> pdb=" O LEU A2526 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2553 Processing helix chain 'A' and resid 2559 through 2576 Processing helix chain 'A' and resid 2583 through 2601 Proline residue: A2598 - end of helix Processing helix chain 'A' and resid 2606 through 2627 removed outlier: 3.535A pdb=" N ARG A2617 " --> pdb=" O ASN A2613 " (cutoff:3.500A) removed outlier: 3.917A 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 2653 Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2668 - end of helix Processing helix chain 'A' and resid 2715 through 2739 removed outlier: 3.633A pdb=" N GLU A2719 " --> pdb=" O PRO A2715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A2720 " --> pdb=" O GLU A2716 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A2721 " --> pdb=" O LYS A2717 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A2724 " --> pdb=" O TYR A2720 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A2737 " --> pdb=" O TRP A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 3.546A pdb=" N ILE A2771 " --> pdb=" O LYS A2767 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR A2772 " --> pdb=" O GLU A2768 " (cutoff:3.500A) Proline residue: A2775 - end of helix removed outlier: 3.595A pdb=" N LYS A2781 " --> pdb=" O LYS A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2835 through 2862 removed outlier: 3.703A pdb=" N ALA A2854 " --> pdb=" O HIS A2850 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.726A pdb=" N ASP A2886 " --> pdb=" O GLU A2882 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS A2889 " --> pdb=" O LYS A2885 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP A2892 " --> pdb=" O GLU A2888 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A2894 " --> pdb=" O ALA A2890 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A2896 " --> pdb=" O ASP A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2983 through 3003 Proline residue: A2990 - end of helix Processing helix chain 'A' and resid 3010 through 3028 Processing helix chain 'A' and resid 3035 through 3052 Processing helix chain 'A' and resid 3062 through 3080 removed outlier: 3.859A pdb=" N GLU A3070 " --> pdb=" O ALA A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3101 through 3115 removed outlier: 3.515A pdb=" N PHE A3110 " --> pdb=" O LEU A3106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A3113 " --> pdb=" O LEU A3109 " (cutoff:3.500A) Processing helix chain 'A' and resid 3125 through 3144 removed outlier: 3.662A pdb=" N THR A3136 " --> pdb=" O TYR A3132 " (cutoff:3.500A) Processing helix chain 'A' and resid 3150 through 3165 removed outlier: 3.561A pdb=" N CYS A3159 " --> pdb=" O ALA A3155 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A3161 " --> pdb=" O GLY A3157 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A3165 " --> pdb=" O ALA A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3171 through 3182 removed outlier: 3.547A pdb=" N HIS A3175 " --> pdb=" O PHE A3171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A3177 " --> pdb=" O GLU A3173 " (cutoff:3.500A) Processing helix chain 'A' and resid 3614 through 3630 removed outlier: 4.082A pdb=" N ILE A3630 " --> pdb=" O GLU A3626 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3646 removed outlier: 4.466A pdb=" N LYS A3640 " --> pdb=" O TYR A3636 " (cutoff:3.500A) Processing helix chain 'A' and resid 3663 through 3677 removed outlier: 3.589A pdb=" N PHE A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3686 through 3698 removed outlier: 3.892A pdb=" N ASP A3694 " --> pdb=" O MET A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3734 removed outlier: 3.723A pdb=" N MET A3720 " --> pdb=" O GLU A3716 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A3732 " --> pdb=" O GLN A3728 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) Processing helix chain 'A' and resid 3736 through 3748 removed outlier: 3.710A pdb=" N MET A3740 " --> pdb=" O GLY A3736 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A3742 " --> pdb=" O ALA A3738 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A3746 " --> pdb=" O LEU A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3768 Processing helix chain 'A' and resid 3771 through 3785 removed outlier: 3.596A pdb=" N LEU A3779 " --> pdb=" O GLN A3775 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A3782 " --> pdb=" O MET A3778 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A3785 " --> pdb=" O TYR A3781 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3799 Processing helix chain 'A' and resid 3806 through 3812 Processing helix chain 'A' and resid 3834 through 3849 removed outlier: 3.678A pdb=" N ASP A3839 " --> pdb=" O GLU A3835 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS A3848 " --> pdb=" O LEU A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3862 removed outlier: 3.807A pdb=" N ARG A3860 " --> pdb=" O GLN A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3870 through 3893 removed outlier: 3.557A pdb=" N VAL A3876 " --> pdb=" O ILE A3872 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A3885 " --> pdb=" O ARG A3881 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A3891 " --> pdb=" O SER A3887 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A3892 " --> pdb=" O ASP A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3900 through 3926 removed outlier: 3.674A pdb=" N LYS A3909 " --> pdb=" O ARG A3905 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A3913 " --> pdb=" O LYS A3909 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A3916 " --> pdb=" O GLN A3912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A3919 " --> pdb=" O LYS A3915 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A3925 " --> pdb=" O LEU A3921 " (cutoff:3.500A) Processing helix chain 'A' and resid 3929 through 3938 removed outlier: 3.531A pdb=" N HIS A3938 " --> pdb=" O GLN A3934 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3960 removed outlier: 3.769A pdb=" N ALA A3944 " --> pdb=" O ARG A3940 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A3954 " --> pdb=" O HIS A3950 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A3956 " --> pdb=" O PHE A3952 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A3958 " --> pdb=" O HIS A3954 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3987 removed outlier: 3.510A pdb=" N GLU A3971 " --> pdb=" O GLU A3967 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A3982 " --> pdb=" O ASP A3978 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A3983 " --> pdb=" O MET A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 3.751A pdb=" N MET A4000 " --> pdb=" O ILE A3996 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A4004 " --> pdb=" O MET A4000 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A4005 " --> pdb=" O VAL A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4007 through 4026 removed outlier: 3.908A pdb=" N VAL A4011 " --> pdb=" O SER A4007 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A4012 " --> pdb=" O SER A4008 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A4013 " --> pdb=" O ASN A4009 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A4014 " --> pdb=" O ASN A4010 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A4023 " --> pdb=" O ASP A4019 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A4024 " --> pdb=" O MET A4020 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A4025 " --> pdb=" O PHE A4021 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A4026 " --> pdb=" O LEU A4022 " (cutoff:3.500A) Processing helix chain 'A' and resid 4045 through 4054 removed outlier: 3.710A pdb=" N GLU A4054 " --> pdb=" O HIS A4050 " (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 4086 removed outlier: 3.631A pdb=" N VAL A4085 " --> pdb=" O TYR A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4091 through 4110 removed outlier: 4.154A pdb=" N ILE A4095 " --> pdb=" O PRO A4091 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A4098 " --> pdb=" O ASP A4094 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4122 removed outlier: 3.765A pdb=" N PHE A4119 " --> pdb=" O ARG A4115 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A4122 " --> pdb=" O THR A4118 " (cutoff:3.500A) Processing helix chain 'A' and resid 4123 through 4131 removed outlier: 3.679A pdb=" N TYR A4129 " --> pdb=" O SER A4125 " (cutoff:3.500A) Processing helix chain 'A' and resid 4154 through 4163 removed outlier: 3.957A pdb=" N GLU A4162 " --> pdb=" O ARG A4158 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS A4163 " --> pdb=" O THR A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4181 removed outlier: 3.553A pdb=" N GLN A4172 " --> pdb=" O GLU A4168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A4176 " --> pdb=" O GLN A4172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A4178 " --> pdb=" O ILE A4174 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A4180 " --> pdb=" O ASP A4176 " (cutoff:3.500A) Processing helix chain 'A' and resid 4182 through 4205 removed outlier: 3.961A pdb=" N MET A4187 " --> pdb=" O GLU A4183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A4188 " --> pdb=" O LYS A4184 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A4191 " --> pdb=" O MET A4187 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A4192 " --> pdb=" O GLU A4188 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A4196 " --> pdb=" O ASN A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4487 through 4499 removed outlier: 3.549A pdb=" N PHE A4496 " --> pdb=" O LEU A4492 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A4497 " --> pdb=" O LEU A4493 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A4498 " --> pdb=" O ASN A4494 " (cutoff:3.500A) Processing helix chain 'A' and resid 4499 through 4519 removed outlier: 3.525A pdb=" N LEU A4508 " --> pdb=" O ARG A4504 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A4513 " --> pdb=" O PHE A4509 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4592 removed outlier: 3.673A pdb=" N ILE A4578 " --> pdb=" O ARG A4574 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A4588 " --> pdb=" O SER A4584 " (cutoff:3.500A) Processing helix chain 'A' and resid 4595 through 4613 removed outlier: 3.610A pdb=" N LYS A4610 " --> pdb=" O GLU A4606 " (cutoff:3.500A) Processing helix chain 'A' and resid 4626 through 4631 Processing helix chain 'A' and resid 4632 through 4638 removed outlier: 4.043A pdb=" N ILE A4636 " --> pdb=" O ARG A4633 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A4637 " --> pdb=" O LEU A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4646 removed outlier: 3.703A pdb=" N TYR A4645 " --> pdb=" O PRO A4642 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP A4646 " --> pdb=" O ASN A4643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4642 through 4646' 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 4659 removed outlier: 3.695A pdb=" N MET A4655 " --> pdb=" O LYS A4651 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4672 removed outlier: 3.510A pdb=" N ILE A4667 " --> pdb=" O GLY A4663 " (cutoff:3.500A) Processing helix chain 'A' and resid 4697 through 4702 removed outlier: 4.199A pdb=" N ILE A4702 " --> pdb=" O VAL A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 Processing helix chain 'A' and resid 4717 through 4736 Processing helix chain 'A' and resid 4738 through 4744 removed outlier: 3.560A pdb=" N ALA A4741 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A4743 " --> pdb=" O PHE A4740 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A4744 " --> pdb=" O ALA A4741 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4751 removed outlier: 3.737A pdb=" N MET A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A4751 " --> pdb=" O ILE A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4754 through 4764 removed outlier: 3.721A pdb=" N LEU A4758 " --> pdb=" O LEU A4754 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A4762 " --> pdb=" O LEU A4758 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A4764 " --> pdb=" O SER A4760 " (cutoff:3.500A) Processing helix chain 'A' and resid 4764 through 4790 removed outlier: 4.167A pdb=" N LEU A4770 " --> pdb=" O LYS A4766 " (cutoff:3.500A) Processing helix chain 'A' and resid 4791 through 4794 removed outlier: 3.633A 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 removed outlier: 3.617A pdb=" N HIS A4817 " --> pdb=" O CYS A4813 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A4818 " --> pdb=" O TYR A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4855 removed outlier: 4.475A pdb=" N TYR A4843 " --> pdb=" O GLU A4839 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A4850 " --> pdb=" O ILE A4846 " (cutoff:3.500A) Processing helix chain 'A' and resid 4858 through 4888 removed outlier: 3.510A pdb=" N ILE A4863 " --> pdb=" O LEU A4859 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A4867 " --> pdb=" O ILE A4863 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A4881 " --> pdb=" O GLN A4877 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A4886 " --> pdb=" O LYS A4882 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4900 Processing helix chain 'A' and resid 4904 through 4912 removed outlier: 3.726A pdb=" N THR A4908 " --> pdb=" O HIS A4904 " (cutoff:3.500A) Processing helix chain 'A' and resid 4916 through 4929 removed outlier: 3.627A pdb=" N LEU A4920 " --> pdb=" O LEU A4916 " (cutoff:3.500A) Processing helix chain 'A' and resid 4935 through 4948 Processing helix chain 'A' and resid 4958 through 4963 removed outlier: 3.577A pdb=" N TYR A4963 " --> pdb=" O PHE A4959 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.600A pdb=" N ILE B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 65 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.591A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 270 through 273 removed outlier: 3.707A pdb=" N SER B 273 " --> pdb=" O HIS B 270 " (cutoff:3.500A) No H-bonds generated for '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: 3.592A pdb=" N ALA B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 3.554A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.628A pdb=" N LEU B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.539A pdb=" N SER B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.948A pdb=" N CYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 549 " --> pdb=" O ARG B 545 " (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: 4.111A 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: 3.551A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.649A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.603A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.779A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.606A pdb=" N CYS B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 removed outlier: 3.614A pdb=" N ALA B 825 " --> pdb=" O CYS B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 899 removed outlier: 3.967A pdb=" N ARG B 880 " --> pdb=" O PRO B 876 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 881 " --> pdb=" O HIS B 877 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 899 " --> pdb=" O MET B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 946 removed outlier: 4.608A pdb=" N MET B 935 " --> pdb=" O TYR B 931 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1011 Processing helix chain 'B' and resid 1039 through 1060 removed outlier: 3.536A pdb=" N LYS B1043 " --> pdb=" O ASP B1039 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B1045 " --> pdb=" O ARG B1041 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B1049 " --> pdb=" O SER B1045 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B1057 " --> pdb=" O ALA B1053 " (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: 3.553A pdb=" N HIS B1575 " --> pdb=" O PHE B1571 " (cutoff:3.500A) removed outlier: 3.531A 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 removed outlier: 3.725A pdb=" N HIS B1654 " --> pdb=" O LEU B1650 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1681 removed outlier: 3.654A pdb=" N ALA B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 removed outlier: 3.673A pdb=" N LEU B1685 " --> pdb=" O ASP B1681 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B1690 " --> pdb=" O LEU B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1710 removed outlier: 3.517A pdb=" N HIS B1710 " --> pdb=" O LEU B1706 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 3.914A pdb=" N MET B1720 " --> pdb=" O THR B1716 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.816A pdb=" N ALA B1789 " --> pdb=" O ASP B1785 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B1790 " --> pdb=" O ILE B1786 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B1792 " --> pdb=" O LYS B1788 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B1800 " --> pdb=" O THR B1796 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B1801 " --> pdb=" O GLU B1797 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1831 Proline residue: B1820 - end of helix removed outlier: 3.801A 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: 3.774A pdb=" N TYR B1913 " --> pdb=" O LEU B1909 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B1914 " --> pdb=" O LEU B1910 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B1932 " --> pdb=" O ALA B1928 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B1935 " --> pdb=" O ASP B1931 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B1939 " --> pdb=" O ALA B1935 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B1940 " --> pdb=" O LYS B1936 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2009 Processing helix chain 'B' and resid 2025 through 2039 removed outlier: 3.589A pdb=" N ARG B2029 " --> pdb=" O THR B2025 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B2030 " --> pdb=" O ILE B2026 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B2035 " --> pdb=" O LEU B2031 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B2039 " --> pdb=" O GLU B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2059 through 2074 removed outlier: 3.797A pdb=" N MET B2067 " --> pdb=" O ILE B2063 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B2073 " --> pdb=" O ARG B2069 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B2074 " --> pdb=" O TRP B2070 " (cutoff:3.500A) Processing helix chain 'B' and resid 2078 through 2094 removed outlier: 3.946A pdb=" N VAL B2082 " --> pdb=" O ASP B2078 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B2087 " --> pdb=" O ARG B2083 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B2088 " --> pdb=" O ALA B2084 " (cutoff:3.500A) Processing helix chain 'B' and resid 2096 through 2103 removed outlier: 3.626A pdb=" N ALA B2102 " --> pdb=" O GLY B2098 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2131 removed outlier: 3.817A pdb=" N THR B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B2119 " --> pdb=" O GLU B2115 " (cutoff:3.500A) Processing helix chain 'B' and resid 2139 through 2153 removed outlier: 3.962A pdb=" N MET B2143 " --> pdb=" O GLU B2139 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B2144 " --> pdb=" O GLU B2140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B2152 " --> pdb=" O GLY B2148 " (cutoff:3.500A) Processing helix chain 'B' and resid 2159 through 2167 removed outlier: 3.778A pdb=" N MET B2163 " --> pdb=" O HIS B2159 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2180 Processing helix chain 'B' and resid 2192 through 2206 removed outlier: 3.738A pdb=" N ASN B2196 " --> pdb=" O LYS B2192 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B2197 " --> pdb=" O MET B2193 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B2205 " --> pdb=" O LEU B2201 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B2206 " --> pdb=" O CYS B2202 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2217 removed outlier: 3.753A pdb=" N ALA B2214 " --> pdb=" O GLN B2210 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET B2215 " --> pdb=" O ASN B2211 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B2217 " --> pdb=" O LYS B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2218 through 2226 removed outlier: 3.719A pdb=" N GLU B2224 " --> pdb=" O SER B2220 " (cutoff:3.500A) Processing helix chain 'B' and resid 2240 through 2247 removed outlier: 3.507A pdb=" N ALA B2244 " --> pdb=" O PRO B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2251 through 2258 Processing helix chain 'B' and resid 2259 through 2273 removed outlier: 3.853A pdb=" N LEU B2263 " --> pdb=" O ARG B2259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B2266 " --> pdb=" O ASP B2262 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B2269 " --> pdb=" O LYS B2265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B2273 " --> pdb=" O TYR B2269 " (cutoff:3.500A) Processing helix chain 'B' and resid 2295 through 2308 removed outlier: 4.119A pdb=" N TYR B2299 " --> pdb=" O GLU B2295 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B2307 " --> pdb=" O LEU B2303 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) Processing helix chain 'B' and resid 2314 through 2326 removed outlier: 3.645A pdb=" N VAL B2320 " --> pdb=" O GLU B2316 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B2322 " --> pdb=" O ALA B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2344 through 2354 removed outlier: 3.634A pdb=" N MET B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B2351 " --> pdb=" O ALA B2347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B2352 " --> pdb=" O MET B2348 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS B2353 " --> pdb=" O GLU B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2402 removed outlier: 3.684A pdb=" N TYR B2393 " --> pdb=" O ILE B2389 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B2394 " --> pdb=" O MET B2390 " (cutoff:3.500A) Processing helix chain 'B' and resid 2418 through 2426 Processing helix chain 'B' and resid 2432 through 2440 removed outlier: 3.609A pdb=" N VAL B2436 " --> pdb=" O ASP B2432 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2462 through 2477 removed outlier: 4.304A pdb=" N LYS B2466 " --> pdb=" O CYS B2462 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2482 through 2488 removed outlier: 3.630A pdb=" N LEU B2488 " --> pdb=" O PHE B2484 " (cutoff:3.500A) Processing helix chain 'B' and resid 2493 through 2499 Processing helix chain 'B' and resid 2500 through 2503 removed outlier: 4.337A pdb=" N LEU B2503 " --> pdb=" O ALA B2500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2500 through 2503' Processing helix chain 'B' and resid 2512 through 2524 removed outlier: 3.996A pdb=" N ASN B2518 " --> pdb=" O ALA B2514 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B2519 " --> pdb=" O LEU B2515 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS B2522 " --> pdb=" O ASN B2518 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2529 removed outlier: 3.678A pdb=" N LEU B2529 " --> pdb=" O LEU B2526 " (cutoff:3.500A) Processing helix chain 'B' and resid 2535 through 2553 Processing helix chain 'B' and resid 2559 through 2576 Processing helix chain 'B' and resid 2583 through 2601 Proline residue: B2598 - end of helix Processing helix chain 'B' and resid 2606 through 2627 removed outlier: 3.532A pdb=" N ARG B2617 " --> pdb=" O ASN B2613 " (cutoff:3.500A) removed outlier: 3.915A 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 2653 Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2668 - end of helix Processing helix chain 'B' and resid 2715 through 2739 removed outlier: 3.633A pdb=" N GLU B2719 " --> pdb=" O PRO B2715 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B2720 " --> pdb=" O GLU B2716 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B2721 " --> pdb=" O LYS B2717 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B2724 " --> pdb=" O TYR B2720 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B2737 " --> pdb=" O TRP B2733 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 3.547A pdb=" N ILE B2771 " --> pdb=" O LYS B2767 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR B2772 " --> pdb=" O GLU B2768 " (cutoff:3.500A) Proline residue: B2775 - end of helix removed outlier: 3.593A pdb=" N LYS B2781 " --> pdb=" O LYS B2777 " (cutoff:3.500A) Processing helix chain 'B' and resid 2835 through 2862 removed outlier: 3.700A pdb=" N ALA B2854 " --> pdb=" O HIS B2850 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.731A pdb=" N ASP B2886 " --> pdb=" O GLU B2882 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS B2889 " --> pdb=" O LYS B2885 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B2892 " --> pdb=" O GLU B2888 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B2894 " --> pdb=" O ALA B2890 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B2896 " --> pdb=" O ASP B2892 " (cutoff:3.500A) Processing helix chain 'B' and resid 2983 through 3003 Proline residue: B2990 - end of helix Processing helix chain 'B' and resid 3010 through 3028 Processing helix chain 'B' and resid 3035 through 3052 Processing helix chain 'B' and resid 3062 through 3080 removed outlier: 3.857A pdb=" N GLU B3070 " --> pdb=" O ALA B3066 " (cutoff:3.500A) Processing helix chain 'B' and resid 3101 through 3115 removed outlier: 3.513A pdb=" N PHE B3110 " --> pdb=" O LEU B3106 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B3113 " --> pdb=" O LEU B3109 " (cutoff:3.500A) Processing helix chain 'B' and resid 3125 through 3144 removed outlier: 3.664A pdb=" N THR B3136 " --> pdb=" O TYR B3132 " (cutoff:3.500A) Processing helix chain 'B' and resid 3150 through 3165 removed outlier: 3.560A pdb=" N CYS B3159 " --> pdb=" O ALA B3155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B3161 " --> pdb=" O GLY B3157 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B3165 " --> pdb=" O ALA B3161 " (cutoff:3.500A) Processing helix chain 'B' and resid 3171 through 