Starting phenix.real_space_refine on Thu Mar 21 05:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yzg_6864/03_2024/5yzg_6864_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 425 5.49 5 Mg 7 5.21 5 S 335 5.16 5 C 61171 2.51 5 N 19997 2.21 5 O 21964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1283": "OE1" <-> "OE2" Residue "A PHE 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A TYR 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J GLU 200": "OE1" <-> "OE2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "J TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L GLU 229": "OE1" <-> "OE2" Residue "L GLU 230": "OE1" <-> "OE2" Residue "L GLU 753": "OE1" <-> "OE2" Residue "L GLU 759": "OE1" <-> "OE2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O GLU 69": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R GLU 316": "OE1" <-> "OE2" Residue "S TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "T GLU 474": "OE1" <-> "OE2" Residue "V ARG 457": "NH1" <-> "NH2" Residue "V ARG 545": "NH1" <-> "NH2" Residue "V ARG 602": "NH1" <-> "NH2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "W GLU 169": "OE1" <-> "OE2" Residue "W GLU 176": "OE1" <-> "OE2" Residue "W GLU 183": "OE1" <-> "OE2" Residue "W GLU 212": "OE1" <-> "OE2" Residue "X ARG 34": "NH1" <-> "NH2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q GLU 31": "OE1" <-> "OE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ARG 119": "NH1" <-> "NH2" Residue "q GLU 123": "OE1" <-> "OE2" Residue "q ARG 128": "NH1" <-> "NH2" Residue "r GLU 26": "OE1" <-> "OE2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 129": "OE1" <-> "OE2" Residue "t ARG 119": "NH1" <-> "NH2" Residue "t GLU 123": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 106": "OE1" <-> "OE2" Residue "u ARG 173": "NH1" <-> "NH2" Residue "u GLU 188": "OE1" <-> "OE2" Residue "u GLU 224": "OE1" <-> "OE2" Residue "u GLU 227": "OE1" <-> "OE2" Residue "u GLU 259": "OE1" <-> "OE2" Residue "u GLU 261": "OE1" <-> "OE2" Residue "u ARG 324": "NH1" <-> "NH2" Residue "u ARG 390": "NH1" <-> "NH2" Residue "u GLU 393": "OE1" <-> "OE2" Residue "u GLU 402": "OE1" <-> "OE2" Residue "v GLU 27": "OE1" <-> "OE2" Residue "v PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 51": "OE1" <-> "OE2" Residue "w GLU 83": "OE1" <-> "OE2" Residue "w GLU 126": "OE1" <-> "OE2" Residue "i GLU 47": "OE1" <-> "OE2" Residue "i GLU 75": "OE1" <-> "OE2" Residue "j ARG 61": "NH1" <-> "NH2" Residue "k ARG 61": "NH1" <-> "NH2" Residue "k GLU 68": "OE1" <-> "OE2" Residue "k ARG 102": "NH1" <-> "NH2" Residue "m GLU 28": "OE1" <-> "OE2" Residue "m ARG 73": "NH1" <-> "NH2" Residue "l ARG 76": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "e ARG 76": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 103906 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 17519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2253, 17519 Classifications: {'peptide': 2253} Incomplete info: {'backbone_only': 254, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 126, 'TRANS': 2126} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1244 Unresolved non-hydrogen angles: 1787 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 324 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 12, 'TYR:plan': 15, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 12, 'PHE:plan': 11, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 640 Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1768 Classifications: {'RNA': 84} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 39} Link IDs: {'rna2p': 13, 'rna3p': 70} Chain breaks: 1 Chain: "C" Number of atoms: 6795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6795 Classifications: {'peptide': 862} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 808} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 7632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1908, 7632 Classifications: {'peptide': 1908} Incomplete info: {'backbone_only': 1822} Link IDs: {'CIS': 1, 'PTRANS': 81, 'TRANS': 1825} Chain breaks: 3 Unresolved chain link angles: 81 Unresolved non-hydrogen bonds: 8049 Unresolved non-hydrogen angles: 11607 Unresolved non-hydrogen dihedrals: 5166 Unresolved non-hydrogen chiralities: 2409 Planarities with less than four sites: {'GLN:plan1': 93, 'HIS:plan': 56, 'TYR:plan': 66, 'ASN:plan1': 74, 'TRP:plan': 20, 'ASP:plan': 105, 'PHE:plan': 72, 'GLU:plan': 141, 'ARG:plan': 101} Unresolved non-hydrogen planarities: 3725 Chain: "E" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 15, 'rna3p': 81} Chain: "G" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1641 Classifications: {'RNA': 88} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 33, 'rna3p_pyr': 38} Link IDs: {'rna2p': 17, 'rna3p': 70} Chain breaks: 3 Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {' G%rna3p_pur:plan2': 7, ' C%rna3p_pyr:plan': 6, ' A%rna3p_pur:plan2': 3, ' U%rna3p_pyr:plan': 8, ' C%rna3p_pyr:plan2': 6, ' G%rna3p_pur:plan': 7, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 251 Chain: "H" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2946 Classifications: {'RNA': 139} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 14, 'rna3p_pur': 59, 'rna3p_pyr': 59} Link IDs: {'rna2p': 21, 'rna3p': 117} Chain breaks: 6 Chain: "I" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 2757 Classifications: {'peptide': 559} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 468} Link IDs: {'PTRANS': 17, 'TRANS': 541} Chain breaks: 32 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1903 Unresolved non-hydrogen angles: 2446 Unresolved non-hydrogen dihedrals: 1593 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 14, 'TYR:plan': 27, 'ASN:plan1': 16, 'TRP:plan': 9, 'ASP:plan': 35, 'PHE:plan': 22, 'GLU:plan': 56, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1165 Chain: "J" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 3829 Classifications: {'peptide': 571} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 268} Link IDs: {'PTRANS': 17, 'TRANS': 553} Chain breaks: 20 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1149 Unresolved non-hydrogen angles: 1458 Unresolved non-hydrogen dihedrals: 974 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 45, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 716 Chain: "K" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 979 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "L" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 2885 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 18, 'TRANS': 400} Chain breaks: 8 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 335 Chain: "y" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 704 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 135 Chain: "M" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 775 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "N" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "O" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2277 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 17, 'TRANS': 265} Chain breaks: 1 Chain: "P" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 829 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "R" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1962 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "T" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2461 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "Q" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 5288 Classifications: {'peptide': 1322} Incomplete info: {'backbone_only': 1266} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 5844 Unresolved non-hydrogen angles: 8405 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 1651 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2938 Chain: "U" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "V" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3410 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 439} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 192 Chain: "W" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 2310 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 285} Link IDs: {'PTRANS': 18, 'TRANS': 421} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1322 Unresolved non-hydrogen angles: 1904 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 363 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 21, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 12, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 657 Chain: "X" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 91 Chain: "Y" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1426 Classifications: {'peptide': 204} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 75} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 213 Chain: "Z" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 2540 Classifications: {'peptide': 635} Incomplete info: {'backbone_only': 595} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 11 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 2562 Unresolved non-hydrogen angles: 3708 Unresolved non-hydrogen dihedrals: 1631 Unresolved non-hydrogen chiralities: 785 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 15, 'TYR:plan': 25, 'ASN:plan1': 20, 'TRP:plan': 5, 'ASP:plan': 37, 'PHE:plan': 24, 'GLU:plan': 39, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1162 Chain: "q" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 918 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 6, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "r" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 901 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 6, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "s" Number of atoms: 1497 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 1496 Classifications: {'peptide': 374} Incomplete info: {'backbone_only': 352} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 2144 Unresolved non-hydrogen dihedrals: 926 Unresolved non-hydrogen chiralities: 471 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 6, 'HIS:plan': 15, 'PHE:plan': 16, 'GLU:plan': 16, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 662 Conformer: "B" Number of residues, atoms: 374, 1496 Classifications: {'peptide': 374} Incomplete info: {'backbone_only': 352} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 2144 Unresolved non-hydrogen dihedrals: 926 Unresolved non-hydrogen chiralities: 471 Planarities with less than four sites: {'GLN:plan1': 18, 'ARG:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 6, 'HIS:plan': 15, 'PHE:plan': 16, 'GLU:plan': 16, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 662 bond proxies already assigned to first conformer: 1491 Chain: "t" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 476 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'HIS:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "u" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3126 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 377} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "v" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "w" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 730 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "x" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "h" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 621 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "m" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "l" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 652 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "n" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 533 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1277 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "p" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 760 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 609 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 675 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "c" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "d" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 768 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "f" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "e" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 652 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 569 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "1" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 972 Classifications: {'peptide': 243} Incomplete info: {'backbone_only': 217} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 958 Unresolved non-hydrogen angles: 1376 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 18, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 476 Chain: "2" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 1664 Classifications: {'peptide': 416} Incomplete info: {'backbone_only': 384} Link IDs: {'PTRANS': 16, 'TRANS': 399} Chain breaks: 13 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1736 Unresolved non-hydrogen angles: 2496 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 499 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 19, 'TYR:plan': 11, 'ASN:plan1': 20, 'TRP:plan': 6, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 27, 'ASP:plan': 25} Unresolved non-hydrogen planarities: 843 Chain: "3" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 684 Classifications: {'peptide': 171} Incomplete info: {'backbone_only': 153} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 981 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 8, 'PHE:plan': 16, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 357 Chain: "4" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 184 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 55540 SG CYS N 105 74.414 171.945 109.337 1.00 55.60 S ATOM 55634 SG CYS N 117 75.142 168.523 108.018 1.00 75.95 S ATOM 55648 SG CYS N 119 71.928 170.122 109.042 1.00 51.58 S ATOM 55767 SG CYS N 134 74.471 168.570 111.320 1.00104.87 S ATOM 55509 SG CYS N 101 71.078 173.409 108.817 1.00 58.20 S ATOM 55515 SG CYS N 102 74.203 174.954 110.633 1.00 37.17 S ATOM 55540 SG CYS N 105 74.414 171.945 109.337 1.00 55.60 S ATOM 55790 SG CYS N 137 72.049 173.332 112.464 1.00 97.64 S ATOM 55509 SG CYS N 101 71.078 173.409 108.817 1.00 58.20 S ATOM 55648 SG CYS N 119 71.928 170.122 109.042 1.00 51.58 S ATOM 55800 SG CYS N 139 68.366 171.162 109.667 1.00106.33 S ATOM 55821 SG CYS N 142 70.163 171.851 106.562 1.00 78.90 S ATOM 55875 SG CYS O 24 83.107 137.149 112.354 1.00 60.57 S ATOM 55897 SG CYS O 27 82.434 140.801 112.616 1.00 50.06 S ATOM 56340 SG CYS O 81 85.777 139.758 113.263 1.00 64.02 S ATOM 56362 SG CYS O 84 82.274 139.214 115.052 1.00 74.16 S ATOM 56046 SG CYS O 45 96.759 143.338 120.329 1.00104.07 S ATOM 56069 SG CYS O 48 99.846 142.041 119.134 1.00 63.54 S ATOM 56265 SG CYS O 71 97.938 142.547 116.999 1.00 68.80 S ATOM 56287 SG CYS O 74 97.049 140.079 118.564 1.00 83.74 S ATOM 57008 SG CYS O 165 69.486 155.417 126.619 1.00 81.09 S ATOM 57074 SG CYS O 173 67.294 158.366 126.264 1.00125.31 S ATOM 57122 SG CYS O 179 68.924 156.696 123.240 1.00126.83 S ATOM 76618 SG CYS Y 43 127.404 143.366 171.500 1.00 0.00 S ATOM 76640 SG CYS Y 46 126.336 141.567 169.562 1.00 0.00 S ATOM 76931 SG CYS Y 80 127.140 144.904 168.171 1.00 0.00 S ATOM 76955 SG CYS Y 83 124.150 143.380 169.870 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N HIS D1502 " occ=0.92 ... (2 atoms not shown) pdb=" O HIS D1502 " occ=0.92 residue: pdb=" N MET Q 79 " occ=0.50 ... (2 atoms not shown) pdb=" O MET Q 79 " occ=0.50 residue: pdb=" N MET Q 326 " occ=0.58 ... (2 atoms not shown) pdb=" O MET Q 326 " occ=0.58 Time building chain proxies: 43.42, per 1000 atoms: 0.42 Number of scatterers: 103906 At special positions: 0 Unit cell: (263.586, 322.458, 327.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 335 16.00 P 425 15.00 Mg 7 11.99 O 21964 8.00 N 19997 7.00 C 61171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 308 " distance=2.74 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: 35.03 Conformation dependent library (CDL) restraints added in 15.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 117 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 134 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 102 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 137 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 101 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 101 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 142 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 139 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 27 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 24 " pdb=" ZN O 502 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 71 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 48 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 45 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 74 " pdb=" ZN O 503 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 165 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 173 " pdb="ZN ZN O 503 " - pdb=" NE2 HIS O 183 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 179 " pdb=" ZN Y 400 " pdb="ZN ZN Y 400 " - pdb=" SG CYS Y 46 " pdb="ZN ZN Y 400 " - pdb=" SG CYS Y 83 " pdb="ZN ZN Y 400 " - pdb=" SG CYS Y 43 " pdb="ZN ZN Y 400 " - pdb=" SG CYS Y 80 " Number of angles added : 39 29726 Ramachandran restraints generated. 