3182 removed outlier: 3.544A pdb=" N HIS B3175 " --> pdb=" O PHE B3171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B3177 " --> pdb=" O GLU B3173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3614 through 3630 removed outlier: 4.082A pdb=" N ILE B3630 " --> pdb=" O GLU B3626 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3646 removed outlier: 4.449A pdb=" N LYS B3640 " --> pdb=" O TYR B3636 " (cutoff:3.500A) Processing helix chain 'B' and resid 3663 through 3677 removed outlier: 3.595A pdb=" N PHE B3672 " --> pdb=" O LEU B3668 " (cutoff:3.500A) Processing helix chain 'B' and resid 3686 through 3698 removed outlier: 3.898A pdb=" N ASP B3694 " --> pdb=" O MET B3690 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3734 removed outlier: 3.721A pdb=" N MET B3720 " --> pdb=" O GLU B3716 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B3732 " --> pdb=" O GLN B3728 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) Processing helix chain 'B' and resid 3736 through 3748 removed outlier: 3.698A pdb=" N MET B3740 " --> pdb=" O GLY B3736 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B3742 " --> pdb=" O ALA B3738 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B3746 " --> pdb=" O LEU B3742 " (cutoff:3.500A) Processing helix chain 'B' and resid 3753 through 3768 Processing helix chain 'B' and resid 3771 through 3785 removed outlier: 3.590A pdb=" N LEU B3779 " --> pdb=" O GLN B3775 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B3782 " --> pdb=" O MET B3778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B3785 " --> pdb=" O TYR B3781 " (cutoff:3.500A) Processing helix chain 'B' and resid 3788 through 3799 Processing helix chain 'B' and resid 3806 through 3812 Processing helix chain 'B' and resid 3834 through 3849 removed outlier: 3.683A pdb=" N ASP B3839 " --> pdb=" O GLU B3835 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS B3848 " --> pdb=" O LEU B3844 " (cutoff:3.500A) Processing helix chain 'B' and resid 3852 through 3862 removed outlier: 3.809A pdb=" N ARG B3860 " --> pdb=" O GLN B3856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3870 through 3893 removed outlier: 3.564A pdb=" N VAL B3876 " --> pdb=" O ILE B3872 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B3885 " --> pdb=" O ARG B3881 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B3890 " --> pdb=" O ILE B3886 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP B3891 " --> pdb=" O SER B3887 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B3892 " --> pdb=" O ASP B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3900 through 3926 removed outlier: 3.674A pdb=" N LYS B3909 " --> pdb=" O ARG B3905 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B3913 " --> pdb=" O LYS B3909 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B3916 " --> pdb=" O GLN B3912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B3919 " --> pdb=" O LYS B3915 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B3925 " --> pdb=" O LEU B3921 " (cutoff:3.500A) Processing helix chain 'B' and resid 3929 through 3938 removed outlier: 3.540A pdb=" N HIS B3938 " --> pdb=" O GLN B3934 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3960 removed outlier: 3.771A pdb=" N ALA B3944 " --> pdb=" O ARG B3940 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B3954 " --> pdb=" O HIS B3950 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B3956 " --> pdb=" O PHE B3952 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B3958 " --> pdb=" O HIS B3954 " (cutoff:3.500A) Processing helix chain 'B' and resid 3965 through 3987 removed outlier: 3.509A pdb=" N GLU B3971 " --> pdb=" O GLU B3967 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B3982 " --> pdb=" O ASP B3978 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B3983 " --> pdb=" O MET B3979 " (cutoff:3.500A) Processing helix chain 'B' and resid 3994 through 4007 removed outlier: 3.744A pdb=" N MET B4000 " --> pdb=" O ILE B3996 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B4005 " --> pdb=" O VAL B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4007 through 4026 removed outlier: 3.918A pdb=" N VAL B4011 " --> pdb=" O SER B4007 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B4012 " --> pdb=" O SER B4008 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET B4013 " --> pdb=" O ASN B4009 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B4014 " --> pdb=" O ASN B4010 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B4023 " --> pdb=" O ASP B4019 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B4024 " --> pdb=" O MET B4020 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B4025 " --> pdb=" O PHE B4021 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B4026 " --> pdb=" O LEU B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4045 through 4054 removed outlier: 3.722A pdb=" N GLU B4054 " --> pdb=" O HIS B4050 " (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 4086 removed outlier: 3.622A pdb=" N VAL B4085 " --> pdb=" O TYR B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4091 through 4110 removed outlier: 4.145A pdb=" N ILE B4095 " --> pdb=" O PRO B4091 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B4098 " --> pdb=" O ASP B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4113 through 4122 removed outlier: 3.761A pdb=" N PHE B4119 " --> pdb=" O ARG B4115 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B4122 " --> pdb=" O THR B4118 " (cutoff:3.500A) Processing helix chain 'B' and resid 4123 through 4131 removed outlier: 3.681A pdb=" N TYR B4129 " --> pdb=" O SER B4125 " (cutoff:3.500A) Processing helix chain 'B' and resid 4154 through 4163 removed outlier: 3.962A pdb=" N GLU B4162 " --> pdb=" O ARG B4158 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B4163 " --> pdb=" O THR B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4165 through 4181 removed outlier: 3.548A pdb=" N GLN B4172 " --> pdb=" O GLU B4168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B4178 " --> pdb=" O ILE B4174 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B4180 " --> pdb=" O ASP B4176 " (cutoff:3.500A) Processing helix chain 'B' and resid 4182 through 4205 removed outlier: 3.966A pdb=" N MET B4187 " --> pdb=" O GLU B4183 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B4188 " --> pdb=" O LYS B4184 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B4191 " --> pdb=" O MET B4187 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B4192 " --> pdb=" O GLU B4188 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP B4196 " --> pdb=" O ASN B4192 " (cutoff:3.500A) Processing helix chain 'B' and resid 4487 through 4499 removed outlier: 3.547A pdb=" N PHE B4496 " --> pdb=" O LEU B4492 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B4497 " --> pdb=" O LEU B4493 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B4498 " --> pdb=" O ASN B4494 " (cutoff:3.500A) Processing helix chain 'B' and resid 4499 through 4519 removed outlier: 3.526A pdb=" N LEU B4508 " --> pdb=" O ARG B4504 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B4513 " --> pdb=" O PHE B4509 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4592 removed outlier: 3.675A pdb=" N ILE B4578 " --> pdb=" O ARG B4574 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B4588 " --> pdb=" O SER B4584 " (cutoff:3.500A) Processing helix chain 'B' and resid 4595 through 4613 removed outlier: 3.608A pdb=" N LYS B4610 " --> pdb=" O GLU B4606 " (cutoff:3.500A) Processing helix chain 'B' and resid 4626 through 4631 Processing helix chain 'B' and resid 4632 through 4638 removed outlier: 4.058A pdb=" N ILE B4636 " --> pdb=" O ARG B4633 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B4637 " --> pdb=" O LEU B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4646 removed outlier: 3.710A pdb=" N TYR B4645 " --> pdb=" O PRO B4642 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP B4646 " --> pdb=" O ASN B4643 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4642 through 4646' 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 4659 removed outlier: 3.702A pdb=" N MET B4655 " --> pdb=" O LYS B4651 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4672 removed outlier: 3.505A pdb=" N ILE B4667 " --> pdb=" O GLY B4663 " (cutoff:3.500A) Processing helix chain 'B' and resid 4697 through 4702 removed outlier: 4.184A pdb=" N ILE B4702 " --> pdb=" O VAL B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 Processing helix chain 'B' and resid 4717 through 4736 Processing helix chain 'B' and resid 4738 through 4744 removed outlier: 3.566A pdb=" N ALA B4741 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B4743 " --> pdb=" O PHE B4740 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B4744 " --> pdb=" O ALA B4741 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4751 removed outlier: 3.744A pdb=" N MET B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B4751 " --> pdb=" O ILE B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4754 through 4764 removed outlier: 3.722A pdb=" N LEU B4758 " --> pdb=" O LEU B4754 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B4762 " --> pdb=" O LEU B4758 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B4764 " --> pdb=" O SER B4760 " (cutoff:3.500A) Processing helix chain 'B' and resid 4764 through 4790 removed outlier: 4.164A pdb=" N LEU B4770 " --> pdb=" O LYS B4766 " (cutoff:3.500A) Processing helix chain 'B' and resid 4791 through 4794 removed outlier: 3.642A 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 removed outlier: 3.616A pdb=" N HIS B4817 " --> pdb=" O CYS B4813 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B4818 " --> pdb=" O TYR B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4855 removed outlier: 4.483A pdb=" N TYR B4843 " --> pdb=" O GLU B4839 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B4850 " --> pdb=" O ILE B4846 " (cutoff:3.500A) Processing helix chain 'B' and resid 4858 through 4888 removed outlier: 3.507A pdb=" N ILE B4863 " --> pdb=" O LEU B4859 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B4867 " --> pdb=" O ILE B4863 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B4881 " --> pdb=" O GLN B4877 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B4886 " --> pdb=" O LYS B4882 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4900 Processing helix chain 'B' and resid 4904 through 4912 removed outlier: 3.725A pdb=" N THR B4908 " --> pdb=" O HIS B4904 " (cutoff:3.500A) Processing helix chain 'B' and resid 4916 through 4929 removed outlier: 3.632A pdb=" N LEU B4920 " --> pdb=" O LEU B4916 " (cutoff:3.500A) Processing helix chain 'B' and resid 4935 through 4948 Processing helix chain 'B' and resid 4958 through 4963 removed outlier: 3.569A pdb=" N TYR B4963 " --> pdb=" O PHE B4959 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.593A pdb=" N ILE C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 65 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 65' Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.598A pdb=" N GLN C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 270 through 273 removed outlier: 3.705A pdb=" N SER C 273 " --> pdb=" O HIS C 270 " (cutoff:3.500A) No H-bonds generated for '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: 3.592A pdb=" N ALA C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 428 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 3.563A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.634A pdb=" N LEU C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 489 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 Processing helix chain 'C' and resid 525 through 540 removed outlier: 3.535A pdb=" N SER C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.963A pdb=" N CYS C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 549 " --> pdb=" O ARG C 545 " (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: 4.102A 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: 3.551A pdb=" N LEU C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 581 " --> pdb=" O CYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 587 removed outlier: 3.644A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.603A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.782A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.608A pdb=" N CYS C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 removed outlier: 3.600A pdb=" N ALA C 825 " --> pdb=" O CYS C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.957A pdb=" N ARG C 880 " --> pdb=" O PRO C 876 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 881 " --> pdb=" O HIS C 877 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 899 " --> pdb=" O MET C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 946 removed outlier: 4.617A pdb=" N MET C 935 " --> pdb=" O TYR C 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 946 " --> pdb=" O THR C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1011 Processing helix chain 'C' and resid 1039 through 1060 removed outlier: 3.535A pdb=" N LYS C1043 " --> pdb=" O ASP C1039 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN C1046 " --> pdb=" O THR C1042 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C1049 " --> pdb=" O SER C1045 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C1050 " --> pdb=" O ASN C1046 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C1057 " --> pdb=" O ALA C1053 " (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: 3.554A pdb=" N HIS C1575 " --> pdb=" O PHE C1571 " (cutoff:3.500A) removed outlier: 3.516A 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 removed outlier: 3.735A pdb=" N HIS C1654 " --> pdb=" O LEU C1650 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1681 removed outlier: 3.654A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 removed outlier: 3.668A pdb=" N LEU C1685 " --> pdb=" O ASP C1681 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C1690 " --> pdb=" O LEU C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1695 through 1710 removed outlier: 3.521A pdb=" N HIS C1710 " --> pdb=" O LEU C1706 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 3.922A pdb=" N MET C1720 " --> pdb=" O THR C1716 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.813A pdb=" N ALA C1789 " --> pdb=" O ASP C1785 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C1790 " --> pdb=" O ILE C1786 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C1792 " --> pdb=" O LYS C1788 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C1800 " --> pdb=" O THR C1796 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU C1801 " --> pdb=" O GLU C1797 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1831 Proline residue: C1820 - end of helix removed outlier: 3.795A 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: 3.773A pdb=" N TYR C1913 " --> pdb=" O LEU C1909 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C1914 " --> pdb=" O LEU C1910 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C1932 " --> pdb=" O ALA C1928 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C1935 " --> pdb=" O ASP C1931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C1939 " --> pdb=" O ALA C1935 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C1940 " --> pdb=" O LYS C1936 " (cutoff:3.500A) Processing helix chain 'C' and resid 2000 through 2009 Processing helix chain 'C' and resid 2025 through 2039 removed outlier: 3.594A pdb=" N ARG C2029 " --> pdb=" O THR C2025 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C2030 " --> pdb=" O ILE C2026 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C2035 " --> pdb=" O LEU C2031 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C2039 " --> pdb=" O GLU C2035 " (cutoff:3.500A) Processing helix chain 'C' and resid 2059 through 2074 removed outlier: 3.793A pdb=" N MET C2067 " --> pdb=" O ILE C2063 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C2073 " --> pdb=" O ARG C2069 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C2074 " --> pdb=" O TRP C2070 " (cutoff:3.500A) Processing helix chain 'C' and resid 2078 through 2094 removed outlier: 3.943A pdb=" N VAL C2082 " --> pdb=" O ASP C2078 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C2087 " --> pdb=" O ARG C2083 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C2088 " --> pdb=" O ALA C2084 " (cutoff:3.500A) Processing helix chain 'C' and resid 2096 through 2103 removed outlier: 3.634A pdb=" N ALA C2102 " --> pdb=" O GLY C2098 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2131 removed outlier: 3.815A pdb=" N THR C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C2119 " --> pdb=" O GLU C2115 " (cutoff:3.500A) Processing helix chain 'C' and resid 2139 through 2153 removed outlier: 3.963A pdb=" N MET C2143 " --> pdb=" O GLU C2139 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C2144 " --> pdb=" O GLU C2140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C2152 " --> pdb=" O GLY C2148 " (cutoff:3.500A) Processing helix chain 'C' and resid 2159 through 2167 removed outlier: 3.782A pdb=" N MET C2163 " --> pdb=" O HIS C2159 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2180 Processing helix chain 'C' and resid 2192 through 2206 removed outlier: 3.744A pdb=" N ASN C2196 " --> pdb=" O LYS C2192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C2197 " --> pdb=" O MET C2193 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C2205 " --> pdb=" O LEU C2201 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C2206 " --> pdb=" O CYS C2202 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2217 removed outlier: 3.758A pdb=" N ALA C2214 " --> pdb=" O GLN C2210 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET C2215 " --> pdb=" O ASN C2211 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C2217 " --> pdb=" O LYS C2213 " (cutoff:3.500A) Processing helix chain 'C' and resid 2218 through 2226 removed outlier: 3.721A pdb=" N GLU C2224 " --> pdb=" O SER C2220 " (cutoff:3.500A) Processing helix chain 'C' and resid 2240 through 2247 removed outlier: 3.507A pdb=" N ALA C2244 " --> pdb=" O PRO C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2251 through 2258 Processing helix chain 'C' and resid 2259 through 2273 removed outlier: 3.854A pdb=" N LEU C2263 " --> pdb=" O ARG C2259 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C2266 " --> pdb=" O ASP C2262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR C2269 " --> pdb=" O LYS C2265 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS C2273 " --> pdb=" O TYR C2269 " (cutoff:3.500A) Processing helix chain 'C' and resid 2295 through 2308 removed outlier: 4.110A pdb=" N TYR C2299 " --> pdb=" O GLU C2295 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C2307 " --> pdb=" O LEU C2303 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2326 removed outlier: 3.644A pdb=" N VAL C2320 " --> pdb=" O GLU C2316 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C2322 " --> pdb=" O ALA C2318 " (cutoff:3.500A) Processing helix chain 'C' and resid 2344 through 2354 removed outlier: 3.640A pdb=" N MET C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C2351 " --> pdb=" O ALA C2347 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C2352 " --> pdb=" O MET C2348 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS C2353 " --> pdb=" O GLU C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2387 through 2402 removed outlier: 3.691A pdb=" N TYR C2393 " --> pdb=" O ILE C2389 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C2394 " --> pdb=" O MET C2390 " (cutoff:3.500A) Processing helix chain 'C' and resid 2418 through 2426 Processing helix chain 'C' and resid 2432 through 2440 removed outlier: 3.612A pdb=" N VAL C2436 " --> pdb=" O ASP C2432 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C2437 " --> pdb=" O LEU C2433 " (cutoff:3.500A) Processing helix chain 'C' and resid 2462 through 2477 removed outlier: 4.308A pdb=" N LYS C2466 " --> pdb=" O CYS C2462 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C2467 " --> pdb=" O PRO C2463 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2482 through 2488 removed outlier: 3.638A pdb=" N LEU C2488 " --> pdb=" O PHE C2484 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2499 Processing helix chain 'C' and resid 2500 through 2503 removed outlier: 4.327A pdb=" N LEU C2503 " --> pdb=" O ALA C2500 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2500 through 2503' Processing helix chain 'C' and resid 2512 through 2523 removed outlier: 3.994A pdb=" N ASN C2518 " --> pdb=" O ALA C2514 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C2519 " --> pdb=" O LEU C2515 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C2522 " --> pdb=" O ASN C2518 " (cutoff:3.500A) Processing helix chain 'C' and resid 2525 through 2529 removed outlier: 3.665A pdb=" N LEU C2529 " --> pdb=" O LEU C2526 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2553 Processing helix chain 'C' and resid 2559 through 2576 Processing helix chain 'C' and resid 2583 through 2601 Proline residue: C2598 - end of helix Processing helix chain 'C' and resid 2606 through 2627 removed outlier: 3.530A pdb=" N ARG C2617 " --> pdb=" O ASN C2613 " (cutoff:3.500A) removed outlier: 3.923A 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 2653 Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2668 - end of helix Processing helix chain 'C' and resid 2715 through 2739 removed outlier: 3.636A pdb=" N GLU C2719 " --> pdb=" O PRO C2715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C2720 " --> pdb=" O GLU C2716 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C2721 " --> pdb=" O LYS C2717 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C2724 " --> pdb=" O TYR C2720 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C2737 " --> pdb=" O TRP C2733 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 3.550A pdb=" N ILE C2771 " --> pdb=" O LYS C2767 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR C2772 " --> pdb=" O GLU C2768 " (cutoff:3.500A) Proline residue: C2775 - end of helix removed outlier: 3.592A pdb=" N LYS C2781 " --> pdb=" O LYS C2777 " (cutoff:3.500A) Processing helix chain 'C' and resid 2835 through 2862 removed outlier: 3.699A pdb=" N ALA C2854 " --> pdb=" O HIS C2850 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.726A pdb=" N ASP C2886 " --> pdb=" O GLU C2882 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS C2889 " --> pdb=" O LYS C2885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C2892 " --> pdb=" O GLU C2888 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C2894 " --> pdb=" O ALA C2890 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C2896 " --> pdb=" O ASP C2892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2983 through 3003 Proline residue: C2990 - end of helix Processing helix chain 'C' and resid 3010 through 3028 Processing helix chain 'C' and resid 3035 through 3052 Processing helix chain 'C' and resid 3062 through 3080 removed outlier: 3.863A pdb=" N GLU C3070 " --> pdb=" O ALA C3066 " (cutoff:3.500A) Processing helix chain 'C' and resid 3101 through 3115 removed outlier: 3.516A pdb=" N PHE C3110 " --> pdb=" O LEU C3106 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C3113 " --> pdb=" O LEU C3109 " (cutoff:3.500A) Processing helix chain 'C' and resid 3125 through 3144 removed outlier: 3.660A pdb=" N THR C3136 " --> pdb=" O TYR C3132 " (cutoff:3.500A) Processing helix chain 'C' and resid 3150 through 3165 removed outlier: 3.567A pdb=" N CYS C3159 " --> pdb=" O ALA C3155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C3161 " --> pdb=" O GLY C3157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C3165 " --> pdb=" O ALA C3161 " (cutoff:3.500A) Processing helix chain 'C' and resid 3171 through 3182 removed outlier: 3.544A pdb=" N HIS C3175 " --> pdb=" O PHE C3171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C3177 " --> pdb=" O GLU C3173 " (cutoff:3.500A) Processing helix chain 'C' and resid 3614 through 3630 removed outlier: 4.082A pdb=" N ILE C3630 " --> pdb=" O GLU C3626 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3646 removed outlier: 4.456A pdb=" N LYS C3640 " --> pdb=" O TYR C3636 " (cutoff:3.500A) Processing helix chain 'C' and resid 3663 through 3677 removed outlier: 3.587A pdb=" N PHE C3672 " --> pdb=" O LEU C3668 " (cutoff:3.500A) Processing helix chain 'C' and resid 3686 through 3698 removed outlier: 3.889A pdb=" N ASP C3694 " --> pdb=" O MET C3690 " (cutoff:3.500A) Processing helix chain 'C' and resid 3715 through 3734 removed outlier: 3.729A pdb=" N MET C3720 " --> pdb=" O GLU C3716 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C3732 " --> pdb=" O GLN C3728 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) Processing helix chain 'C' and resid 3736 through 3748 removed outlier: 3.707A pdb=" N MET C3740 " --> pdb=" O GLY C3736 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C3742 " --> pdb=" O ALA C3738 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C3746 " --> pdb=" O LEU C3742 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3768 Processing helix chain 'C' and resid 3771 through 3785 removed outlier: 3.597A pdb=" N LEU C3779 " --> pdb=" O GLN C3775 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C3782 " --> pdb=" O MET C3778 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C3785 " --> pdb=" O TYR C3781 " (cutoff:3.500A) Processing helix chain 'C' and resid 3788 through 3799 Processing helix chain 'C' and resid 3806 through 3812 Processing helix chain 'C' and resid 3834 through 3849 removed outlier: 3.684A pdb=" N ASP C3839 " --> pdb=" O GLU C3835 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS C3848 " --> pdb=" O LEU C3844 " (cutoff:3.500A) Processing helix chain 'C' and resid 3852 through 3862 removed outlier: 3.805A pdb=" N ARG C3860 " --> pdb=" O GLN C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3870 through 3893 