14863 Oldfield, 0 Emsley, 14863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18124 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 538 helices and 142 sheets defined 49.0% alpha, 16.2% beta 90 base pairs and 179 stacking pairs defined. Time for finding SS restraints: 82.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 46 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.334A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 4.860A pdb=" N LYS A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.727A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.940A pdb=" N ILE A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 303' Processing helix chain 'A' and resid 309 through 317 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.670A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.747A pdb=" N ASN A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 413' Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.945A pdb=" N ILE A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix No H-bonds generated for 'chain 'A' and resid 420 through 425' Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.595A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 removed outlier: 3.638A pdb=" N HIS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 removed outlier: 4.046A pdb=" N SER A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 Processing helix chain 'A' and resid 531 through 539 Processing helix chain 'A' and resid 541 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 590 through 596 removed outlier: 4.131A pdb=" N TYR A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.480A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 676 through 697 removed outlier: 3.716A pdb=" N LEU A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 695 " --> pdb=" O HIS A 691 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 removed outlier: 3.514A pdb=" N CYS A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 853 removed outlier: 4.116A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 874 Proline residue: A 874 - end of helix Processing helix chain 'A' and resid 875 through 887 Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 962 Processing helix chain 'A' and resid 983 through 988 removed outlier: 5.375A pdb=" N LYS A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.816A pdb=" N ARG A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1015 removed outlier: 3.662A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 5.052A pdb=" N HIS A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1118 Proline residue: A1118 - end of helix Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.031A pdb=" N GLY A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A1128 " --> pdb=" O ASN A1124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1123 through 1128' Processing helix chain 'A' and resid 1143 through 1162 removed outlier: 3.624A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Proline residue: A1162 - end of helix Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 4.776A pdb=" N PHE A1174 " --> pdb=" O TRP A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1252 removed outlier: 5.273A pdb=" N GLY A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 removed outlier: 3.627A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1282 removed outlier: 4.340A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A1281 " --> pdb=" O ALA A1277 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLN A1282 " --> pdb=" O VAL A1278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1282' Processing helix chain 'A' and resid 1283 through 1304 removed outlier: 3.639A pdb=" N ASN A1304 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1312 removed outlier: 3.858A pdb=" N PHE A1311 " --> pdb=" O MET A1307 " (cutoff:3.500A) Proline residue: A1312 - end of helix No H-bonds generated for 'chain 'A' and resid 1307 through 1312' Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 4.597A pdb=" N GLN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 3.901A pdb=" N TYR A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A1372 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN A1373 " --> pdb=" O TYR A1369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1367 through 1373' Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1404 through 1410 removed outlier: 6.370A pdb=" N LEU A1408 " --> pdb=" O THR A1404 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A1410 " --> pdb=" O GLU A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 4.572A pdb=" N LEU A1422 " --> pdb=" O ARG A1418 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A1423 " --> pdb=" O ILE A1419 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1424 " --> pdb=" O ASN A1420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1418 through 1424' Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 5.548A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 3.761A pdb=" N ASP A1441 " --> pdb=" O ARG A1437 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 3.622A pdb=" N ARG A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1489 removed outlier: 4.088A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR A1488 " --> pdb=" O ILE A1484 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A1489 " --> pdb=" O LEU A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 removed outlier: 3.964A pdb=" N GLU A1511 " --> pdb=" O SER A1507 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A1512 " --> pdb=" O GLY A1508 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP A1515 " --> pdb=" O GLU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1528 removed outlier: 3.524A pdb=" N ASN A1527 " --> pdb=" O ARG A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1539 removed outlier: 3.994A pdb=" N LEU A1536 " --> pdb=" O ARG A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1580 through 1605 removed outlier: 3.663A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A1603 " --> pdb=" O GLN A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1690 Processing helix chain 'A' and resid 1721 through 1736 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1764 through 1772 removed outlier: 4.234A pdb=" N TYR A1768 " --> pdb=" O SER A1764 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A1769 " --> pdb=" O SER A1765 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU A1770 " --> pdb=" O GLN A1766 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A1771 " --> pdb=" O ASN A1767 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE A1772 " --> pdb=" O TYR A1768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1764 through 1772' Processing helix chain 'A' and resid 1823 through 1828 removed outlier: 4.760A pdb=" N TRP A1827 " --> pdb=" O HIS A1823 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1828 " --> pdb=" O THR A1824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1823 through 1828' Processing helix chain 'A' and resid 1833 through 1853 Proline residue: A1853 - end of helix Processing helix chain 'A' and resid 1865 through 1877 removed outlier: 4.374A pdb=" N LEU A1869 " --> pdb=" O ARG A1865 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP A1870 " --> pdb=" O LYS A1866 " (cutoff:3.500A) Proline residue: A1871 - end of helix removed outlier: 3.500A pdb=" N LEU A1877 " --> pdb=" O GLU A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1899 removed outlier: 4.050A pdb=" N CYS A1896 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A1897 " --> pdb=" O PHE A1893 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A1898 " --> pdb=" O GLN A1894 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A1899 " --> pdb=" O ALA A1895 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1899' Processing helix chain 'A' and resid 1900 through 1909 Processing helix chain 'A' and resid 1922 through 1927 removed outlier: 4.614A pdb=" N THR A1926 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1947 through 1956 Proline residue: A1956 - end of helix Processing helix chain 'A' and resid 1972 through 1996 removed outlier: 3.590A pdb=" N ASP A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2003 removed outlier: 3.907A pdb=" N LEU A2002 " --> pdb=" O ASN A1998 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR A2003 " --> pdb=" O VAL A1999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1998 through 2003' Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2070 through 2090 removed outlier: 3.666A pdb=" N ARG A2074 " --> pdb=" O LYS A2070 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A2076 " --> pdb=" O GLU A2072 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A2088 " --> pdb=" O HIS A2084 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS A2089 " --> pdb=" O LEU A2085 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2119 removed outlier: 3.674A pdb=" N LEU A2111 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A2118 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP A2119 " --> pdb=" O ILE A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 4.457A pdb=" N GLU A2171 " --> pdb=" O GLU A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2203 removed outlier: 3.650A pdb=" N ASP A2202 " --> pdb=" O LYS A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2257 removed outlier: 4.681A pdb=" N TYR A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A2257 " --> pdb=" O PRO A2253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2252 through 2257' Processing helix chain 'A' and resid 2284 through 2289 removed outlier: 4.127A pdb=" N HIS A2288 " --> pdb=" O MET A2284 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP A2289 " --> pdb=" O GLY A2285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2284 through 2289' Processing helix chain 'A' and resid 2306 through 2311 removed outlier: 3.786A pdb=" N ARG A2310 " --> pdb=" O HIS A2306 " (cutoff:3.500A) Proline residue: A2311 - end of helix No H-bonds generated for 'chain 'A' and resid 2306 through 2311' Processing helix chain 'A' and resid 2321 through 2326 removed outlier: 4.662A pdb=" N VAL A2325 " --> pdb=" O GLN A2321 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A2326 " --> pdb=" O GLU A2322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2321 through 2326' Processing helix chain 'A' and resid 1615 through 1620 removed outlier: 4.702A pdb=" N SER A1619 " --> pdb=" O PRO A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.061A pdb=" N ALA A 201 " --> pdb=" O ASP A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.918A pdb=" N TYR C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.713A pdb=" N ASP C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Proline residue: C 155 - end of helix Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.971A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.571A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 294 removed outlier: 3.837A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.535A pdb=" N PHE C 339 " --> pdb=" O ASN C 335 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 5.238A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.850A pdb=" N LEU C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 424 Processing helix chain 'C' and resid 427 through 437 removed outlier: 4.169A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 removed outlier: 3.761A pdb=" N ALA C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 3.516A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 468 removed outlier: 5.817A pdb=" N GLU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 523 removed outlier: 4.346A pdb=" N SER C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLN C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 518 through 523' Processing helix chain 'C' and resid 596 through 615 removed outlier: 3.944A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Proline residue: C 601 - end of helix Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 633 through 646 Processing helix chain 'C' and resid 693 through 703 removed outlier: 4.017A pdb=" N ALA C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 750 through 755 removed outlier: 5.032A pdb=" N ASP C 755 " --> pdb=" O PRO C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 777 removed outlier: 4.008A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 824 removed outlier: 4.707A pdb=" N ILE C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 854 removed outlier: 3.581A pdb=" N VAL C 843 " --> pdb=" O PRO C 839 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ALA C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 881 removed outlier: 4.128A pdb=" N PHE C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 892 Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'D' and resid 107 through 124 removed outlier: 4.230A pdb=" N VAL D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 150 through 162 removed outlier: 5.206A pdb=" N ARG D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 removed outlier: 5.922A pdb=" N TYR D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 171 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.870A pdb=" N ILE D 263 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP D 264 " --> pdb=" O PRO D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 264' Processing helix chain 'D' and resid 266 through 276 removed outlier: 4.184A pdb=" N PHE D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 295 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.693A pdb=" N LEU D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'D' and resid 326 through 338 removed outlier: 5.444A pdb=" N GLN D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'D' and resid 356 through 365 Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.914A pdb=" N LEU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 410 through 415' Processing helix chain 'D' and resid 468 through 473 removed outlier: 3.559A pdb=" N GLN D 472 " --> pdb=" O PRO D 468 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 468 through 473' Processing helix chain 'D' and resid 482 through 494 removed outlier: 5.462A pdb=" N ARG D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA D 491 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 525 removed outlier: 4.315A pdb=" N VAL D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 520 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS D 524 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 559 removed outlier: 3.672A pdb=" N LYS D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 4.898A pdb=" N ILE D 580 " --> pdb=" O CYS D 576 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR D 583 " --> pdb=" O GLU D 579 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN D 584 " --> pdb=" O ILE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 600 Processing helix chain 'D' and resid 601 through 606 removed outlier: 4.197A pdb=" N TYR D 605 " --> pdb=" O GLY D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 4.384A pdb=" N ASP D 622 " --> pdb=" O HIS D 618 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 623' Processing helix chain 'D' and resid 624 through 643 removed outlier: 3.994A pdb=" N LEU D 628 " --> pdb=" O ARG D 624 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET D 641 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 696 through 717 removed outlier: 4.104A pdb=" N GLN D 702 " --> pdb=" O ILE D 698 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN D 705 " --> pdb=" O PHE D 701 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 746 removed outlier: 4.956A pdb=" N GLY D 732 " --> pdb=" O ARG D 728 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 735 " --> pdb=" O THR D 731 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA D 737 " --> pdb=" O LYS D 733 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 738 " --> pdb=" O THR D 734 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP D 746 " --> pdb=" O CYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 768 removed outlier: 3.802A pdb=" N THR D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN D 768 " --> pdb=" O THR D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 781 removed outlier: 3.894A pdb=" N LEU D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Proline residue: D 779 - end of helix Processing helix chain 'D' and resid 790 through 804 removed outlier: 5.141A pdb=" N ARG D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR D 795 " --> pdb=" O ARG D 791 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 818 removed outlier: 3.984A pdb=" N ALA D 816 " --> pdb=" O THR D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.590A pdb=" N ILE D 849 " --> pdb=" O GLY D 845 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 855 " --> pdb=" O GLN D 851 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA D 856 " --> pdb=" O MET D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 885 removed outlier: 4.305A pdb=" N GLN D 877 " --> pdb=" O HIS D 873 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR D 878 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 883 " --> pdb=" O TYR D 879 