removed outlier: 3.562A pdb=" N VAL C3876 " --> pdb=" O ILE C3872 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C3885 " --> pdb=" O ARG C3881 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C3890 " --> pdb=" O ILE C3886 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP C3891 " --> pdb=" O SER C3887 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C3892 " --> pdb=" O ASP C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3900 through 3926 removed outlier: 3.682A pdb=" N LYS C3909 " --> pdb=" O ARG C3905 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C3913 " --> pdb=" O LYS C3909 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C3916 " --> pdb=" O GLN C3912 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C3919 " --> pdb=" O LYS C3915 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C3925 " --> pdb=" O LEU C3921 " (cutoff:3.500A) Processing helix chain 'C' and resid 3929 through 3938 removed outlier: 3.541A pdb=" N HIS C3938 " --> pdb=" O GLN C3934 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3960 removed outlier: 3.773A pdb=" N ALA C3944 " --> pdb=" O ARG C3940 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C3954 " --> pdb=" O HIS C3950 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C3956 " --> pdb=" O PHE C3952 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C3958 " --> pdb=" O HIS C3954 " (cutoff:3.500A) Processing helix chain 'C' and resid 3965 through 3987 removed outlier: 3.506A pdb=" N GLU C3971 " --> pdb=" O GLU C3967 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C3982 " --> pdb=" O ASP C3978 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C3983 " --> pdb=" O MET C3979 " (cutoff:3.500A) Processing helix chain 'C' and resid 3994 through 4007 removed outlier: 3.753A pdb=" N MET C4000 " --> pdb=" O ILE C3996 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C4004 " --> pdb=" O MET C4000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C4005 " --> pdb=" O VAL C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4007 through 4026 removed outlier: 3.916A pdb=" N VAL C4011 " --> pdb=" O SER C4007 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C4012 " --> pdb=" O SER C4008 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET C4013 " --> pdb=" O ASN C4009 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C4014 " --> pdb=" O ASN C4010 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C4023 " --> pdb=" O ASP C4019 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C4024 " --> pdb=" O MET C4020 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C4025 " --> pdb=" O PHE C4021 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C4026 " --> pdb=" O LEU C4022 " (cutoff:3.500A) Processing helix chain 'C' and resid 4045 through 4054 removed outlier: 3.714A pdb=" N GLU C4054 " --> pdb=" O HIS C4050 " (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 4086 removed outlier: 3.618A pdb=" N VAL C4085 " --> pdb=" O TYR C4081 " (cutoff:3.500A) Processing helix chain 'C' and resid 4091 through 4110 removed outlier: 4.144A pdb=" N ILE C4095 " --> pdb=" O PRO C4091 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C4098 " --> pdb=" O ASP C4094 " (cutoff:3.500A) Processing helix chain 'C' and resid 4113 through 4122 removed outlier: 3.756A pdb=" N PHE C4119 " --> pdb=" O ARG C4115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C4122 " --> pdb=" O THR C4118 " (cutoff:3.500A) Processing helix chain 'C' and resid 4123 through 4131 removed outlier: 3.672A pdb=" N TYR C4129 " --> pdb=" O SER C4125 " (cutoff:3.500A) Processing helix chain 'C' and resid 4154 through 4163 removed outlier: 3.958A pdb=" N GLU C4162 " --> pdb=" O ARG C4158 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS C4163 " --> pdb=" O THR C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4165 through 4181 removed outlier: 3.562A pdb=" N GLN C4172 " --> pdb=" O GLU C4168 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C4176 " --> pdb=" O GLN C4172 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C4178 " --> pdb=" O ILE C4174 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C4180 " --> pdb=" O ASP C4176 " (cutoff:3.500A) Processing helix chain 'C' and resid 4182 through 4205 removed outlier: 3.967A pdb=" N MET C4187 " --> pdb=" O GLU C4183 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C4188 " --> pdb=" O LYS C4184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C4191 " --> pdb=" O MET C4187 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C4192 " --> pdb=" O GLU C4188 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C4196 " --> pdb=" O ASN C4192 " (cutoff:3.500A) Processing helix chain 'C' and resid 4487 through 4499 removed outlier: 3.560A pdb=" N PHE C4496 " --> pdb=" O LEU C4492 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C4497 " --> pdb=" O LEU C4493 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C4498 " --> pdb=" O ASN C4494 " (cutoff:3.500A) Processing helix chain 'C' and resid 4499 through 4519 removed outlier: 3.526A pdb=" N LEU C4508 " --> pdb=" O ARG C4504 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C4513 " --> pdb=" O PHE C4509 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4592 removed outlier: 3.670A pdb=" N ILE C4578 " --> pdb=" O ARG C4574 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C4588 " --> pdb=" O SER C4584 " (cutoff:3.500A) Processing helix chain 'C' and resid 4595 through 4613 removed outlier: 3.614A pdb=" N LYS C4610 " --> pdb=" O GLU C4606 " (cutoff:3.500A) Processing helix chain 'C' and resid 4626 through 4631 Processing helix chain 'C' and resid 4632 through 4638 removed outlier: 4.048A pdb=" N ILE C4636 " --> pdb=" O ARG C4633 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C4637 " --> pdb=" O LEU C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4646 removed outlier: 3.718A pdb=" N TYR C4645 " --> pdb=" O PRO C4642 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP C4646 " --> pdb=" O ASN C4643 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4642 through 4646' 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 4659 removed outlier: 3.698A pdb=" N MET C4655 " --> pdb=" O LYS C4651 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4672 removed outlier: 3.507A pdb=" N ILE C4667 " --> pdb=" O GLY C4663 " (cutoff:3.500A) Processing helix chain 'C' and resid 4697 through 4702 removed outlier: 4.196A pdb=" N ILE C4702 " --> pdb=" O VAL C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 Processing helix chain 'C' and resid 4717 through 4736 Processing helix chain 'C' and resid 4738 through 4744 removed outlier: 3.570A pdb=" N ALA C4741 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C4743 " --> pdb=" O PHE C4740 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C4744 " --> pdb=" O ALA C4741 " (cutoff:3.500A) Processing helix chain 'C' and resid 4745 through 4751 removed outlier: 3.748A pdb=" N MET C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C4751 " --> pdb=" O ILE C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4754 through 4764 removed outlier: 3.719A pdb=" N LEU C4758 " --> pdb=" O LEU C4754 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C4762 " --> pdb=" O LEU C4758 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C4764 " --> pdb=" O SER C4760 " (cutoff:3.500A) Processing helix chain 'C' and resid 4764 through 4790 removed outlier: 4.178A pdb=" N LEU C4770 " --> pdb=" O LYS C4766 " (cutoff:3.500A) Processing helix chain 'C' and resid 4791 through 4794 removed outlier: 3.652A 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 removed outlier: 3.622A pdb=" N HIS C4817 " --> pdb=" O CYS C4813 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C4818 " --> pdb=" O TYR C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4840 through 4855 removed outlier: 3.740A pdb=" N THR C4850 " --> pdb=" O ILE C4846 " (cutoff:3.500A) Processing helix chain 'C' and resid 4858 through 4888 removed outlier: 3.509A pdb=" N ILE C4863 " --> pdb=" O LEU C4859 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C4867 " --> pdb=" O ILE C4863 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C4881 " --> pdb=" O GLN C4877 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C4886 " --> pdb=" O LYS C4882 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4900 Processing helix chain 'C' and resid 4904 through 4912 removed outlier: 3.725A pdb=" N THR C4908 " --> pdb=" O HIS C4904 " (cutoff:3.500A) Processing helix chain 'C' and resid 4916 through 4929 removed outlier: 3.634A pdb=" N LEU C4920 " --> pdb=" O LEU C4916 " (cutoff:3.500A) Processing helix chain 'C' and resid 4935 through 4948 Processing helix chain 'C' and resid 4958 through 4963 removed outlier: 3.568A pdb=" N TYR C4963 " --> pdb=" O PHE C4959 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.592A pdb=" N ILE D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS D 65 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.612A pdb=" N GLN D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.705A pdb=" N SER D 273 " --> pdb=" O HIS D 270 " (cutoff:3.500A) No H-bonds generated for '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: 3.593A pdb=" N ALA D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 428 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 3.560A pdb=" N ILE D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.629A pdb=" N LEU D 488 " --> pdb=" O ASN D 484 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE D 489 " --> pdb=" O ARG D 485 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 506 Processing helix chain 'D' and resid 525 through 540 removed outlier: 3.536A pdb=" N SER D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.961A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 549 " --> pdb=" O ARG D 545 " (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: 4.105A 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: 3.545A pdb=" N LEU D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 587 removed outlier: 3.639A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.606A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.788A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.611A pdb=" N CYS D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 636 " --> pdb=" O ILE D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 removed outlier: 3.597A pdb=" N ALA D 825 " --> pdb=" O CYS D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 899 removed outlier: 3.959A pdb=" N ARG D 880 " --> pdb=" O PRO D 876 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 881 " --> pdb=" O HIS D 877 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 898 " --> pdb=" O VAL D 894 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU D 899 " --> pdb=" O MET D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 946 removed outlier: 4.615A pdb=" N MET D 935 " --> pdb=" O TYR D 931 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 936 " --> pdb=" O ASN D 932 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 946 " --> pdb=" O THR D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1011 Processing helix chain 'D' and resid 1039 through 1060 removed outlier: 3.537A pdb=" N LYS D1043 " --> pdb=" O ASP D1039 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER D1045 " --> pdb=" O ARG D1041 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D1049 " --> pdb=" O SER D1045 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D1050 " --> pdb=" O ASN D1046 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D1057 " --> pdb=" O ALA D1053 " (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: 3.549A pdb=" N HIS D1575 " --> pdb=" O PHE D1571 " (cutoff:3.500A) removed outlier: 3.514A 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 removed outlier: 3.730A pdb=" N HIS D1654 " --> pdb=" O LEU D1650 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1681 removed outlier: 3.650A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 removed outlier: 3.669A pdb=" N LEU D1685 " --> pdb=" O ASP D1681 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D1690 " --> pdb=" O LEU D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1710 removed outlier: 3.517A pdb=" N HIS D1710 " --> pdb=" O LEU D1706 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 3.930A pdb=" N MET D1720 " --> pdb=" O THR D1716 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.812A pdb=" N ALA D1789 " --> pdb=" O ASP D1785 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D1790 " --> pdb=" O ILE D1786 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D1792 " --> pdb=" O LYS D1788 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D1800 " --> pdb=" O THR D1796 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D1801 " --> pdb=" O GLU D1797 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1831 Proline residue: D1820 - end of helix removed outlier: 3.794A 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: 