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 908 removed outlier: 4.114A pdb=" N LYS D 896 " --> pdb=" O GLN D 892 " (cutoff:3.500A) Proline residue: D 898 - end of helix Processing helix chain 'D' and resid 912 through 924 removed outlier: 3.721A pdb=" N TYR D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 923 " --> pdb=" O TRP D 919 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 939 through 947 Proline residue: D 947 - end of helix Processing helix chain 'D' and resid 949 through 968 removed outlier: 4.421A pdb=" N VAL D 957 " --> pdb=" O ARG D 953 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS D 958 " --> pdb=" O LEU D 954 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 959 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 992 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.738A pdb=" N GLN D 999 " --> pdb=" O ASN D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1026 removed outlier: 3.852A pdb=" N ARG D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D1021 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER D1022 " --> pdb=" O PHE D1018 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLU D1023 " --> pdb=" O SER D1019 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS D1025 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN D1026 " --> pdb=" O SER D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1031 through 1042 removed outlier: 4.204A pdb=" N LEU D1035 " --> pdb=" O GLU D1031 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU D1036 " --> pdb=" O GLU D1032 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D1038 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D1039 " --> pdb=" O LEU D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1069 Processing helix chain 'D' and resid 1078 through 1103 removed outlier: 3.750A pdb=" N GLY D1089 " --> pdb=" O THR D1085 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1121 Processing helix chain 'D' and resid 1127 through 1133 removed outlier: 4.693A pdb=" N GLN D1131 " --> pdb=" O CYS D1127 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG D1133 " --> pdb=" O LEU D1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1127 through 1133' Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.670A pdb=" N LYS D1146 " --> pdb=" O LYS D1142 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN D1147 " --> pdb=" O ILE D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1149 through 1157 removed outlier: 4.137A pdb=" N LEU D1153 " --> pdb=" O PRO D1149 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D1154 " --> pdb=" O PHE D1150 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP D1155 " --> pdb=" O GLU D1151 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D1156 " --> pdb=" O ARG D1152 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN D1157 " --> pdb=" O LEU D1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1149 through 1157' Processing helix chain 'D' and resid 1158 through 1166 removed outlier: 3.875A pdb=" N GLY D1162 " --> pdb=" O HIS D1158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D1164 " --> pdb=" O GLU D1160 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE D1165 " --> pdb=" O ILE D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1182 removed outlier: 3.867A pdb=" N GLY D1171 " --> pdb=" O MET D1167 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS D1172 " --> pdb=" O PRO D1168 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR D1173 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS D1175 " --> pdb=" O GLY D1171 " (cutoff:3.500A) Proline residue: D1182 - end of helix Processing helix chain 'D' and resid 1314 through 1322 removed outlier: 4.446A pdb=" N LEU D1320 " --> pdb=" O ALA D1316 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D1321 " --> pdb=" O PHE D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1329 through 1340 removed outlier: 4.789A pdb=" N ASN D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR D1338 " --> pdb=" O GLN D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1355 through 1371 removed outlier: 3.665A pdb=" N CYS D1359 " --> pdb=" O GLY D1355 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D1363 " --> pdb=" O CYS D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1382 through 1397 removed outlier: 3.773A pdb=" N ASP D1392 " --> pdb=" O GLN D1388 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D1395 " --> pdb=" O MET D1391 " (cutoff:3.500A) Processing helix chain 'D' and resid 1411 through 1422 removed outlier: 4.907A pdb=" N GLY D1420 " --> pdb=" O LEU D1416 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS D1421 " --> pdb=" O LYS D1417 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D1422 " --> pdb=" O LEU D1418 " (cutoff:3.500A) Processing helix chain 'D' and resid 1428 through 1437 removed outlier: 3.666A pdb=" N LEU D1435 " --> pdb=" O LYS D1431 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER D1436 " --> pdb=" O TRP D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1438 through 1443 removed outlier: 3.890A pdb=" N ARG D1442 " --> pdb=" O ARG D1438 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D1443 " --> pdb=" O TRP D1439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1438 through 1443' Processing helix chain 'D' and resid 1455 through 1462 removed outlier: 4.803A pdb=" N ILE D1459 " --> pdb=" O GLU D1455 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY D1460 " --> pdb=" O VAL D1456 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY D1461 " --> pdb=" O HIS D1457 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU D1462 " --> pdb=" O LEU D1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1455 through 1462' Processing helix chain 'D' and resid 1463 through 1482 removed outlier: 4.103A pdb=" N LEU D1467 " --> pdb=" O ASN D1463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1505 removed outlier: 3.663A pdb=" N VAL D1500 " --> pdb=" O ASN D1496 " (cutoff:3.500A) Processing helix chain 'D' and resid 1507 through 1512 removed outlier: 5.532A pdb=" N PHE D1512 " --> pdb=" O ALA D1508 " (cutoff:3.500A) Processing helix chain 'D' and resid 1534 through 1553 removed outlier: 3.840A pdb=" N ALA D1543 " --> pdb=" O LEU D1539 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS D1544 " --> pdb=" O LEU D1540 " (cutoff:3.500A) Proline residue: D1545 - end of helix Processing helix chain 'D' and resid 1566 through 1584 removed outlier: 4.901A pdb=" N ARG D1570 " --> pdb=" O ARG D1566 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D1571 " --> pdb=" O LYS D1567 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D1582 " --> pdb=" O THR D1578 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D1583 " --> pdb=" O THR D1579 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D1584 " --> pdb=" O CYS D1580 " (cutoff:3.500A) Processing helix chain 'D' and resid 1593 through 1604 removed outlier: 3.851A pdb=" N LEU D1597 " --> pdb=" O THR D1593 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D1598 " --> pdb=" O GLU D1594 " (cutoff:3.500A) Proline residue: D1599 - end of helix removed outlier: 4.738A pdb=" N LYS D1603 " --> pdb=" O PRO D1599 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU D1604 " --> pdb=" O TYR D1600 " (cutoff:3.500A) Processing helix chain 'D' and resid 1606 through 1616 removed outlier: 3.579A pdb=" N LYS D1610 " --> pdb=" O ASP D1606 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D1611 " --> pdb=" O SER D1607 " (cutoff:3.500A) Processing helix chain 'D' and resid 1625 through 1639 Processing helix chain 'D' and resid 1647 through 1652 removed outlier: 4.179A pdb=" N CYS D1651 " --> pdb=" O SER D1647 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRP D1652 " --> pdb=" O ARG D1648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1647 through 1652' Processing helix chain 'D' and resid 1680 through 1691 removed outlier: 4.109A pdb=" N ALA D1691 " --> pdb=" O MET D1687 " (cutoff:3.500A) Processing helix chain 'D' and resid 1707 through 1720 removed outlier: 4.560A pdb=" N ASP D1712 " --> pdb=" O GLY D1708 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE D1713 " --> pdb=" O SER D1709 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D1714 " --> pdb=" O LYS D1710 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR D1719 " --> pdb=" O LYS D1715 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D1720 " --> pdb=" O LYS D1716 " (cutoff:3.500A) Processing helix chain 'D' and resid 1727 through 1732 removed outlier: 3.810A pdb=" N MET D1732 " --> pdb=" O LEU D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1733 through 1743 Processing helix chain 'D' and resid 1747 through 1758 removed outlier: 3.619A pdb=" N TRP D1757 " --> pdb=" O ASP D1753 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D1758 " --> pdb=" O TYR D1754 " (cutoff:3.500A) Processing helix chain 'D' and resid 1759 through 1767 removed outlier: 4.503A pdb=" N THR D1765 " --> pdb=" O TYR D1761 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN D1766 " --> pdb=" O ARG D1762 " (cutoff:3.500A) Processing helix chain 'D' and resid 1777 through 1800 removed outlier: 3.546A pdb=" N LYS D1800 " --> pdb=" O LEU D1796 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1823 Processing helix chain 'D' and resid 1825 through 1836 Processing helix chain 'D' and resid 1841 through 1852 removed outlier: 3.677A pdb=" N GLU D1847 " --> pdb=" O ARG D1843 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D1852 " --> pdb=" O ILE D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1853 through 1858 removed outlier: 4.283A pdb=" N ASN D1857 " --> pdb=" O ALA D1853 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE D1858 " --> pdb=" O GLU D1854 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1853 through 1858' Processing helix chain 'D' and resid 1863 through 1876 removed outlier: 4.380A pdb=" N LEU D1867 " --> pdb=" O HIS D1863 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D1868 " --> pdb=" O GLU D1864 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D1869 " --> pdb=" O ASP D1865 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS D1874 " --> pdb=" O GLN D1870 " (cutoff:3.500A) Proline residue: D1876 - end of helix Processing helix chain 'D' and resid 1886 through 1901 Processing helix chain 'D' and resid 1905 through 1934 removed outlier: 3.745A pdb=" N ASP D1911 " --> pdb=" O GLU D1907 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D1918 " --> pdb=" O GLU D1914 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE D1920 " --> pdb=" O LEU D1916 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG D1921 " --> pdb=" O SER D1917 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D1922 " --> pdb=" O LYS D1918 " (cutoff:3.500A) Processing helix chain 'D' and resid 1935 through 1952 removed outlier: 3.559A pdb=" N ALA D1939 " --> pdb=" O TRP D1935 " (cutoff:3.500A) Processing helix chain 'D' and resid 1967 through 1978 removed outlier: 3.784A pdb=" N ILE D1971 " --> pdb=" O THR D1967 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS D1972 " --> pdb=" O SER D1968 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D1973 " --> pdb=" O GLU D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 1981 through 1989 removed outlier: 3.588A pdb=" N ILE D1985 " --> pdb=" O SER D1981 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D1987 " --> pdb=" O PHE D1983 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET D1988 " --> pdb=" O ASP D1984 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU D1989 " --> pdb=" O ILE D1985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 1998 removed outlier: 5.121A pdb=" N ASN D1994 " --> pdb=" O ASP D1990 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN D1998 " --> pdb=" O ASN D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2000 through 2014 removed outlier: 3.716A pdb=" N PHE D2010 " --> pdb=" O ASP D2006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.989A pdb=" N LEU D1312 " --> pdb=" O VAL D1309 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG D1313 " --> pdb=" O SER D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1958 through 1964 removed outlier: 3.658A pdb=" N LYS D1961 " --> pdb=" O SER D1958 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D1962 " --> pdb=" O TYR D1959 " (cutoff:3.500A) Proline residue: D1964 - end of helix Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 1211 through 1216 removed outlier: 3.695A pdb=" N GLY D1216 " --> pdb=" O ASP D1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1211 through 1216' Processing helix chain 'I' and resid 156 through 166 Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 172 through 183 Proline residue: I 177 - end of helix Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.595A pdb=" N THR I 202 " --> pdb=" O GLN I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 222 through 234 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 236 through 251 removed outlier: 3.727A pdb=" N ARG I 250 " --> pdb=" O GLY I 246 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE I 251 " --> pdb=" O GLY I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 267 removed outlier: 3.567A pdb=" N LEU I 258 " --> pdb=" O GLN I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 283 removed outlier: 3.692A pdb=" N GLU I 273 " --> pdb=" O SER I 269 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG I 276 " --> pdb=" O PHE I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 Processing helix chain 'I' and resid 303 through 316 removed outlier: 5.048A pdb=" N GLU I 316 " --> pdb=" O GLU I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 334 Processing helix chain 'I' and resid 337 through 352 Proline residue: I 342 - end of helix Processing helix chain 'I' and resid 356 through 366 removed outlier: 3.573A pdb=" N ARG I 363 " --> pdb=" O GLU I 359 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL I 364 " --> pdb=" O TRP I 360 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA I 365 " --> pdb=" O HIS I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 375 through 383 Processing helix chain 'I' and resid 387 through 398 removed outlier: 4.280A pdb=" N THR I 391 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Proline residue: I 394 - end of helix Processing helix chain 'I' and resid 403 through 416 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 440 through 460 removed outlier: 4.255A pdb=" N ARG I 457 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS I 458 " --> pdb=" O ARG I 454 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 484 Proline residue: I 475 - end of helix Processing helix chain 'I' and resid 487 through 502 removed outlier: 5.628A pdb=" N SER I 502 " --> pdb=" O GLY I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 525 Proline residue: I 518 - end of helix removed outlier: 5.346A pdb=" N ALA I 525 " --> pdb=" O VAL I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 527 through 542 removed outlier: 3.578A pdb=" N HIS I 531 " --> pdb=" O PHE I 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 534 " --> pdb=" O GLU I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 560 Proline residue: I 551 - end of helix removed outlier: 3.524A pdb=" N TRP I 557 " --> pdb=" O VAL I 553 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER I 558 " --> pdb=" O SER I 554 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR I 560 " --> pdb=" O ILE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 580 removed outlier: 4.396A pdb=" N LEU I 573 " --> pdb=" O GLY I 569 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG I 577 " --> pdb=" O LEU I 573 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE I 580 " --> pdb=" O ALA I 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 599 Proline residue: I 588 - end of helix Processing helix chain 'I' and resid 600 through 616 removed outlier: 4.491A pdb=" N GLU I 604 " --> pdb=" O ALA I 600 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA I 614 " --> pdb=" O ARG I 610 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR I 616 " --> pdb=" O ALA I 612 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 636 removed outlier: 3.855A pdb=" N ALA I 622 " --> pdb=" O ARG I 618 " (cutoff:3.500A) Proline residue: I 625 - end of helix removed outlier: 3.530A pdb=" N TYR I 635 " --> pdb=" O MET I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 653 removed outlier: 4.109A pdb=" N GLY I 644 " --> pdb=" O ALA I 640 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN I 653 " --> pdb=" O ARG I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 663 through 676 removed outlier: 3.694A pdb=" N MET I 667 " --> pdb=" O HIS I 663 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU I 675 " --> pdb=" O PHE I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 679 through 689 removed outlier: 3.523A pdb=" N ARG I 683 " --> pdb=" O GLY I 679 " (cutoff:3.500A) Processing helix chain 'I' and resid 706 through 721 Processing helix chain 'I' and resid 722 through 733 removed outlier: 4.017A pdb=" N ILE I 726 " --> pdb=" O GLU I 722 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG I 727 " --> pdb=" O MET I 723 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL I 730 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN I 731 " --> pdb=" O ARG I 727 " (cutoff:3.500A) Processing helix chain 'I' and resid 740 through 753 removed outlier: 3.751A pdb=" N GLN I 744 " --> pdb=" O PHE I 740 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER I 751 " --> pdb=" O LYS I 747 " (cutoff:3.500A) Processing helix chain 'I' and resid 760 through 775 removed outlier: 3.737A pdb=" N ARG I 775 " --> pdb=" O LEU I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 779 through 793 Proline residue: I 788 - end of helix removed outlier: 4.141A pdb=" N SER I 793 " --> pdb=" O LEU I 789 " (cutoff:3.500A) Processing helix chain 'I' and resid 797 through 819 Proline residue: I 816 - end of helix removed outlier: 5.519A pdb=" N ILE I 819 " --> pdb=" O ASN I 815 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 202 removed outlier: 4.272A pdb=" N LEU J 194 " --> pdb=" O THR J 190 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU J 195 " --> pdb=" O ALA J 191 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 239 removed outlier: 4.371A pdb=" N ASN J 221 " --> pdb=" O GLU J 217 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR J 223 " --> pdb=" O GLU J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 256 removed outlier: 4.170A pdb=" N TRP J 245 " --> pdb=" O VAL J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 273 Processing helix chain 'J' and resid 275 through 290 Processing helix chain 'J' and resid 291 through 306 Processing helix chain 'J' and resid 309 through 324 removed outlier: 3.779A pdb=" N TRP J 313 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 340 removed outlier: 3.506A pdb=" N GLU J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN J 340 " --> pdb=" O TRP J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 357 removed outlier: 4.086A pdb=" N TYR J 356 " --> pdb=" O PHE J 352 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 374 removed outlier: 4.065A pdb=" N LEU J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Proline residue: J 374 - end of helix Processing helix chain 'J' and resid 375 through 390 Processing helix chain 'J' and resid 391 through 407 Processing helix chain 'J' and resid 412 through 427 removed outlier: 3.786A pdb=" N TYR J 416 " --> pdb=" O ASP J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 444 removed outlier: 4.559A pdb=" N SER J 444 " --> pdb=" O LEU J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 467 Processing helix chain 'J' and resid 477 through 491 removed outlier: 3.917A pdb=" N GLU J 481 " --> pdb=" O ARG J 477 " (cutoff:3.500A) Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 495 through 513 removed outlier: 4.563A pdb=" N ARG J 499 " --> pdb=" O PHE J 495 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 535 removed outlier: 3.875A pdb=" N TYR J 535 " --> pdb=" O LYS J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 555 removed outlier: 4.129A pdb=" N LEU J 542 " --> pdb=" O ILE J 538 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR J 543 " --> pdb=" O ASN J 539 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA J 548 " --> pdb=" O GLU J 544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP J 550 " --> pdb=" O LEU J 546 " (cutoff:3.500A) Proline residue: J 551 - end of helix Processing helix chain 'J' and resid 559 through 569 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 573 through 586 removed outlier: 3.732A pdb=" N PHE J 582 " --> pdb=" O LEU J 578 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU J 583 " --> pdb=" O TYR J 579 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG J 585 " --> pdb=" O GLN J 581 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLN J 586 " --> pdb=" O PHE J 582 " (cutoff:3.500A) Processing helix chain 'J' and resid 592 through 605 removed outlier: 3.923A pdb=" N THR J 598 " --> pdb=" O ARG J 594 " (cutoff:3.500A) Proline residue: J 604 - end of helix Processing helix chain 'J' and resid 609 through 624 removed outlier: 3.551A pdb=" N ILE J 613 " --> pdb=" O PHE J 609 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG J 624 " --> pdb=" O ARG J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 631 through 644 removed outlier: 3.869A pdb=" N PHE J 635 " --> pdb=" O LYS J 631 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY J 636 " --> pdb=" O PHE J 632 " (cutoff:3.500A) Proline residue: J 637 - end of helix removed outlier: 3.870A pdb=" N TRP J 643 " --> pdb=" O ASN J 639 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE J 644 " --> pdb=" O CYS J 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 660 removed outlier: 3.981A pdb=" N ILE J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU J 653 " --> pdb=" O LEU J 649 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG J 660 " --> pdb=" O ILE J 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 679 Proline residue: J 670 - end of helix removed outlier: 3.697A pdb=" N MET J 674 " --> pdb=" O PRO J 670 " (cutoff:3.500A) Proline residue: J 675 - end of helix removed outlier: 3.657A pdb=" N LEU J 678 " --> pdb=" O MET J 674 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP J 679 " --> pdb=" O PRO J 675 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 697 removed outlier: 4.158A pdb=" N ASN J 697 " --> pdb=" O GLU J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 699 through 710 removed outlier: 3.834A pdb=" N LEU J 703 " --> pdb=" O TYR J 699 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL J 709 " --> pdb=" O ARG J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 731 Processing helix chain 'J' and resid 740 through 756 removed outlier: 3.762A pdb=" N ASN J 744 " --> pdb=" O LYS J 740 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 755 " --> pdb=" O ARG J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 762 through 776 removed outlier: 4.035A pdb=" N GLY J 766 " --> pdb=" O GLU J 762 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR J 767 " --> pdb=" O GLU J 763 " (cutoff:3.500A) Processing helix chain 'J' and resid 780 through 802 removed outlier: 3.778A pdb=" N LYS J 784 " --> pdb=" O GLU J 780 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 801 " --> pdb=" O GLY J 797 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE J 802 " --> pdb=" O TRP J 798 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 43 Processing helix chain 'K' and resid 65 through 78 removed outlier: 4.181A pdb=" N GLU K 69 " --> pdb=" O ILE K 65 " (cutoff:3.500A) Proline residue: K 78 - end of helix Processing helix chain 'K' and resid 105 through 131 removed outlier: 3.572A pdb=" N GLU K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET K 127 " --> pdb=" O ASN K 123 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS K 130 " --> pdb=" O LEU K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 199 removed outlier: 3.665A pdb=" N TYR K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS K 148 " --> pdb=" O HIS K 144 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN K 169 " --> pdb=" O TRP K 165 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR K 193 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 26 Processing helix chain 'L' and resid 30 through 39 removed outlier: 3.718A pdb=" N SER L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU L 38 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N HIS L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 53 Processing helix chain 'L' and resid 64 through 79 Proline residue: L 79 - end of helix Processing helix chain 'L' and resid 81 through 90 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 92 through 108 Processing helix chain 'L' and resid 145 through 162 removed outlier: 3.982A pdb=" N LEU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR L 162 " --> pdb=" O ARG L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 195 removed outlier: 4.146A pdb=" N GLU L 178 " --> pdb=" O LYS L 174 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA L 179 " --> pdb=" O GLN L 175 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG L 180 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 212 removed outlier: 4.281A pdb=" N TYR L 210 " --> pdb=" O ARG L 206 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN L 211 " --> pdb=" O GLY L 207 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA L 212 " --> pdb=" O VAL L 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 212' Processing helix chain 'L' and resid 506 through 529 removed outlier: 3.557A pdb=" N THR L 510 " --> pdb=" O GLU L 506 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE L 525 " --> pdb=" O ARG L 521 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA L 528 " --> pdb=" O ALA L 524 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU L 529 " --> pdb=" O ILE L 525 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 552 Proline residue: L 548 - end of helix Processing helix chain 'L' and resid 556 through 571 removed outlier: 3.634A pdb=" N ASN L 560 " --> pdb=" O LEU L 556 " (cutoff:3.500A) Proline residue: L 563 - end of helix removed outlier: 3.836A pdb=" N SER L 571 " --> pdb=" O ASP L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 608 removed outlier: 3.591A pdb=" N ASN L 597 " --> pdb=" O GLU L 593 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 629 Proline residue: L 620 - end of helix Processing helix chain 'L' and resid 690 through 721 removed outlier: 4.080A pdb=" N LYS L 694 " --> pdb=" O GLU L 690 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG L 695 " --> pdb=" O SER L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 722 through 795 removed outlier: 3.695A pdb=" N GLN L 734 " --> pdb=" O GLY L 730 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU L 735 " --> pdb=" O LEU L 731 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP L 740 " --> pdb=" O ASN L 736 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE L 742 " --> pdb=" O LEU L 738 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN L 744 " --> pdb=" O ASP L 740 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER L 761 " --> pdb=" O LYS L 757 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 762 " --> pdb=" O HIS L 758 " (cutoff:3.500A) Proline residue: L 764 - end of helix removed outlier: 3.515A pdb=" N ARG L 780 " --> pdb=" O ARG L 776 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 785 " --> pdb=" O GLU L 781 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS L 786 " --> pdb=" O LYS L 782 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 787 " --> pdb=" O GLU L 783 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR L 788 " --> pdb=" O LEU L 784 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU L 792 " --> pdb=" O TYR L 788 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 793 " --> pdb=" O ALA L 789 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU L 794 " --> pdb=" O ASP L 790 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 795 " --> pdb=" O LEU L 791 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 10 removed outlier: 3.944A pdb=" N LYS y 7 " --> pdb=" O ARG y 3 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET y 9 " --> pdb=" O ALA y 5 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR y 10 " --> pdb=" O GLU y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 22 removed outlier: 3.845A pdb=" N GLN y 17 " --> pdb=" O ALA y 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU y 22 " --> pdb=" O ALA y 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 38 through 62 removed outlier: 3.592A pdb=" N ALA y 42 " --> pdb=" O GLU y 38 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS y 44 " --> pdb=" O PRO y 40 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG y 47 " --> pdb=" O GLU y 43 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU y 52 " --> pdb=" O GLN y 48 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN y 61 " --> pdb=" O VAL y 57 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN y 62 " --> pdb=" O ALA y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 66 through 88 Processing helix chain 'y' and resid 161 through 192 Proline residue: y 165 - end of helix Processing helix chain 'M' and resid 126 through 142 removed outlier: 3.657A pdb=" N ALA M 130 " --> pdb=" O ASP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 157 removed outlier: 4.222A pdb=" N LYS M 155 " --> pdb=" O ARG M 151 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 196 removed outlier: 3.880A pdb=" N ILE M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET M 182 " --> pdb=" O GLU M 178 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR M 196 " --> pdb=" O LYS M 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 35 removed outlier: 4.057A pdb=" N ILE N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Proline residue: N 20 - end of helix Processing helix chain 'N' and resid 41 through 65 removed outlier: 4.916A pdb=" N SER N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP N 47 " --> pdb=" O VAL N 43 " (cutoff:3.500A) Proline residue: N 48 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.646A pdb=" N GLY N 82 " --> pdb=" O CYS N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 95 removed outlier: 3.519A pdb=" N ILE N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLN N 95 " --> pdb=" O LYS N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 107 removed outlier: 4.509A pdb=" N ILE N 106 " --> pdb=" O CYS N 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 102 through 107' Processing helix chain 'N' and resid 117 through 122 removed outlier: 4.063A pdb=" N VAL N 121 " --> pdb=" O CYS N 117 " (cutoff:3.500A) Proline residue: N 122 - end of helix No H-bonds generated for 'chain 'N' and resid 117 through 122' Processing helix chain 'O' and resid 24 through 29 removed outlier: 4.044A pdb=" N GLY O 29 " --> pdb=" O GLN O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 79 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 111 through 129 removed outlier: 5.438A pdb=" N ASP O 129 " --> pdb=" O ILE O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 141 removed outlier: 4.328A pdb=" N GLY O 138 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS O 139 " --> pdb=" O GLY O 135 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR O 141 " --> pdb=" O LEU O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 151 Processing helix chain 'O' and resid 165 through 171 removed outlier: 4.075A pdb=" N LYS O 170 " --> pdb=" O SER O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 197 through 204 Processing helix chain 'O' and resid 207 through 220 removed outlier: 3.806A pdb=" N THR O 219 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET O 220 " --> pdb=" O ARG O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 253 removed outlier: 3.921A pdb=" N LEU O 248 " --> pdb=" O THR O 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 276 through 288 removed outlier: 3.617A pdb=" N ALA O 280 " --> pdb=" O THR O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.780A pdb=" N ASP O 195 " --> pdb=" O PRO O 192 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN O 196 " --> pdb=" O LEU O 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 57 removed outlier: 3.519A pdb=" N ASN P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 78 removed outlier: 3.506A pdb=" N GLU P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 210 removed outlier: 5.547A pdb=" N PHE P 210 " --> pdb=" O LYS P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'R' and resid 99 through 104 removed outlier: 3.701A pdb=" N ARG R 103 " --> pdb=" O ASP R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 121 removed outlier: 3.962A pdb=" N LEU R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 160 removed outlier: 3.541A pdb=" N ILE R 140 " --> pdb=" O ASP R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 removed outlier: 7.236A pdb=" N ASN R 189 " --> pdb=" O GLY R 185 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER R 190 " --> pdb=" O VAL R 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 185 through 190' Processing helix chain 'R' and resid 238 through 246 removed outlier: 3.785A pdb=" N LYS R 246 " --> pdb=" O GLN R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 281 through 316 removed outlier: 5.052A pdb=" N ALA R 285 " --> pdb=" O ASN R 281 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 46 Processing helix chain 'S' and resid 135 through 145 removed outlier: 3.593A pdb=" N VAL S 145 " --> pdb=" O ARG S 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 30 Processing helix chain 'Q' and resid 42 through 58 removed outlier: 4.048A pdb=" N ILE Q 46 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG Q 58 " --> pdb=" O ILE Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 71 Processing helix chain 'Q' and resid 76 through 81 removed outlier: 3.639A pdb=" N ASN Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 105 Processing helix chain 'Q' and resid 109 through 116 Proline residue: Q 116 - end of helix Processing helix chain 'Q' and resid 118 through 132 Processing helix chain 'Q' and resid 139 through 157 removed outlier: 3.737A pdb=" N LEU Q 157 " --> pdb=" O CYS Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 170 removed outlier: 3.938A pdb=" N GLN Q 165 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU Q 169 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 179 removed outlier: 4.485A pdb=" N TRP Q 175 " --> pdb=" O SER Q 171 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET Q 176 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY Q 177 " --> pdb=" O PRO Q 173 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU Q 178 " --> pdb=" O MET Q 174 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN Q 179 " --> pdb=" O TRP Q 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 171 through 179' Processing helix chain 'Q' and resid 180 through 191 Proline residue: Q 191 - end of helix Processing helix chain 'Q' and resid 192 through 208 removed outlier: 4.357A pdb=" N PHE Q 196 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU Q 205 " --> pdb=" O LYS Q 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS Q 206 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET Q 207 " --> pdb=" O ASN Q 203 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP Q 208 " --> pdb=" O ASP Q 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 236 removed outlier: 4.870A pdb=" N LEU Q 222 " --> pdb=" O GLU Q 218 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER Q 223 " --> pdb=" O ARG Q 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL Q 236 " --> pdb=" O VAL Q 232 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 264 removed outlier: 3.682A pdb=" N VAL Q 247 " --> pdb=" O THR Q 243 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU Q 264 " --> pdb=" O LEU Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 278 removed outlier: 5.204A pdb=" N TRP Q 269 " --> pdb=" O PRO Q 265 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE Q 270 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR Q 272 " --> pdb=" O ARG Q 268 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE Q 273 " --> pdb=" O TRP Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 287 through 292 removed outlier: 5.408A pdb=" N GLU Q 292 " --> pdb=" O LEU Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 311 Processing helix chain 'Q' and resid 322 through 344 Processing helix chain 'Q' and resid 345 through 354 removed outlier: 3.626A pdb=" N TYR Q 349 " --> pdb=" O PHE Q 345 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP Q 350 " --> pdb=" O PRO Q 346 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE Q 351 " --> pdb=" O GLU Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 355 through 360 removed outlier: 3.589A pdb=" N VAL Q 359 " --> pdb=" O ASN Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 370 Processing helix chain 'Q' and resid 373 through 385 Processing helix chain 'Q' and resid 399 through 412 Processing helix chain 'Q' and resid 416 through 424 removed outlier: 3.793A pdb=" N MET Q 424 " --> pdb=" O GLN Q 420 " (cutoff:3.500A) Processing helix chain 'Q' and resid 429 through 435 removed outlier: 4.453A pdb=" N TRP Q 434 " --> pdb=" O GLU Q 430 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP Q 435 " --> pdb=" O LYS Q 431 " (cutoff:3.500A) Processing helix chain 'Q' and resid 461 through 493 removed outlier: 3.513A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU Q 480 " --> pdb=" O GLU Q 476 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS Q 493 " --> pdb=" O VAL Q 489 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 556 removed outlier: 3.657A pdb=" N LEU Q 556 " --> pdb=" O GLU Q 552 " (cutoff:3.500A) Processing helix chain 'Q' and resid 582 through 588 Processing helix chain 'Q' and resid 630 through 644 Processing helix chain 'Q' and resid 648 through 653 removed outlier: 4.256A pdb=" N THR Q 652 " --> pdb=" O ASP Q 648 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE Q 653 " --> pdb=" O VAL Q 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 648 through 653' Processing helix chain 'Q' and resid 660 through 680 removed outlier: 4.308A pdb=" N ASN Q 665 " --> pdb=" O PRO Q 661 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE Q 666 " --> pdb=" O LYS Q 662 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS Q 667 " --> pdb=" O GLU Q 663 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA Q 668 " --> pdb=" O ASN Q 664 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP Q 680 " --> pdb=" O LEU Q 676 " (cutoff:3.500A) Processing helix chain 'Q' and resid 684 through 693 removed outlier: 4.792A pdb=" N ASP Q 689 " --> pdb=" O ASP Q 685 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ILE Q 690 " --> pdb=" O TRP Q 686 " (cutoff:3.500A) Processing helix chain 'Q' and resid 701 through 706 Proline residue: Q 706 - end of helix Processing helix chain 'Q' and resid 720 through 729 removed outlier: 3.551A pdb=" N PHE Q 728 " --> pdb=" O LEU Q 724 " (cutoff:3.500A) Proline residue: Q 729 - end of helix Processing helix chain 'Q' and resid 803 through 816 Proline residue: Q 816 - end of helix Processing helix chain 'Q' and resid 828 through 844 Processing helix chain 'Q' and resid 855 through 870 removed outlier: 3.578A pdb=" N LEU Q 859 " --> pdb=" O SER Q 855 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Q 868 " --> pdb=" O GLU Q 864 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Q 869 " --> pdb=" O LYS Q 865 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP Q 870 " --> pdb=" O ILE Q 866 " (cutoff:3.500A) Processing helix chain 'Q' and resid 872 through 877 removed outlier: 3.981A pdb=" N LEU Q 876 " --> pdb=" O ASP Q 872 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU Q 877 " --> pdb=" O GLU Q 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 872 through 877' Processing helix chain 'Q' and resid 893 through 920 Processing helix chain 'Q' and resid 928 through 952 removed outlier: 4.172A pdb=" N MET Q 941 " --> pdb=" O LEU Q 937 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER Q 942 " --> pdb=" O TYR Q 938 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Q 943 " --> pdb=" O GLN Q 939 " (cutoff:3.500A) Processing helix chain 'Q' and resid 960 through 968 removed outlier: 3.874A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE Q 968 " --> pdb=" O VAL Q 964 " (cutoff:3.500A) Processing helix chain 'Q' and resid 970 through 975 Processing helix chain 'Q' and resid 986 through 1018 removed outlier: 4.838A pdb=" N ALA Q1013 " --> pdb=" O GLU Q1009 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER Q1014 " --> pdb=" O GLU Q1010 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU Q1015 " --> pdb=" O PHE Q1011 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG Q1018 " --> pdb=" O SER Q1014 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1019 through 1030 Processing helix chain 'Q' and resid 1038 through 1046 Processing helix chain 'Q' and resid 1047 through 1053 Processing helix chain 'Q' and resid 1063 through 1068 removed outlier: 3.618A pdb=" N ILE Q1067 " --> pdb=" O GLU Q1063 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU Q1068 " --> pdb=" O ALA Q1064 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1063 through 1068' Processing helix chain 'Q' and resid 1069 through 1078 Proline residue: Q1075 - end of helix removed outlier: 3.916A pdb=" N LEU Q1078 " --> pdb=" O ILE Q1074 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1106 through 1113 removed outlier: 4.220A pdb=" N GLN Q1110 " --> pdb=" O ASN Q1106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1118 through 1127 Processing helix chain 'Q' and resid 1140 through 1148 removed outlier: 4.199A pdb=" N LEU Q1146 " --> pdb=" O SER Q1142 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR Q1147 " --> pdb=" O LEU Q1143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1157 through 1163 Processing helix chain 'Q' and resid 1200 through 1218 Processing helix chain 'Q' and resid 1220 through 1225 removed outlier: 3.766A pdb=" N ILE Q1224 " --> pdb=" O PRO Q1220 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER Q1225 " --> pdb=" O ALA Q1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1220 through 1225' Processing helix chain 'Q' and resid 1230 through 1245 Processing helix chain 'Q' and resid 1259 through 1264 removed outlier: 3.745A pdb=" N GLN Q1264 " --> pdb=" O VAL Q1260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1286 through 1296 removed outlier: 3.682A pdb=" N ARG Q1296 " --> pdb=" O VAL Q1292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1306 through 1314 removed outlier: 3.753A pdb=" N PHE Q1310 " --> pdb=" O ARG Q1306 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS Q1313 " --> pdb=" O LEU Q1309 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE Q1314 " --> pdb=" O PHE Q1310 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1316 through 1327 removed outlier: 4.235A pdb=" N GLN Q1322 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Q1325 " --> pdb=" O SER Q1321 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG Q1326 " --> pdb=" O GLN Q1322 " (cutoff:3.500A) Proline residue: Q1327 - end of helix Processing helix chain 'Q' and resid 1357 through 1376 removed outlier: 3.617A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 173 Processing helix chain 'V' and resid 177 through 189 removed outlier: 3.539A pdb=" N GLN V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU V 188 " --> pdb=" O GLU V 184 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 209 Proline residue: V 209 - end of helix Processing helix chain 'V' and resid 210 through 226 removed outlier: 6.210A pdb=" N VAL V 214 " --> pdb=" O ILE V 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS V 225 " --> pdb=" O ILE V 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 248 Processing helix chain 'V' and resid 249 through 267 Processing helix chain 'V' and resid 270 through 285 removed outlier: 4.472A pdb=" N CYS V 274 " --> pdb=" O HIS V 270 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG V 284 " --> pdb=" O LEU V 280 " (cutoff:3.500A) Proline residue: V 285 - end of helix Processing helix chain 'V' and resid 286 through 301 removed outlier: 3.579A pdb=" N GLU V 299 " --> pdb=" O GLY V 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 308 Processing helix chain 'V' and resid 309 through 325 Processing helix chain 'V' and resid 329 through 346 Processing helix chain 'V' and resid 379 through 384 removed outlier: 4.479A pdb=" N ASN V 383 " --> pdb=" O GLU V 379 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 379 through 384' Processing helix chain 'V' and resid 390 through 406 removed outlier: 3.571A pdb=" N GLU V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 449 through 467 removed outlier: 3.702A pdb=" N PHE V 455 " --> pdb=" O ASN V 451 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG V 456 " --> pdb=" O LEU V 452 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER V 466 " --> pdb=" O ALA V 462 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU V 467 " --> pdb=" O ILE V 463 " (cutoff:3.500A) Processing helix chain 'V' and resid 468 through 480 removed outlier: 4.955A pdb=" N CYS V 472 " --> pdb=" O ASP V 468 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 473 " --> pdb=" O PHE V 469 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU V 480 " --> pdb=" O LEU V 476 " (cutoff:3.500A) Processing helix chain 'V' and resid 482 through 501 removed outlier: 4.299A pdb=" N THR V 486 " --> pdb=" O PRO V 482 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS V 487 " --> pdb=" O GLU V 483 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU V 488 " --> pdb=" O SER V 484 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS V 490 " --> pdb=" O THR V 486 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG V 501 " --> pdb=" O CYS V 497 " (cutoff:3.500A) Processing helix chain 'V' and resid 504 through 519 removed outlier: 4.171A pdb=" N GLY V 508 " --> pdb=" O GLU V 504 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA V 511 " --> pdb=" O PHE V 507 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY V 512 " --> pdb=" O GLY V 508 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS V 515 " --> pdb=" O ALA V 511 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS V 518 " --> pdb=" O PHE V 514 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS V 519 " --> pdb=" O CYS V 515 " (cutoff:3.500A) Processing helix chain 'V' and resid 520 through 536 removed outlier: 3.584A pdb=" N GLN V 532 " --> pdb=" O ILE V 528 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR V 533 " --> pdb=" O PHE V 529 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP V 534 " --> pdb=" O LYS V 530 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR V 535 " --> pdb=" O GLU V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 540 through 558 removed outlier: 3.786A pdb=" N LEU V 544 " --> pdb=" O GLU V 540 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG V 545 " --> pdb=" O THR V 541 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN V 546 " --> pdb=" O ASN V 542 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS V 549 " --> pdb=" O ARG V 545 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU V 554 " --> pdb=" O MET V 550 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR V 557 " --> pdb=" O HIS V 553 " (cutoff:3.500A) Processing helix chain 'V' and resid 576 through 595 removed outlier: 4.200A pdb=" N GLU V 592 " --> pdb=" O GLN V 588 " (cutoff:3.500A) Processing helix chain 'V' and resid 596 through 607 removed outlier: 3.764A pdb=" N ASN V 600 " --> pdb=" O LEU V 596 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR V 607 " --> pdb=" O LEU V 603 " (cutoff:3.500A) Processing helix chain 'V' and resid 620 through 635 Processing helix chain 'V' and resid 640 through 648 Processing helix chain 'V' and resid 562 through 568 removed outlier: 3.879A pdb=" N CYS V 567 " --> pdb=" O VAL V 564 " (cutoff:3.500A) Processing helix chain 'V' and resid 608 through 613 removed outlier: 4.938A pdb=" N GLU V 613 " --> pdb=" O LEU V 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 608 through 613' Processing helix chain 'W' and resid 84 through 89 Processing helix chain 'W' and resid 101 through 106 removed outlier: 3.784A pdb=" N ALA W 106 " --> pdb=" O GLN W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 135 Processing helix chain 'W' and resid 156 through 162 removed outlier: 3.530A pdb=" N LYS W 161 " --> pdb=" O GLU W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 217 removed outlier: 3.733A pdb=" N LYS W 214 " --> pdb=" O GLU W 210 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU W 215 " --> pdb=" O GLU W 211 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP W 217 " --> pdb=" O GLN W 213 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 11 removed outlier: 4.295A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER X 11 " --> pdb=" O ASN X 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 5 through 11' Processing helix chain 'X' and resid 16 through 61 removed outlier: 3.793A pdb=" N ALA X 26 " --> pdb=" O LYS X 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS X 35 " --> pdb=" O GLU X 31 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU X 52 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N MET X 53 " --> pdb=" O ALA X 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 129 removed outlier: 4.394A pdb=" N LEU Y 113 " --> pdb=" O GLN Y 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU Y 115 " --> pdb=" O GLU Y 111 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Y 117 " --> pdb=" O LEU Y 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS Y 119 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG Y 120 " --> pdb=" O GLU Y 116 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL Y 121 " --> pdb=" O GLU Y 117 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN Y 122 " --> pdb=" O GLU Y 118 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS Y 123 " --> pdb=" O LYS Y 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Y 124 " --> pdb=" O ARG Y 120 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG Y 125 " --> pdb=" O VAL Y 121 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU Y 126 " --> pdb=" O GLN Y 122 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP Y 127 " --> pdb=" O LYS Y 123 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU Y 128 " --> pdb=" O GLU Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 165 removed outlier: 4.409A pdb=" N MET Y 134 " --> pdb=" O LEU Y 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU Y 160 " --> pdb=" O GLU Y 156 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASN Y 161 " --> pdb=" O LEU Y 157 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN Y 162 " --> pdb=" O LYS Y 158 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG Y 163 " --> pdb=" O ASP Y 159 " (cutoff:3.500A) Processing helix chain 'Y' and resid 166 through 205 removed outlier: 3.551A pdb=" N GLU Y 189 " --> pdb=" O ARG Y 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 509 removed outlier: 3.621A pdb=" N MET Z 509 " --> pdb=" O PHE Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 522 through 532 removed outlier: 4.119A pdb=" N LEU Z 532 " --> pdb=" O GLN Z 528 " (cutoff:3.500A) Processing helix chain 'Z' and resid 533 through 538 removed outlier: 3.674A pdb=" N VAL Z 537 " --> pdb=" O PRO Z 533 " (cutoff:3.500A) Processing helix chain 'Z' and resid 539 through 548 Processing helix chain 'Z' and resid 562 through 574 removed outlier: 3.779A pdb=" N THR Z 566 " --> pdb=" O THR Z 562 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN Z 567 " --> pdb=" O THR Z 563 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU Z 571 " --> pdb=" O GLN Z 567 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY Z 573 " --> pdb=" O LEU Z 569 " (cutoff:3.500A) Processing helix chain 'Z' and resid 586 through 602 Processing helix chain 'Z' and resid 629 through 641 Processing helix chain 'Z' and resid 658 through 672 Processing helix chain 'Z' and resid 689 through 696 Processing helix chain 'Z' and resid 722 through 735 Processing helix chain 'Z' and resid 749 through 766 Processing helix chain 'Z' and resid 783 through 792 removed outlier: 3.576A pdb=" N ILE Z 790 " --> pdb=" O LEU Z 786 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE Z 791 " --> pdb=" O GLN Z 787 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN Z 792 " --> pdb=" O ALA Z 788 " (cutoff:3.500A) Processing helix chain 'Z' and resid 805 through 811 removed outlier: 4.372A pdb=" N GLU Z 809 " --> pdb=" O THR Z 805 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR Z 810 " --> pdb=" O ASN Z 806 " (cutoff:3.500A) Processing helix chain 'Z' and resid 846 through 859 removed outlier: 4.021A pdb=" N ALA Z 857 " --> pdb=" O ARG Z 853 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY Z 858 " --> pdb=" O SER Z 854 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG Z 859 " --> pdb=" O GLY Z 855 " (cutoff:3.500A) Processing helix chain 'Z' and resid 870 through 876 Processing helix chain 'Z' and resid 891 through 902 removed outlier: 4.597A pdb=" N GLY Z 902 " --> pdb=" O LEU Z 898 " (cutoff:3.500A) Processing helix chain 'Z' and resid 916 through 931 Processing helix chain 'Z' and resid 940 through 950 removed outlier: 3.733A pdb=" N PHE Z 949 " --> pdb=" O LEU Z 945 " (cutoff:3.500A) Proline residue: Z 950 - end of helix Processing helix chain 'Z' and resid 952 through 966 removed outlier: 4.219A pdb=" N CYS Z 963 " --> pdb=" O LEU Z 959 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP Z 964 " --> pdb=" O ILE Z 960 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY Z 966 " --> pdb=" O SER Z 962 " (cutoff:3.500A) Processing helix chain 'Z' and resid 967 through 981 removed outlier: 3.696A pdb=" N VAL Z 980 " --> pdb=" O SER Z 976 " (cutoff:3.500A) Proline residue: Z 981 - end of helix Processing helix chain 'Z' and resid 990 through 1002 removed outlier: 3.823A pdb=" N PHE Z1001 " --> pdb=" O ILE Z 997 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1006 through 1022 removed outlier: 3.576A pdb=" N ASN Z1021 " --> pdb=" O GLN Z1017 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN Z1022 " --> pdb=" O TRP Z1018 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1024 through 1032 Processing helix chain 'Z' and resid 1034 through 1056 Processing helix chain 'Z' and resid 1064 through 1077 Processing helix chain 'Z' and resid 1106 through 1111 removed outlier: 4.264A pdb=" N MET Z1110 " --> pdb=" O SER Z1106 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY Z1111 " --> pdb=" O LEU Z1107 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 1106 through 1111' Processing helix chain 'Z' and resid 1137 through 1145 Processing helix chain 'q' and resid 26 through 37 removed outlier: 3.722A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 5.295A pdb=" N ILE q 53 " --> pdb=" O GLU q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 133 removed outlier: 3.729A pdb=" N LEU q 87 " --> pdb=" O ASP q 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE q 90 " --> pdb=" O MET q 86 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU q 92 " --> pdb=" O HIS q 88 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN q 95 " --> pdb=" O THR q 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR q 98 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN q 101 " --> pdb=" O GLN q 97 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG q 115 " --> pdb=" O ASP q 111 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR q 125 " --> pdb=" O THR q 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR q 133 " --> pdb=" O GLU q 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 37 Processing helix chain 'r' and resid 69 through 75 Processing helix chain 'r' and resid 78 through 133 removed outlier: 3.603A pdb=" N HIS r 88 " --> pdb=" O ALA r 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR r 125 " --> pdb=" O THR r 121 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA r 126 " --> pdb=" O LYS r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 71 through 134 removed outlier: 3.639A pdb=" N LEU s 75 " --> pdb=" O ILE s 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA s 84 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR s 91 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN s 95 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU s 102 " --> pdb=" O THR s 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU s 129 " --> pdb=" O THR s 125 " (cutoff:3.500A) Processing helix chain 's' and resid 200 through 207 removed outlier: 3.994A pdb=" N LYS s 206 " --> pdb=" O GLU s 202 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR s 207 " --> pdb=" O GLU s 203 " (cutoff:3.500A) Processing helix chain 's' and resid 483 through 488 removed outlier: 6.761A pdb=" N LYS s 488 " --> pdb=" O PHE s 483 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 483 through 488' Processing helix chain 't' and resid 71 through 132 removed outlier: 3.706A pdb=" N LYS t 76 " --> pdb=" O PRO t 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU t 87 " --> pdb=" O ASP t 83 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU t 92 " --> pdb=" O HIS t 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG t 93 " --> pdb=" O SER t 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN t 95 " --> pdb=" O THR t 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN t 109 " --> pdb=" O HIS t 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS t 114 " --> pdb=" O HIS t 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA t 118 " --> pdb=" O CYS t 114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG t 119 " --> pdb=" O ARG t 115 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 44 removed outlier: 3.876A pdb=" N MET u 43 " --> pdb=" O THR u 39 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY u 44 " --> pdb=" O PHE u 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 39 through 44' Processing helix chain 'u' and resid 46 through 57 Processing helix chain 'u' and resid 62 through 75 removed outlier: 3.678A pdb=" N ILE u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS u 70 " --> pdb=" O GLN u 66 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN u 71 " --> pdb=" O ARG u 67 " (cutoff:3.500A) Processing helix chain 'u' and resid 87 through 100 Processing helix chain 'u' and resid 115 through 131 Processing helix chain 'u' and resid 145 through 156 Processing helix chain 'u' and resid 163 through 174 Processing helix chain 'u' and resid 188 through 194 Processing helix chain 'u' and resid 195 through 209 removed outlier: 7.460A pdb=" N GLU u 199 " --> pdb=" O LYS u 195 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN u 200 " --> pdb=" O GLY u 196 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR u 207 " --> pdb=" O ASP u 203 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU u 208 " --> pdb=" O VAL u 204 " (cutoff:3.500A) Proline residue: u 209 - end of helix Processing helix chain 'u' and resid 222 through 233 removed outlier: 3.558A pdb=" N MET u 228 " --> pdb=" O GLU u 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR u 229 " --> pdb=" O ILE u 225 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN u 230 " --> pdb=" O LEU u 226 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS u 231 " --> pdb=" O GLU u 227 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) Processing helix chain 'u' and resid 242 through 247 removed outlier: 4.581A pdb=" N THR u 247 " --> pdb=" O ARG u 243 " (cutoff:3.500A) Processing helix chain 'u' and resid 260 through 276 removed outlier: 3.925A pdb=" N LYS u 264 " --> pdb=" O ARG u 260 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE u 265 " --> pdb=" O GLU u 261 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP u 266 " --> pdb=" O GLU u 262 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP u 273 " --> pdb=" O CYS u 269 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR u 274 " --> pdb=" O ASP u 270 " (cutoff:3.500A) Processing helix chain 'u' and resid 286 through 301 removed outlier: 3.501A pdb=" N ALA u 300 " --> pdb=" O LYS u 296 " (cutoff:3.500A) Processing helix chain 'u' and resid 312 through 326 Processing helix chain 'u' and resid 334 through 339 removed outlier: 4.040A pdb=" N ALA u 338 " --> pdb=" O THR u 334 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG u 339 " --> pdb=" O ASP u 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 334 through 339' Processing helix chain 'u' and resid 357 through 370 removed outlier: 3.629A pdb=" N TYR u 361 " --> pdb=" O ASN u 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE u 362 " --> pdb=" O ARG u 358 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER u 368 " --> pdb=" O ARG u 364 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY u 369 " --> pdb=" O ILE u 365 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG u 370 " --> pdb=" O GLY u 366 " (cutoff:3.500A) Processing helix chain 'u' and resid 384 through 397 removed outlier: 4.299A pdb=" N ILE u 388 " --> pdb=" O ASP u 384 " (cutoff:3.500A) Processing helix chain 'v' and resid 55 through 70 Processing helix chain 'v' and resid 108 through 115 Processing helix chain 'v' and resid 117 through 144 removed outlier: 4.108A pdb=" N VAL v 123 " --> pdb=" O GLU v 119 " (cutoff:3.500A) Processing helix chain 'w' and resid 85 through 94 Processing helix chain 'w' and resid 123 through 134 Processing helix chain 'x' and resid 171 through 176 removed outlier: 5.615A pdb=" N ARG x 176 " --> pdb=" O ASP x 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 14 removed outlier: 3.616A pdb=" N GLU h 14 " --> pdb=" O LEU h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 64 through 69 removed outlier: 3.501A pdb=" N ILE h 68 " --> pdb=" O ARG h 64 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG h 69 " --> pdb=" O GLY h 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 64 through 69' Processing helix chain 'h' and resid 74 through 79 removed outlier: 4.841A pdb=" N LYS h 78 " --> pdb=" O PRO h 74 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN h 79 " --> pdb=" O ASP h 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 74 through 79' Processing helix chain 'i' and resid 6 through 14 removed outlier: 4.263A pdb=" N LEU i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP i 14 " --> pdb=" O LEU i 10 " (cutoff:3.500A) Processing helix chain 'i' and resid 73 through 78 removed outlier: 3.792A pdb=" N LEU i 77 " --> pdb=" O ARG i 73 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL i 78 " --> pdb=" O GLY i 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 73 through 78' Processing helix chain 'j' and resid 2 through 11 removed outlier: 4.032A pdb=" N PHE j 6 " --> pdb=" O LYS j 2 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER j 11 " --> pdb=" O LEU j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 75 through 81 removed outlier: 3.655A pdb=" N VAL j 81 " --> pdb=" O ASP j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 27 Processing helix chain 'k' and resid 28 through 39 removed outlier: 4.808A pdb=" N LEU k 32 " --> pdb=" O PRO k 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 16 removed outlier: 5.813A pdb=" N GLY m 16 " --> pdb=" O ASN m 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 16 removed outlier: 5.812A pdb=" N GLY f 16 " --> pdb=" O ASN f 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'l' and resid 80 through 85 removed outlier: 4.509A pdb=" N ILE l 84 " --> pdb=" O LYS l 80 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR l 85 " --> pdb=" O GLY l 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 80 through 85' Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'e' and resid 80 through 85 removed outlier: 4.511A pdb=" N ILE e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR e 85 " --> pdb=" O GLY e 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 80 through 85' Processing helix chain 'n' and resid 63 through 68 removed outlier: 3.686A pdb=" N ILE n 67 " --> pdb=" O ARG n 63 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE n 68 " --> pdb=" O GLY n 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 63 through 68' Processing helix chain 'o' and resid 5 through 12 removed outlier: 3.512A pdb=" N GLN o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 87 removed outlier: 3.573A pdb=" N ALA o 86 " --> pdb=" O GLY o 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 102 through 113 removed outlier: 3.767A pdb=" N LEU o 106 " --> pdb=" O GLU o 102 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP o 107 " --> pdb=" O LEU o 103 " (cutoff:3.500A) Proline residue: o 108 - end of helix removed outlier: 4.647A pdb=" N SER o 111 " --> pdb=" O ASP o 107 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU o 112 " --> pdb=" O PRO o 108 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS o 113 " --> pdb=" O LEU o 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 102 through 113' Processing helix chain 'o' and resid 123 through 128 removed outlier: 4.534A pdb=" N ASN o 127 " --> pdb=" O ASN o 123 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS o 128 " --> pdb=" O PRO o 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 123 through 128' Processing helix chain 'o' and resid 130 through 139 Processing helix chain 'o' and resid 151 through 163 removed outlier: 4.599A pdb=" N PHE o 162 " --> pdb=" O ALA o 158 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 33 removed outlier: 4.194A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 69 removed outlier: 3.517A pdb=" N SER p 62 " --> pdb=" O GLU p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 88 through 96 Processing helix chain 'a' and resid 4 through 14 removed outlier: 3.614A pdb=" N GLU a 14 " --> pdb=" O LEU a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.501A pdb=" N ILE a 68 " --> pdb=" O ARG a 64 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 74 through 79 removed outlier: 4.840A pdb=" N LYS a 78 " --> pdb=" O PRO a 74 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN a 79 " --> pdb=" O ASP a 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 74 through 79' Processing helix chain 'b' and resid 7 through 14 removed outlier: 4.670A pdb=" N HIS b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 78 removed outlier: 3.791A pdb=" N LEU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL b 78 " --> pdb=" O GLY b 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 73 through 78' Processing helix chain 'c' and resid 2 through 11 removed outlier: 4.033A pdb=" N PHE c 6 " --> pdb=" O LYS c 2 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER c 11 " --> pdb=" O LEU c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 75 through 81 removed outlier: 3.655A pdb=" N VAL c 81 " --> pdb=" O ASP c 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 27 Processing helix chain 'd' and resid 28 through 39 removed outlier: 4.811A pdb=" N LEU d 32 " --> pdb=" O PRO d 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 removed outlier: 3.685A pdb=" N ILE g 67 " --> pdb=" O ARG g 63 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE g 68 " --> pdb=" O GLY g 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 68' Processing helix chain '1' and resid 18 through 27 Processing helix chain '1' and resid 56 through 67 Processing helix chain '1' and resid 165 through 178 Processing helix chain '1' and resid 255 through 260 removed outlier: 4.254A pdb=" N ASP 1 259 " --> pdb=" O THR 1 255 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY 1 260 " --> pdb=" O ASP 1 256 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 255 through 260' Processing helix chain '1' and resid 271 through 283 removed outlier: 3.713A pdb=" N GLN 1 281 " --> pdb=" O GLN 1 277 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY 1 282 " --> pdb=" O ILE 1 278 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER 1 283 " --> pdb=" O GLU 1 279 " (cutoff:3.500A) Processing helix chain '2' and resid 512 through 526 Processing helix chain '2' and resid 615 through 625 Processing helix chain '2' and resid 411 through 416 removed outlier: 6.798A pdb=" N ALA 2 416 " --> pdb=" O LYS 2 411 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 411 through 416' Processing helix chain '3' and resid 33 through 46 Processing helix chain '3' and resid 147 through 157 removed outlier: 3.611A pdb=" N GLN 3 157 " --> pdb=" O GLU 3 153 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 13 removed outlier: 3.806A pdb=" N ALA 4 12 " --> pdb=" O GLY 4 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA 4 13 " --> pdb=" O GLY 4 9 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 