3.774A pdb=" N TYR D1913 " --> pdb=" O LEU D1909 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D1914 " --> pdb=" O LEU D1910 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D1932 " --> pdb=" O ALA D1928 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D1935 " --> pdb=" O ASP D1931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP D1939 " --> pdb=" O ALA D1935 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D1940 " --> pdb=" O LYS D1936 " (cutoff:3.500A) Processing helix chain 'D' and resid 2000 through 2009 Processing helix chain 'D' and resid 2025 through 2039 removed outlier: 3.589A pdb=" N ARG D2029 " --> pdb=" O THR D2025 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D2030 " --> pdb=" O ILE D2026 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D2035 " --> pdb=" O LEU D2031 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR D2039 " --> pdb=" O GLU D2035 " (cutoff:3.500A) Processing helix chain 'D' and resid 2059 through 2074 removed outlier: 3.793A pdb=" N MET D2067 " --> pdb=" O ILE D2063 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D2073 " --> pdb=" O ARG D2069 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D2074 " --> pdb=" O TRP D2070 " (cutoff:3.500A) Processing helix chain 'D' and resid 2078 through 2094 removed outlier: 3.930A pdb=" N VAL D2082 " --> pdb=" O ASP D2078 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D2087 " --> pdb=" O ARG D2083 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D2088 " --> pdb=" O ALA D2084 " (cutoff:3.500A) Processing helix chain 'D' and resid 2096 through 2103 removed outlier: 3.625A pdb=" N ALA D2102 " --> pdb=" O GLY D2098 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2131 removed outlier: 3.814A pdb=" N THR D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D2119 " --> pdb=" O GLU D2115 " (cutoff:3.500A) Processing helix chain 'D' and resid 2139 through 2153 removed outlier: 3.960A pdb=" N MET D2143 " --> pdb=" O GLU D2139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D2144 " --> pdb=" O GLU D2140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D2152 " --> pdb=" O GLY D2148 " (cutoff:3.500A) Processing helix chain 'D' and resid 2159 through 2167 removed outlier: 3.784A pdb=" N MET D2163 " --> pdb=" O HIS D2159 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2180 Processing helix chain 'D' and resid 2192 through 2206 removed outlier: 3.744A pdb=" N ASN D2196 " --> pdb=" O LYS D2192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS D2197 " --> pdb=" O MET D2193 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D2205 " --> pdb=" O LEU D2201 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D2206 " --> pdb=" O CYS D2202 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2217 removed outlier: 3.761A pdb=" N ALA D2214 " --> pdb=" O GLN D2210 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET D2215 " --> pdb=" O ASN D2211 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D2217 " --> pdb=" O LYS D2213 " (cutoff:3.500A) Processing helix chain 'D' and resid 2218 through 2226 removed outlier: 3.724A pdb=" N GLU D2224 " --> pdb=" O SER D2220 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2247 removed outlier: 3.510A pdb=" N ALA D2244 " --> pdb=" O PRO D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2251 through 2258 Processing helix chain 'D' and resid 2259 through 2273 removed outlier: 3.860A pdb=" N LEU D2263 " --> pdb=" O ARG D2259 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D2266 " --> pdb=" O ASP D2262 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D2269 " --> pdb=" O LYS D2265 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS D2273 " --> pdb=" O TYR D2269 " (cutoff:3.500A) Processing helix chain 'D' and resid 2295 through 2308 removed outlier: 4.120A pdb=" N TYR D2299 " --> pdb=" O GLU D2295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D2307 " --> pdb=" O LEU D2303 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2326 removed outlier: 3.646A pdb=" N VAL D2320 " --> pdb=" O GLU D2316 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D2322 " --> pdb=" O ALA D2318 " (cutoff:3.500A) Processing helix chain 'D' and resid 2344 through 2354 removed outlier: 3.637A pdb=" N MET D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D2351 " --> pdb=" O ALA D2347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D2352 " --> pdb=" O MET D2348 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS D2353 " --> pdb=" O GLU D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2387 through 2402 removed outlier: 3.696A pdb=" N TYR D2393 " --> pdb=" O ILE D2389 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D2394 " --> pdb=" O MET D2390 " (cutoff:3.500A) Processing helix chain 'D' and resid 2418 through 2426 Processing helix chain 'D' and resid 2432 through 2440 removed outlier: 3.613A pdb=" N VAL D2436 " --> pdb=" O ASP D2432 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2462 through 2477 removed outlier: 4.310A pdb=" N LYS D2466 " --> pdb=" O CYS D2462 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA D2467 " --> pdb=" O PRO D2463 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2482 through 2488 removed outlier: 3.642A pdb=" N LEU D2488 " --> pdb=" O PHE D2484 " (cutoff:3.500A) Processing helix chain 'D' and resid 2493 through 2499 Processing helix chain 'D' and resid 2500 through 2503 removed outlier: 4.320A pdb=" N LEU D2503 " --> pdb=" O ALA D2500 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2500 through 2503' Processing helix chain 'D' and resid 2512 through 2524 removed outlier: 3.992A pdb=" N ASN D2518 " --> pdb=" O ALA D2514 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D2519 " --> pdb=" O LEU D2515 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS D2522 " --> pdb=" O ASN D2518 " (cutoff:3.500A) Processing helix chain 'D' and resid 2525 through 2529 removed outlier: 3.667A pdb=" N LEU D2529 " --> pdb=" O LEU D2526 " (cutoff:3.500A) Processing helix chain 'D' and resid 2535 through 2553 Processing helix chain 'D' and resid 2559 through 2576 Processing helix chain 'D' and resid 2583 through 2601 Proline residue: D2598 - end of helix Processing helix chain 'D' and resid 2606 through 2627 removed outlier: 3.533A pdb=" N ARG D2617 " --> pdb=" O ASN D2613 " (cutoff:3.500A) removed outlier: 3.912A 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 2653 Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2668 - end of helix Processing helix chain 'D' and resid 2715 through 2739 removed outlier: 3.635A pdb=" N GLU D2719 " --> pdb=" O PRO D2715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D2720 " --> pdb=" O GLU D2716 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D2721 " --> pdb=" O LYS D2717 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D2724 " --> pdb=" O TYR D2720 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D2737 " --> pdb=" O TRP D2733 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 3.549A pdb=" N ILE D2771 " --> pdb=" O LYS D2767 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR D2772 " --> pdb=" O GLU D2768 " (cutoff:3.500A) Proline residue: D2775 - end of helix removed outlier: 3.595A pdb=" N LYS D2781 " --> pdb=" O LYS D2777 " (cutoff:3.500A) Processing helix chain 'D' and resid 2835 through 2862 removed outlier: 3.699A pdb=" N ALA D2854 " --> pdb=" O HIS D2850 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.730A pdb=" N ASP D2886 " --> pdb=" O GLU D2882 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS D2889 " --> pdb=" O LYS D2885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D2892 " --> pdb=" O GLU D2888 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D2894 " --> pdb=" O ALA D2890 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE D2896 " --> pdb=" O ASP D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2983 through 3003 Proline residue: D2990 - end of helix Processing helix chain 'D' and resid 3010 through 3028 Processing helix chain 'D' and resid 3035 through 3052 Processing helix chain 'D' and resid 3062 through 3080 removed outlier: 3.857A pdb=" N GLU D3070 " --> pdb=" O ALA D3066 " (cutoff:3.500A) Processing helix chain 'D' and resid 3101 through 3115 removed outlier: 3.519A pdb=" N PHE D3110 " --> pdb=" O LEU D3106 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D3113 " --> pdb=" O LEU D3109 " (cutoff:3.500A) Processing helix chain 'D' and resid 3125 through 3144 removed outlier: 3.661A pdb=" N THR D3136 " --> pdb=" O TYR D3132 " (cutoff:3.500A) Processing helix chain 'D' and resid 3150 through 3165 removed outlier: 3.564A pdb=" N CYS D3159 " --> pdb=" O ALA D3155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D3161 " --> pdb=" O GLY D3157 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D3165 " --> pdb=" O ALA D3161 " (cutoff:3.500A) Processing helix chain 'D' and resid 3171 through 3182 removed outlier: 3.542A pdb=" N HIS D3175 " --> pdb=" O PHE D3171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D3177 " --> pdb=" O GLU D3173 " (cutoff:3.500A) Processing helix chain 'D' and resid 3614 through 3630 removed outlier: 4.083A pdb=" N ILE D3630 " --> pdb=" O GLU D3626 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3646 removed outlier: 4.471A pdb=" N LYS D3640 " --> pdb=" O TYR D3636 " (cutoff:3.500A) Processing helix chain 'D' and resid 3663 through 3677 removed outlier: 3.582A pdb=" N PHE D3672 " --> pdb=" O LEU D3668 " (cutoff:3.500A) Processing helix chain 'D' and resid 3686 through 3698 removed outlier: 3.886A pdb=" N ASP D3694 " --> pdb=" O MET D3690 " (cutoff:3.500A) Processing helix chain 'D' and resid 3715 through 3734 removed outlier: 3.730A pdb=" N MET D3720 " --> pdb=" O GLU D3716 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D3732 " --> pdb=" O GLN D3728 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) Processing helix chain 'D' and resid 3736 through 3748 removed outlier: 3.711A pdb=" N MET D3740 " --> pdb=" O GLY D3736 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D3742 " --> pdb=" O ALA D3738 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D3746 " --> pdb=" O LEU D3742 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3768 Processing helix chain 'D' and resid 3771 through 3785 removed outlier: 3.595A pdb=" N LEU D3779 " --> pdb=" O GLN D3775 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D3782 " --> pdb=" O MET D3778 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D3785 " --> pdb=" O TYR D3781 " (cutoff:3.500A) Processing helix chain 'D' and resid 3788 through 3799 Processing helix chain 'D' and resid 3806 through 3812 Processing helix chain 'D' and resid 3834 through 3849 removed outlier: 3.682A pdb=" N ASP D3839 " --> pdb=" O GLU D3835 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS D3848 " --> pdb=" O LEU D3844 " (cutoff:3.500A) Processing helix chain 'D' and resid 3852 through 3862 removed outlier: 3.805A pdb=" N ARG D3860 " --> pdb=" O GLN D3856 " (cutoff:3.500A) Processing helix chain 'D' and resid 3870 through 3893 removed outlier: 3.558A pdb=" N VAL D3876 " --> pdb=" O ILE D3872 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D3885 " --> pdb=" O ARG D3881 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP D3891 " --> pdb=" O SER D3887 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D3892 " --> pdb=" O ASP D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3900 through 3926 removed outlier: 3.676A pdb=" N LYS D3909 " --> pdb=" O ARG D3905 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D3913 " --> pdb=" O LYS D3909 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D3916 " --> pdb=" O GLN D3912 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D3919 " --> pdb=" O LYS D3915 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D3925 " --> pdb=" O LEU D3921 " (cutoff:3.500A) Processing helix chain 'D' and resid 3929 through 3938 removed outlier: 3.536A pdb=" N HIS D3938 " --> pdb=" O GLN D3934 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3960 removed outlier: 3.769A pdb=" N ALA D3944 " --> pdb=" O ARG D3940 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS D3954 " --> pdb=" O HIS D3950 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D3956 " --> pdb=" O PHE D3952 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS D3958 " --> pdb=" O HIS D3954 " (cutoff:3.500A) Processing helix chain 'D' and resid 3965 through 3987 removed outlier: 3.507A pdb=" N GLU D3971 " --> pdb=" O GLU D3967 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D3982 " --> pdb=" O ASP D3978 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D3983 " --> pdb=" O MET D3979 " (cutoff:3.500A) Processing helix chain 'D' and resid 3994 through 4007 removed outlier: 3.757A pdb=" N MET D4000 " --> pdb=" O ILE D3996 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D4004 " --> pdb=" O MET D4000 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D4005 " --> pdb=" O VAL