13' Processing helix chain '4' and resid 14 through 21 removed outlier: 3.809A pdb=" N ALA 4 21 " --> pdb=" O ALA 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 38 removed outlier: 6.532A pdb=" N ALA 4 33 " --> pdb=" O ALA 4 29 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= 2, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.254A pdb=" N GLN A 226 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR A 418 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG A 414 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 516 through 519 removed outlier: 4.323A pdb=" N ASN A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 904 through 911 removed outlier: 4.445A pdb=" N HIS A 904 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 1086 through 1091 Processing sheet with id= 6, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 8.688A pdb=" N THR A1225 " --> pdb=" O LYS A1199 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A1212 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 1333 through 1338 removed outlier: 6.566A pdb=" N VAL A1333 " --> pdb=" O GLY A1356 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A1356 " --> pdb=" O VAL A1333 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 1607 through 1611 removed outlier: 4.812A pdb=" N THR A1699 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY A1700 " --> pdb=" O ASN A1717 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 1636 through 1640 Processing sheet with id= 10, first strand: chain 'A' and resid 1785 through 1792 removed outlier: 6.184A pdb=" N VAL A1785 " --> pdb=" O GLY A1805 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A1805 " --> pdb=" O VAL A1785 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP A1782 " --> pdb=" O THR A1864 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1912 through 1919 removed outlier: 7.244A pdb=" N GLY A1815 " --> pdb=" O LEU A1919 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 2222 through 2229 removed outlier: 3.872A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A2124 " --> pdb=" O THR A2180 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN A2260 " --> pdb=" O TYR A2102 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 2270 through 2274 Processing sheet with id= 14, first strand: chain 'A' and resid 1805 through 1812 removed outlier: 3.619A pdb=" N GLN A1816 " --> pdb=" O ASN A1811 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 2126 through 2129 Processing sheet with id= 16, first strand: chain 'C' and resid 183 through 189 removed outlier: 6.415A pdb=" N GLY C 136 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 252 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 306 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 474 through 479 removed outlier: 7.614A pdb=" N LEU C 474 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU C 567 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN C 505 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'C' and resid 480 through 483 removed outlier: 3.623A pdb=" N LYS C 480 " --> pdb=" O PHE C 493 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 529 " --> pdb=" O GLU C 553 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 499 through 502 removed outlier: 6.717A pdb=" N GLY C 499 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 617 through 622 removed outlier: 3.634A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL C 587 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL C 660 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS C 589 " --> pdb=" O PRO C 658 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 591 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASP C 652 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 40.203A pdb=" N ILE C 653 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 35.336A pdb=" N ALA C 838 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 32.825A pdb=" N VAL C 655 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 28.871A pdb=" N VAL C 836 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 25.540A pdb=" N ASP C 657 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 21.507A pdb=" N VAL C 834 " --> pdb=" O ASP C 657 " (cutoff:3.500A) removed outlier: 16.147A pdb=" N VAL C 659 " --> pdb=" O TYR C 832 " (cutoff:3.500A) removed outlier: 12.741A pdb=" N TYR C 832 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR C 661 " --> pdb=" O PRO C 830 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS C 872 " --> pdb=" O THR C 858 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS C 856 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 673 through 678 removed outlier: 4.554A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET C 687 " --> pdb=" O CYS C 674 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 676 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASN C 683 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN C 743 " --> pdb=" O GLY C 736 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 736 " --> pdb=" O ASN C 743 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 682 through 686 removed outlier: 8.807A pdb=" N LYS C 682 " --> pdb=" O ALA C 797 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 797 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 827 through 838 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'C' and resid 859 through 862 Processing sheet with id= 25, first strand: chain 'D' and resid 434 through 438 removed outlier: 3.982A pdb=" N ALA D 449 " --> pdb=" O LEU D 685 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU D 685 " --> pdb=" O ALA D 449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 826 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 498 through 503 removed outlier: 3.961A pdb=" N ALA D 567 " --> pdb=" O ILE D 585 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 831 through 835 removed outlier: 7.963A pdb=" N THR D 831 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 1183 through 1192 removed outlier: 5.509A pdb=" N LYS D1183 " --> pdb=" O ASP D1207 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 1235 through 1242 removed outlier: 7.927A pdb=" N ALA D1220 " --> pdb=" O ASP D1273 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 1345 through 1350 removed outlier: 3.553A pdb=" N ILE D1424 " --> pdb=" O LYS D1404 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 1522 through 1529 removed outlier: 4.327A pdb=" N GLY D1618 " --> pdb=" O VAL D1643 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 1666 through 1671 removed outlier: 7.947A pdb=" N THR D1666 " --> pdb=" O TYR D1679 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 1802 through 1805 Processing sheet with id= 34, first strand: chain 'D' and resid 2017 through 2024 removed outlier: 4.962A pdb=" N VAL D2036 " --> pdb=" O VAL D2024 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D2043 " --> pdb=" O GLN D2086 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLN D2086 " --> pdb=" O ARG D2043 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 2078 through 2083 removed outlier: 6.755A pdb=" N GLY D2063 " --> pdb=" O ASP D2111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS D2102 " --> pdb=" O VAL D2124 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 59 through 63 removed outlier: 4.864A pdb=" N MET E 60 " --> pdb=" O MET E 353 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE E 341 " --> pdb=" O HIS E 336 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 70 through 75 removed outlier: 5.326A pdb=" N THR E 80 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER E 79 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E 92 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP E 100 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'E' and resid 113 through 118 removed outlier: 5.768A pdb=" N MET E 123 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER E 122 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 135 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 142 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 156 through 160 removed outlier: 4.888A pdb=" N LEU E 166 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY E 174 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 188 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'E' and resid 197 through 202 removed outlier: 5.631A pdb=" N GLN E 207 " --> pdb=" O ASN E 202 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ASP E 206 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY E 212 " --> pdb=" O ASP E 216 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP E 216 " --> pdb=" O GLY E 212 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 240 through 244 removed outlier: 3.783A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR E 249 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER E 248 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 291 through 294 removed outlier: 5.671A pdb=" N LYS E 299 " --> pdb=" O SER E 294 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER E 298 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL E 311 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG E 318 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 89 through 92 removed outlier: 4.669A pdb=" N ALA E 103 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 132 through 135 removed outlier: 3.537A pdb=" N LYS E 145 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 308 through 311 Processing sheet with id= 46, first strand: chain 'O' and resid 36 through 40 Processing sheet with id= 47, first strand: chain 'O' and resid 260 through 265 Processing sheet with id= 48, first strand: chain 'R' and resid 174 through 180 Processing sheet with id= 49, first strand: chain 'S' and resid 54 through 57 removed outlier: 4.343A pdb=" N ILE S 97 " --> pdb=" O THR S 115 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 130 through 133 removed outlier: 6.427A pdb=" N VAL S 24 " --> pdb=" O CYS S 133 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 193 through 197 removed outlier: 6.661A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 208 through 213 removed outlier: 5.467A pdb=" N TRP T 218 " --> pdb=" O GLU T 213 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLN T 217 " --> pdb=" O LEU T 233 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE T 230 " --> pdb=" O LYS T 239 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS T 237 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 250 through 255 removed outlier: 5.073A pdb=" N TYR T 260 " --> pdb=" O SER T 255 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN T 269 " --> pdb=" O GLY T 265 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS T 272 " --> pdb=" O ILE T 281 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 292 through 297 removed outlier: 4.831A pdb=" N VAL T 302 " --> pdb=" O HIS T 297 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE T 314 " --> pdb=" O VAL T 323 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA T 321 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'T' and resid 334 through 339 removed outlier: 4.772A pdb=" N GLN T 344 " --> pdb=" O GLN T 339 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU T 356 " --> pdb=" O ARG T 365 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS T 363 " --> pdb=" O ASP T 358 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 377 through 381 removed outlier: 3.710A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR T 386 " --> pdb=" O HIS T 381 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR T 385 " --> pdb=" O PHE T 400 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE T 400 " --> pdb=" O TYR T 385 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN T 407 " --> pdb=" O GLN T 397 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 417 through 421 removed outlier: 4.219A pdb=" N THR T 418 " --> pdb=" O GLY T 430 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 466 through 471 removed outlier: 5.803A pdb=" N ARG T 476 " --> pdb=" O ASP T 471 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 227 through 230 Processing sheet with id= 60, first strand: chain 'T' and resid 311 through 314 Processing sheet with id= 61, first strand: chain 'T' and resid 353 through 356 removed outlier: 3.655A pdb=" N VAL T 366 " --> pdb=" O LEU T 356 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'T' and resid 476 through 481 removed outlier: 3.508A pdb=" N THR T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 494 through 497 removed outlier: 3.505A pdb=" N GLY Q 501 " --> pdb=" O SER Q 497 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 511 through 514 removed outlier: 5.793A pdb=" N ASN Q 654 " --> pdb=" O ILE Q 514 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG Q 536 " --> pdb=" O VAL Q 520 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Q' and resid 711 through 714 removed outlier: 5.713A pdb=" N PHE Q 747 " --> pdb=" O PHE Q 714 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 1033 through 1037 Processing sheet with id= 67, first strand: chain 'Q' and resid 1176 through 1181 Processing sheet with id= 68, first strand: chain 'Q' and resid 1329 through 1333 Processing sheet with id= 69, first strand: chain 'W' and resid 282 through 285 removed outlier: 4.586A pdb=" N VAL W 566 " --> pdb=" O TRP W 578 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY W 555 " --> pdb=" O CYS W 569 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'W' and resid 293 through 297 removed outlier: 3.671A pdb=" N ALA W 293 " --> pdb=" O CYS W 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE W 297 " --> pdb=" O LEU W 303 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU W 303 " --> pdb=" O PHE W 297 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU W 315 " --> pdb=" O ARG W 326 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG W 326 " --> pdb=" O LEU W 315 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 336 through 341 removed outlier: 5.638A pdb=" N GLN W 346 " --> pdb=" O ASN W 341 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR W 345 " --> pdb=" O THR W 361 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR W 355 " --> pdb=" O ALA W 351 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 378 through 381 removed outlier: 4.264A pdb=" N CYS W 378 " --> pdb=" O GLY W 394 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN W 389 " --> pdb=" O ILE W 405 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS W 399 " --> pdb=" O MET W 395 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN W 402 " --> pdb=" O VAL W 411 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU W 409 " --> pdb=" O ASP W 404 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'W' and resid 423 through 427 removed outlier: 6.977A pdb=" N ARG W 432 " --> pdb=" O VAL W 427 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS W 454 " --> pdb=" O VAL W 444 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'W' and resid 466 through 470 removed outlier: 4.303A pdb=" N ALA W 466 " --> pdb=" O GLN W 479 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TRP W 475 " --> pdb=" O SER W 470 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS W 474 " --> pdb=" O ALA W 490 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN W 484 " --> pdb=" O SER W 480 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'W' and resid 514 through 517 removed outlier: 4.422A pdb=" N TYR W 522 " --> pdb=" O SER W 517 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL W 523 " --> pdb=" O ILE W 534 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE W 534 " --> pdb=" O VAL W 523 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER W 525 " --> pdb=" O LEU W 532 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU W 532 " --> pdb=" O SER W 525 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP W 527 " --> pdb=" O GLY W 530 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'W' and resid 399 through 402 Processing sheet with id= 77, first strand: chain 'Y' and resid 30 through 34 removed outlier: 5.073A pdb=" N PHE Y 74 " --> pdb=" O THR Y 91 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA Y 85 " --> pdb=" O CYS Y 80 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP Y 97 " --> pdb=" O ASP Y 92 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Y' and resid 41 through 44 No H-bonds generated for sheet with id= 78 Processing sheet with id= 79, first strand: chain 'Z' and resid 610 through 613 removed outlier: 6.315A pdb=" N CYS Z 618 " --> pdb=" O TYR Z 611 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Z' and resid 624 through 628 removed outlier: 3.796A pdb=" N ALA Z 648 " --> pdb=" O MET Z 579 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N SER Z 549 " --> pdb=" O LEU Z 678 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Z' and resid 709 through 716 removed outlier: 3.544A pdb=" N SER Z 716 " --> pdb=" O ARG Z 867 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET Z 818 " --> pdb=" O PRO Z 862 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'Z' and resid 742 through 746 Processing sheet with id= 83, first strand: chain 'Z' and resid 827 through 833 Processing sheet with id= 84, first strand: chain 'Z' and