D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4007 through 4026 removed outlier: 3.910A pdb=" N VAL D4011 " --> pdb=" O SER D4007 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D4012 " --> pdb=" O SER D4008 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET D4013 " --> pdb=" O ASN D4009 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D4014 " --> pdb=" O ASN D4010 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D4023 " --> pdb=" O ASP D4019 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D4024 " --> pdb=" O MET D4020 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D4025 " --> pdb=" O PHE D4021 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP D4026 " --> pdb=" O LEU D4022 " (cutoff:3.500A) Processing helix chain 'D' and resid 4045 through 4054 removed outlier: 3.707A pdb=" N GLU D4054 " --> pdb=" O HIS D4050 " (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 4086 removed outlier: 3.625A pdb=" N VAL D4085 " --> pdb=" O TYR D4081 " (cutoff:3.500A) Processing helix chain 'D' and resid 4091 through 4110 removed outlier: 4.150A pdb=" N ILE D4095 " --> pdb=" O PRO D4091 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D4098 " --> pdb=" O ASP D4094 " (cutoff:3.500A) Processing helix chain 'D' and resid 4113 through 4122 removed outlier: 3.761A pdb=" N PHE D4119 " --> pdb=" O ARG D4115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D4122 " --> pdb=" O THR D4118 " (cutoff:3.500A) Processing helix chain 'D' and resid 4123 through 4131 removed outlier: 3.677A pdb=" N TYR D4129 " --> pdb=" O SER D4125 " (cutoff:3.500A) Processing helix chain 'D' and resid 4154 through 4163 removed outlier: 3.952A pdb=" N GLU D4162 " --> pdb=" O ARG D4158 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS D4163 " --> pdb=" O THR D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4165 through 4181 removed outlier: 3.567A pdb=" N GLN D4172 " --> pdb=" O GLU D4168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D4176 " --> pdb=" O GLN D4172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D4178 " --> pdb=" O ILE D4174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU D4180 " --> pdb=" O ASP D4176 " (cutoff:3.500A) Processing helix chain 'D' and resid 4182 through 4205 removed outlier: 3.963A pdb=" N MET D4187 " --> pdb=" O GLU D4183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D4188 " --> pdb=" O LYS D4184 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL D4191 " --> pdb=" O MET D4187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D4192 " --> pdb=" O GLU D4188 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D4196 " --> pdb=" O ASN D4192 " (cutoff:3.500A) Processing helix chain 'D' and resid 4487 through 4499 removed outlier: 3.556A pdb=" N PHE D4496 " --> pdb=" O LEU D4492 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D4497 " --> pdb=" O LEU D4493 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D4498 " --> pdb=" O ASN D4494 " (cutoff:3.500A) Processing helix chain 'D' and resid 4499 through 4519 removed outlier: 3.523A pdb=" N LEU D4508 " --> pdb=" O ARG D4504 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D4513 " --> pdb=" O PHE D4509 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4592 removed outlier: 3.669A pdb=" N ILE D4578 " --> pdb=" O ARG D4574 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D4588 " --> pdb=" O SER D4584 " (cutoff:3.500A) Processing helix chain 'D' and resid 4595 through 4613 removed outlier: 3.616A pdb=" N LYS D4610 " --> pdb=" O GLU D4606 " (cutoff:3.500A) Processing helix chain 'D' and resid 4626 through 4631 Processing helix chain 'D' and resid 4632 through 4638 removed outlier: 4.051A pdb=" N ILE D4636 " --> pdb=" O ARG D4633 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D4637 " --> pdb=" O LEU D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4646 removed outlier: 3.709A pdb=" N TYR D4645 " --> pdb=" O PRO D4642 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TRP D4646 " --> pdb=" O ASN D4643 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4642 through 4646' 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 4659 removed outlier: 3.689A pdb=" N MET D4655 " --> pdb=" O LYS D4651 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4672 removed outlier: 3.509A pdb=" N ILE D4667 " --> pdb=" O GLY D4663 " (cutoff:3.500A) Processing helix chain 'D' and resid 4697 through 4702 removed outlier: 4.194A pdb=" N ILE D4702 " --> pdb=" O VAL D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 Processing helix chain 'D' and resid 4717 through 4736 Processing helix chain 'D' and resid 4738 through 4744 removed outlier: 3.563A pdb=" N ALA D4741 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS D4743 " --> pdb=" O PHE D4740 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D4744 " --> pdb=" O ALA D4741 " (cutoff:3.500A) Processing helix chain 'D' and resid 4745 through 4751 removed outlier: 3.745A pdb=" N MET D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D4751 " --> pdb=" O ILE D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4754 through 4764 removed outlier: 3.724A pdb=" N LEU D4758 " --> pdb=" O LEU D4754 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D4762 " --> pdb=" O LEU D4758 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D4764 " --> pdb=" O SER D4760 " (cutoff:3.500A) Processing helix chain 'D' and resid 4764 through 4790 removed outlier: 4.181A pdb=" N LEU D4770 " --> pdb=" O LYS D4766 " (cutoff:3.500A) Processing helix chain 'D' and resid 4791 through 4794 removed outlier: 3.645A 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 removed outlier: 3.622A pdb=" N HIS D4817 " --> pdb=" O CYS D4813 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D4818 " --> pdb=" O TYR D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4840 through 4855 removed outlier: 3.736A pdb=" N THR D4850 " --> pdb=" O ILE D4846 " (cutoff:3.500A) Processing helix chain 'D' and resid 4858 through 4888 removed outlier: 3.508A pdb=" N ILE D4863 " --> pdb=" O LEU D4859 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D4867 " --> pdb=" O ILE D4863 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D4881 " --> pdb=" O GLN D4877 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D4886 " --> pdb=" O LYS D4882 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4900 Processing helix chain 'D' and resid 4904 through 4912 removed outlier: 3.725A pdb=" N THR D4908 " --> pdb=" O HIS D4904 " (cutoff:3.500A) Processing helix chain 'D' and resid 4916 through 4929 removed outlier: 3.631A pdb=" N LEU D4920 " --> pdb=" O LEU D4916 " (cutoff:3.500A) Processing helix chain 'D' and resid 4935 through 4948 Processing helix chain 'D' and resid 4958 through 4963 removed outlier: 3.577A pdb=" N TYR D4963 " --> pdb=" O PHE D4959 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 4.414A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 181 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.626A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.633A pdb=" N GLU A 31 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.389A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.187A 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 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 769 through 770 Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB2, first strand: chain 'A' and resid 697 through 698 removed outlier: 3.569A pdb=" N ALA A 698 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB4, first strand: chain 'A' and resid 841 through 842 removed outlier: 3.722A pdb=" N GLY A 852 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1106 " --> pdb=" O ARG A1214 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A1216 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A1104 " --> pdb=" O ASN A1216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A1160 " --> pdb=" O ALA A1107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 841 through 842 removed outlier: 3.722A pdb=" N GLY A 852 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A1106 " --> pdb=" O ARG A1214 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A1216 " --> pdb=" O GLU A1104 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A1104 " --> pdb=" O ASN A1216 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A1175 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A1190 " --> pdb=" O PHE A1175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 903 through 904 removed outlier: 6.304A pdb=" N GLN A 903 " --> pdb=" O HIS A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 5.116A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A1252 " --> pdb=" O ILE A1087 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1257 through 1259 Processing sheet with id=AB9, first strand: chain 'A' and resid 1300 through 1303 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 1525 through 1526 Processing sheet with id=AC3, first strand: chain 'A' and resid 1629 through 1632 Processing sheet with id=AC4, first strand: chain 'A' and resid 1726 through 1728 Processing sheet with id=AC5, first strand: chain 'A' and resid 2743 through 2744 removed outlier: 5.233A pdb=" N ILE A2743 " --> pdb=" O GLN A2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 2791 through 2792 removed outlier: 4.019A pdb=" N GLU A2791 " --> pdb=" O ALA A2903 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 4043 through 4044 Processing sheet with id=AC8, first strand: chain 'A' and resid 4134 through 4139 Processing sheet with id=AC9, first strand: chain 'A' and resid 4521 through 4522 Processing sheet with id=AD1, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.422A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 181 " --> pdb=" O TRP B 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 73 through 74 removed outlier: 6.626A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AD4, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.635A pdb=" N GLU B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 129 through 132 removed outlier: 4.355A pdb=" N VAL B 147 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 203 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AD7, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AD8, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AD9, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AE1, first strand: chain 'B' and resid 693 through 694 Processing sheet with id=AE2, first strand: chain 'B' and resid 697 through 698 removed outlier: 3.569A pdb=" N ALA B 698 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE4, first strand: chain 'B' and resid 841 through 842 removed outlier: 3.720A pdb=" N GLY B 852 " --> pdb=" O GLN B1211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B1106 " --> pdb=" O ARG B1214 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN B1216 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B1160 " --> pdb=" O ALA B1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 841 through 842 removed outlier: 3.720A pdb=" N GLY B 852 " --> pdb=" O GLN B1211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B1106 " --> pdb=" O ARG B1214 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN B1216 " --> pdb=" O GLU B1104 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE B1175 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B1190 " --> pdb=" O PHE B1175 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 903 through 904 removed outlier: 6.301A pdb=" N GLN B 903 " --> pdb=" O HIS B 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 5.117A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B1252 " --> pdb=" O ILE B1087 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1257 through 1259 removed outlier: 3.982A pdb=" N LEU B1595 " --> pdb=" O PHE B1301 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B1301 " --> pdb=" O LEU B1595 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1426 through 1427 Processing sheet with id=AF1, first strand: chain 'B' and resid 1525 through 1526 Processing sheet with id=AF2, first strand: chain 'B' and resid 1629 through 1632 Processing sheet with id=AF3, first strand: chain 'B' and resid 1726 through 1728 Processing sheet with id=AF4, first strand: chain 'B' and resid 2743 through 2744 removed outlier: 5.233A pdb=" N ILE B2743 " --> pdb=" O GLN B2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 2791 through 2792 removed outlier: 4.019A pdb=" N GLU B2791 " --> pdb=" O ALA B2903 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 4043 through 4044 Processing sheet with id=AF7, first strand: chain 'B' and resid 4134 through 4139 Processing sheet with id=AF8, first strand: chain 'B' and resid 4521 through 4522 Processing sheet with id=AF9, first strand: chain 'C' and resid 73 through 74 removed outlier: 4.416A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 181 " --> pdb=" O TRP C 212 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.625A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AG3, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.639A pdb=" N GLU C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 129 through 132 removed outlier: 4.361A pdb=" N VAL C 147 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 203 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AG6, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AG7, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AG8, first strand: chain 'C' and resid 769 through 770 Processing sheet with id=AG9, first strand: chain 'C' and resid 693 through 694 Processing sheet with id=AH1, first strand: chain 'C' and resid 697 through 698 removed outlier: 3.566A pdb=" N ALA C 698 " --> pdb=" O PHE C 789 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AH3, first strand: chain 'C' and resid 841 through 842 removed outlier: 3.717A pdb=" N GLY C 852 " --> pdb=" O GLN C1211 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C1106 " --> pdb=" O ARG C1214 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C1216 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1104 " --> pdb=" O ASN C1216 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C1160 " --> pdb=" O ALA C1107 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 841 through 842 removed outlier: 3.717A pdb=" N GLY C 852 " --> pdb=" O GLN C1211 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C1106 " --> pdb=" O ARG C1214 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C1216 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1104 " --> pdb=" O ASN C1216 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C1175 " --> pdb=" O LEU C1190 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C1190 " --> pdb=" O PHE C1175 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 903 through 904 removed outlier: 6.301A pdb=" N GLN C 903 " --> pdb=" O HIS C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'C' and resid 1149 through 1151 removed outlier: 5.110A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C1252 " --> pdb=" O ILE C1087 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 1257 through 1259 Processing sheet with id=AH8, first strand: chain 'C' and resid 1300 through 1303 Processing sheet with id=AH9, first strand: chain 'C' and resid 1426 through 1427 Processing sheet with id=AI1, first strand: chain 'C' and resid 1525 through 1526 Processing sheet with id=AI2, first strand: chain 'C' and resid 1629 through 1632 Processing sheet with id=AI3, first strand: chain 'C' and resid 1726 through 1728 Processing sheet with id=AI4, first strand: chain 'C' and resid 2743 through 2744 removed outlier: 5.234A pdb=" N ILE C2743 " --> pdb=" O GLN C2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'C' and resid 2791 through 2792 removed outlier: 4.015A pdb=" N GLU C2791 " --> pdb=" O ALA C2903 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 4043 through 4044 Processing sheet with id=AI7, first strand: chain 'C' and resid 4134 through 4139 Processing sheet with id=AI8, first strand: chain 'C' and resid 4521 through 4522 Processing sheet with id=AI9, first strand: chain 'D' and resid 73 through 74 removed outlier: 4.409A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 181 " --> pdb=" O TRP D 212 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 73 through 74 removed outlier: 6.626A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AJ3, first strand: chain 'D' and resid 27 through 28 removed outlier: 3.639A pdb=" N GLU D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 129 through 132 removed outlier: 4.385A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 233 through 234 Processing sheet with id=AJ6, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AJ7, first strand: chain 'D' and resid 305 through 308 Processing sheet with id=AJ8, first strand: chain 'D' and resid 769 through 770 Processing sheet with id=AJ9, first strand: chain 'D' and resid 693 through 694 Processing sheet with id=AK1, first strand: chain 'D' and resid 697 through 698 removed outlier: 3.566A pdb=" N ALA D 698 " --> pdb=" O PHE D 789 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AK3, first strand: chain 'D' and resid 841 through 842 removed outlier: 3.721A pdb=" N GLY D 852 " --> pdb=" O GLN D1211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D1106 " --> pdb=" O ARG D1214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D1216 " --> pdb=" O GLU D1104 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP D1160 " --> pdb=" O ALA D1107 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 841 through 842 removed outlier: 3.721A pdb=" N GLY D 852 " --> pdb=" O GLN D1211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D1106 " --> pdb=" O ARG D1214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN D1216 " --> pdb=" O GLU D1104 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE D1175 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D1190 " --> pdb=" O PHE D1175 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 903 through 904 removed outlier: 6.304A pdb=" N GLN D 903 " --> pdb=" O HIS D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'D' and resid 1149 through 1151 removed outlier: 5.108A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D1252 " --> pdb=" O ILE D1087 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 1257 through 1259 Processing sheet with id=AK8, first strand: chain 'D' and resid 1300 through 1303 Processing sheet with id=AK9, first strand: chain 'D' and resid 1426 through 1427 Processing sheet with id=AL1, first strand: chain 'D' and resid 1525 through 1526 Processing sheet with id=AL2, first strand: chain 'D' and resid 1629 through 1632 Processing sheet with id=AL3, first strand: chain 'D' and resid 1726 through 1728 Processing sheet with id=AL4, first strand: chain 'D' and resid 2743 through 2744 removed outlier: 5.230A pdb=" N ILE D2743 " --> pdb=" O GLN D2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'D' and resid 2791 through 2792 removed outlier: 4.019A pdb=" N GLU D2791 " --> pdb=" O ALA D2903 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'D' and resid 4043 through 4044 Processing sheet with id=AL7, first strand: chain 'D' and resid 4134 through 4139 Processing sheet with id=AL8, first strand: chain 'D' and resid 4521 through 4522 5118 hydrogen bonds defined for protein. 14697 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: 83.86 Time building geometry restraints manager: 33.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.29: 17978 1.29 - 1.48: 43216 1.48 - 1.67: 44826 1.67 - 1.86: 971 1.86 - 2.05: 17 Bond restraints: 107008 Sorted by residual: bond pdb=" C ILE A4849 " pdb=" O ILE A4849 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.19e-02 7.06e+03 2.79e+02 bond pdb=" C ILE D4849 " pdb=" O ILE D4849 " ideal model delta sigma weight residual 1.237 1.435 -0.198 1.19e-02 7.06e+03 2.78e+02 bond pdb=" C ILE C4849 " pdb=" O ILE C4849 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.29e-02 6.01e+03 2.39e+02 bond pdb=" C ILE B4849 " pdb=" O ILE B4849 " ideal model delta sigma weight residual 1.237 1.434 -0.197 1.29e-02 6.01e+03 2.34e+02 bond pdb=" C TYR C4150 " pdb=" O TYR C4150 " ideal model delta sigma weight residual 1.234 1.106 0.128 1.22e-02 6.72e+03 1.10e+02 ... (remaining 107003 not shown) Histogram of bond angle deviations from ideal: 89.17 - 98.57: 139 98.57 - 107.97: 7599 107.97 - 117.36: 70538 117.36 - 126.76: 64857 126.76 - 136.16: 1471 Bond angle restraints: 144604 Sorted by residual: angle pdb=" C GLU B1847 " pdb=" N PRO B1848 " pdb=" CA PRO B1848 " ideal model delta sigma weight residual 119.84 134.84 -15.00 1.25e+00 6.40e-01 1.44e+02 angle pdb=" C GLU A1847 " pdb=" N PRO A1848 " pdb=" CA PRO A1848 " ideal model delta sigma weight residual 119.84 134.83 -14.99 1.25e+00 6.40e-01 1.44e+02 angle pdb=" C GLU D1847 " pdb=" N PRO D1848 " pdb=" CA PRO D1848 " ideal model delta sigma weight residual 119.84 134.79 -14.95 1.25e+00 6.40e-01 1.43e+02 angle pdb=" C GLU C1847 " pdb=" N PRO C1848 " pdb=" CA PRO C1848 " ideal model delta sigma weight residual 119.84 134.62 -14.78 1.25e+00 6.40e-01 1.40e+02 angle pdb=" N PHE B4853 " pdb=" CA PHE B4853 " pdb=" CB PHE B4853 " ideal model delta sigma weight residual 109.98 127.06 -17.08 1.45e+00 4.76e-01 1.39e+02 ... (remaining 144599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 61943 26.44 - 52.89: 1700 52.89 - 79.33: 127 79.33 - 105.77: 13 105.77 - 132.22: 12 Dihedral angle restraints: 63795 sinusoidal: 24175 harmonic: 39620 Sorted by residual: dihedral pdb=" CA GLY D 852 " pdb=" C GLY D 852 " pdb=" N PRO D 853 " pdb=" CA PRO D 853 " ideal model delta harmonic sigma weight residual -180.00 -47.78 -132.22 0 5.00e+00 4.00e-02 6.99e+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 -47.83 -132.17 0 5.00e+00 4.00e-02 6.99e+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 -47.93 -132.07 0 5.00e+00 4.00e-02 6.98e+02 ... (remaining 63792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 11552 0.116 - 0.232: 3726 0.232 - 0.348: 815 0.348 - 0.463: 195 0.463 - 0.579: 40 Chirality restraints: 16328 Sorted by residual: chirality pdb=" CA ASN C3768 " pdb=" N ASN C3768 " pdb=" C ASN C3768 " pdb=" CB ASN C3768 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA ASN B3768 " pdb=" N ASN B3768 " pdb=" C ASN B3768 " pdb=" CB ASN B3768 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" CA ASN D3768 " pdb=" N ASN D3768 " pdb=" C ASN D3768 " pdb=" CB ASN D3768 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.30e+00 ... (remaining 16325 not shown) Planarity restraints: 18540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D4952 " 0.086 2.00e-02 2.50e+03 6.86e-02 8.23e+01 pdb=" CG PHE D4952 " -0.138 2.00e-02 2.50e+03 pdb=" CD1 PHE D4952 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D4952 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE D4952 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D4952 " -0.033 2.00e-02 2.50e+03 pdb=" CZ PHE D4952 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D4853 " -0.089 2.00e-02 2.50e+03 6.73e-02 7.93e+01 pdb=" CG PHE D4853 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D4853 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D4853 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE D4853 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 PHE D4853 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE D4853 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C4853 " -0.087 2.00e-02 2.50e+03 6.72e-02 7.91e+01 pdb=" CG PHE C4853 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE C4853 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C4853 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 PHE C4853 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 PHE C4853 " -0.061 2.00e-02 2.50e+03 pdb=" CZ PHE C4853 " -0.062 2.00e-02 2.50e+03 ... (remaining 18537 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.18: 8 2.18 - 2.86: 34997 2.86 - 3.54: 145925 3.54 - 4.22: 259308 4.22 - 4.90: 407338 Nonbonded interactions: 847576 Sorted by model distance: nonbonded pdb=" NH1 ARG A2419 " pdb=" OE1 GLU D 189 " model vdw 1.505 2.520 nonbonded pdb=" OE1 GLU C 189 " pdb=" NH1 ARG D2419 " model vdw 1.512 2.520 nonbonded pdb=" OE1 GLU A 189 " pdb=" NH1 ARG B2419 " model vdw 1.529 2.520 nonbonded pdb=" OE1 GLU B 189 " pdb=" NH1 ARG C2419 " model vdw 1.544 2.520 nonbonded pdb=" OG SER D3802 " pdb=" O ASP D3833 " model vdw 2.141 2.440 ... (remaining 847571 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: 7.650 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: 0.090 Extract box with map and model: 31.770 Check model and map are aligned: 1.210 Set scattering table: 0.780 Process input model: 269.130 Find NCS groups from input model: 5.120 Set up NCS constraints: 0.560 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 318.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.022 0.239 107008 Z= 1.396 Angle : 1.863 17.084 144604 Z= 1.104 Chirality : 0.122 0.579 16328 Planarity : 0.010 0.106 18540 Dihedral : 12.404 132.215 38051 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.47 % Favored : 90.88 % Rotamer: Outliers : 1.03 % Allowed : 4.70 % Favored : 94.27 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.31 % Twisted General : 0.44 % 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: -4.96 (0.05), residues: 13156 helix: -3.40 (0.04), residues: 6788 sheet: -2.77 (0.14), residues: 1032 loop : -3.02 (0.07), residues: 5336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.012 TRP A4942 HIS 0.033 0.006 HIS A3615 PHE 0.139 0.012 PHE B4952 TYR 0.090 0.013 TYR B3689 ARG 0.039 0.004 ARG C4666 *********************** 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 2395 residues out of total 12064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 2278 time to evaluate : 9.538 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 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