resid 1089 through 1092 removed outlier: 4.065A pdb=" N GLU Z1089 " --> pdb=" O LYS Z1085 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN Z1080 " --> pdb=" O TYR Z1119 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP Z1115 " --> pdb=" O LEU Z1084 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TYR Z1116 " --> pdb=" O VAL Z1136 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS Z1132 " --> pdb=" O HIS Z1120 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Z' and resid 1121 through 1124 Processing sheet with id= 86, first strand: chain 'r' and resid 15 through 18 Processing sheet with id= 87, first strand: chain 's' and resid 210 through 214 removed outlier: 3.970A pdb=" N SER s 498 " --> pdb=" O GLY s 494 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 's' and resid 226 through 230 removed outlier: 5.750A pdb=" N LYS s 236 " --> pdb=" O CYS s 230 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN s 235 " --> pdb=" O LYS s 251 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN s 245 " --> pdb=" O GLY s 241 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL s 248 " --> pdb=" O LEU s 257 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 's' and resid 268 through 273 removed outlier: 5.342A pdb=" N LEU s 278 " --> pdb=" O HIS s 273 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASP s 277 " --> pdb=" O VAL s 293 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE s 290 " --> pdb=" O VAL s 299 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 's' and resid 311 through 315 removed outlier: 3.622A pdb=" N GLY s 311 " --> pdb=" O SER s 324 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR s 320 " --> pdb=" O HIS s 315 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASP s 319 " --> pdb=" O ILE s 335 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR s 329 " --> pdb=" O SER s 325 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE s 332 " --> pdb=" O LEU s 341 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG s 339 " --> pdb=" O ASP s 334 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 's' and resid 355 through 359 removed outlier: 3.831A pdb=" N CYS s 355 " --> pdb=" O GLY s 368 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE s 364 " --> pdb=" O HIS s 359 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N LEU s 363 " --> pdb=" O LEU s 379 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN s 373 " --> pdb=" O THR s 369 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE s 376 " --> pdb=" O VAL s 385 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 's' and resid 396 through 401 removed outlier: 3.508A pdb=" N SER s 397 " --> pdb=" O ALA s 410 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR s 406 " --> pdb=" O SER s 401 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR s 405 " --> pdb=" O LEU s 421 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU s 418 " --> pdb=" O PHE s 427 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 's' and resid 440 through 444 removed outlier: 5.693A pdb=" N TYR s 449 " --> pdb=" O ASP s 444 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR s 448 " --> pdb=" O CYS s 462 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE s 459 " --> pdb=" O ILE s 468 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 's' and resid 245 through 248 Processing sheet with id= 95, first strand: chain 's' and resid 287 through 290 Processing sheet with id= 96, first strand: chain 's' and resid 329 through 332 Processing sheet with id= 97, first strand: chain 's' and resid 373 through 376 removed outlier: 3.511A pdb=" N ALA s 386 " --> pdb=" O ILE s 376 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 's' and resid 414 through 418 removed outlier: 5.664A pdb=" N SER s 414 " --> pdb=" O LEU s 432 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS s 428 " --> pdb=" O LEU s 418 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 's' and resid 456 through 459 Processing sheet with id=100, first strand: chain 'u' and resid 136 through 140 Processing sheet with id=101, first strand: chain 'u' and resid 304 through 307 removed outlier: 5.730A pdb=" N SER u 347 " --> pdb=" O LYS u 374 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA u 257 " --> pdb=" O MET u 403 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'v' and resid 46 through 54 removed outlier: 3.552A pdb=" N VAL v 46 " --> pdb=" O SER v 40 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER v 40 " --> pdb=" O VAL v 46 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY v 32 " --> pdb=" O VAL v 54 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'w' and resid 101 through 104 removed outlier: 3.744A pdb=" N ASN w 101 " --> pdb=" O GLU w 120 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'h' and resid 41 through 44 Processing sheet with id=105, first strand: chain 'h' and resid 54 through 59 removed outlier: 4.558A pdb=" N ARG h 54 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASN h 45 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS h 31 " --> pdb=" O ASN h 45 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS h 16 " --> pdb=" O LEU h 32 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'i' and resid 40 through 43 Processing sheet with id=107, first strand: chain 'i' and resid 63 through 68 removed outlier: 7.785A pdb=" N GLU i 63 " --> pdb=" O ARG i 49 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASP i 44 " --> pdb=" O THR i 30 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR i 30 " --> pdb=" O ASP i 44 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR i 15 " --> pdb=" O PHE i 31 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'j' and resid 52 through 55 removed outlier: 4.276A pdb=" N THR j 23 " --> pdb=" O LEU j 19 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'k' and resid 90 through 96 removed outlier: 3.706A pdb=" N LYS k 50 " --> pdb=" O CYS k 46 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN m 46 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR m 32 " --> pdb=" O ASN m 46 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS m 17 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN f 46 " --> pdb=" O TYR f 32 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR f 32 " --> pdb=" O ASN f 46 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS f 17 " --> pdb=" O LEU f 33 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'l' and resid 69 through 74 removed outlier: 5.724A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASN l 40 " --> pdb=" O SER l 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'e' and resid 69 through 74 removed outlier: 5.724A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN e 40 " --> pdb=" O SER e 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'n' and resid 54 through 57 removed outlier: 5.828A pdb=" N CYS n 45 " --> pdb=" O ILE n 57 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N HIS n 26 " --> pdb=" O MET n 48 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS n 16 " --> pdb=" O LEU n 73 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'o' and resid 13 through 16 removed outlier: 4.347A pdb=" N ALA o 13 " --> pdb=" O ASP o 25 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER o 50 " --> pdb=" O LEU o 26 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN o 72 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR o 96 " --> pdb=" O VAL o 71 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU o 121 " --> pdb=" O LEU o 95 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'p' and resid 39 through 42 removed outlier: 3.519A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE p 72 " --> pdb=" O MET p 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE p 81 " --> pdb=" O GLN p 70 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN p 70 " --> pdb=" O ILE p 81 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'a' and resid 41 through 44 Processing sheet with id=118, first strand: chain 'a' and resid 54 through 59 removed outlier: 4.558A pdb=" N ARG a 54 " --> pdb=" O TYR a 50 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN a 45 " --> pdb=" O LYS a 31 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS a 31 " --> pdb=" O ASN a 45 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS a 16 " --> pdb=" O LEU a 32 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'b' and resid 40 through 43 Processing sheet with id=120, first strand: chain 'b' and resid 63 through 68 removed outlier: 7.787A pdb=" N GLU b 63 " --> pdb=" O ARG b 49 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASP b 44 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR b 30 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR b 15 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'c' and resid 52 through 55 removed outlier: 4.275A pdb=" N THR c 23 " --> pdb=" O LEU c 19 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'd' and resid 89 through 96 removed outlier: 3.707A pdb=" N LYS d 50 " --> pdb=" O CYS d 46 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'g' and resid 53 through 57 removed outlier: 4.013A pdb=" N GLN g 53 " --> pdb=" O ALA g 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N CYS g 45 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS g 26 " --> pdb=" O MET g 48 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS g 16 " --> pdb=" O LEU g 73 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain '1' and resid 34 through 37 removed outlier: 5.610A pdb=" N ARG 1 6 " --> pdb=" O PHE 1 54 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain '1' and resid 197 through 201 removed outlier: 5.400A pdb=" N GLN 1 247 " --> pdb=" O ALA 1 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU 1 233 " --> pdb=" O THR 1 251 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY 1 232 " --> pdb=" O GLU 1 267 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU 1 267 " --> pdb=" O GLY 1 232 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU 1 234 " --> pdb=" O PHE 1 265 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL 1 263 " --> pdb=" O MET 1 236 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE 1 146 " --> pdb=" O ALA 1 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG 1 155 " --> pdb=" O MET 1 144 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET 1 144 " --> pdb=" O ARG 1 155 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN 1 157 " --> pdb=" O VAL 1 142 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL 1 142 " --> pdb=" O GLN 1 157 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU 1 159 " --> pdb=" O PRO 1 140 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN 1 141 " --> pdb=" O TYR 1 300 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain '1' and resid 217 through 220 No H-bonds generated for sheet with id=126 Processing sheet with id=127, first strand: chain '2' and resid 102 through 105 removed outlier: 4.009A pdb=" N LEU 2 429 " --> pdb=" O LYS 2 422 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain '2' and resid 117 through 121 removed outlier: 5.743A pdb=" N LEU 2 133 " --> pdb=" O GLU 2 121 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS 2 149 " --> pdb=" O SER 2 138 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY 2 152 " --> pdb=" O ASP 2 161 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain '2' and resid 171 through 176 removed outlier: 5.342A pdb=" N GLU 2 181 " --> pdb=" O PHE 2 176 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU 2 197 " --> pdb=" O PRO 2 186 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain '2' and resid 232 through 236 removed outlier: 3.594A pdb=" N ASN 2 232 " --> pdb=" O GLY 2 245 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER 2 241 " --> pdb=" O LYS 2 236 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain '2' and resid 250 through 253 Processing sheet with id=132, first strand: chain '2' and resid 275 through 279 removed outlier: 3.838A pdb=" N GLU 2 275 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR 2 284 " --> pdb=" O CYS 2 279 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS 2 293 " --> pdb=" O SER 2 289 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA 2 296 " --> pdb=" O ARG 2 305 " (cutoff:3.500A) Processing sheet with id=133, first strand: chain '2' and resid 319 through 323 removed outlier: 5.250A pdb=" N LEU 2 328 " --> pdb=" O SER 2 323 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLU 2 327 " --> pdb=" O ARG 2 342 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU 2 339 " --> pdb=" O ARG 2 348 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain '2' and resid 365 through 369 removed outlier: 5.707A pdb=" N GLY 2 377 " --> pdb=" O PHE 2 369 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU 2 376 " --> pdb=" O ARG 2 390 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain '2' and resid 534 through 537 removed outlier: 3.662A pdb=" N ARG 2 535 " --> pdb=" O GLN 2 543 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN 2 591 " --> pdb=" O ALA 2 581 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR 2 577 " --> pdb=" O THR 2 595 " (cutoff:3.500A) Processing sheet with id=136, first strand: chain '2' and resid 610 through 613 removed outlier: 6.806A pdb=" N HIS 2 504 " --> pdb=" O THR 2 613 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER 2 493 " --> pdb=" O LYS 2 646 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN 2 642 " --> pdb=" O HIS 2 497 " (cutoff:3.500A) Processing sheet with id=137, first strand: chain '2' and resid 149 through 152 Processing sheet with id=138, first strand: chain '2' and resid 293 through 296 Processing sheet with id=139, first strand: chain '2' and resid 335 through 339 removed outlier: 5.645A pdb=" N LEU 2 335 " --> pdb=" O VAL 2 353 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU 2 349 " --> pdb=" O GLU 2 339 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain '3' and resid 66 through 69 removed outlier: 5.333A pdb=" N GLN 3 123 " --> pdb=" O ALA 3 113 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU 3 109 " --> pdb=" O THR 3 127 " (cutoff:3.500A) Processing sheet with id=141, first strand: chain '3' and resid 142 through 145 removed outlier: 6.586A pdb=" N VAL 3 25 " --> pdb=" O ILE 3 145 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE 3 14 " --> pdb=" O ALA 3 21 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG 3 23 " --> pdb=" O PHE 3 12 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE 3 12 " --> pdb=" O ARG 3 23 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL 3 25 " --> pdb=" O CYS 3 10 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS 3 10 " --> pdb=" O VAL 3 25 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU 3 27 " --> pdb=" O PRO 3 8 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP 3 13 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing sheet with id=142, first strand: chain '3' and resid 10 through 13 removed outlier: 3.611A pdb=" N SER 3 173 " --> pdb=" O ASP 3 13 " (cutoff:3.500A) 5896 hydrogen bonds defined for protein. 17388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 221 hydrogen bonds 418 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 179 stacking parallelities Total time for adding SS restraints: 78.05 Time building geometry restraints manager: 38.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.53: 88401 1.53 - 1.89: 17723 1.89 - 2.26: 2 2.26 - 2.62: 2 2.62 - 2.99: 1 Bond restraints: 106129 Sorted by residual: bond pdb=" N VAL s 481 " pdb=" CA BVAL s 481 " ideal model delta sigma weight residual 1.458 2.461 -1.004 1.18e-02 7.18e+03 7.23e+03 bond pdb=" C GLY 2 187 " pdb=" N SER 2 196 " ideal model delta sigma weight residual 1.335 2.990 -1.655 1.97e-02 2.58e+03 7.06e+03 bond pdb=" N VAL s 481 " pdb=" CA AVAL s 481 " ideal model delta sigma weight residual 1.458 2.429 -0.972 1.18e-02 7.18e+03 6.78e+03 bond pdb=" CD ARG A 642 " pdb=" NE ARG A 642 " ideal model delta sigma weight residual 1.458 1.667 -0.209 1.40e-02 5.10e+03 2.23e+02 bond pdb=" C VAL s 481 " pdb=" CA BVAL s 481 " ideal model delta sigma weight residual 1.522 1.696 -0.174 1.22e-02 6.72e+03 2.04e+02 ... (remaining 106124 not shown) Histogram of bond angle deviations from ideal: 67.51 - 83.32: 2 83.32 - 99.13: 124 99.13 - 114.94: 60159 114.94 - 130.74: 82314 130.74 - 146.55: 480 Bond angle restraints: 143079 Sorted by residual: angle pdb=" O GLY 2 187 " pdb=" C GLY 2 187 " pdb=" N SER 2 196 " ideal model delta sigma weight residual 122.70 84.59 38.11 1.30e+00 5.92e-01 8.59e+02 angle pdb=" N VAL s 481 " pdb=" CA BVAL s 481 " pdb=" C VAL s 481 " ideal model delta sigma weight residual 108.46 67.51 40.95 1.49e+00 4.50e-01 7.55e+02 angle pdb=" N VAL s 481 " pdb=" CA AVAL s 481 " pdb=" C VAL s 481 " ideal model delta sigma weight residual 108.46 68.71 39.75 1.49e+00 4.50e-01 7.12e+02 angle pdb=" PB ATP u 702 " pdb=" O3B ATP u 702 " pdb=" PG ATP u 702 " ideal model delta sigma weight residual 139.87 117.98 21.89 1.00e+00 1.00e+00 4.79e+02 angle pdb=" C GLY 2 187 " pdb=" N SER 2 196 " pdb=" CA SER 2 196 " ideal model delta sigma weight residual 120.17 140.97 -20.80 1.54e+00 4.22e-01 1.82e+02 ... (remaining 143074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 54401 35.89 - 71.78: 2277 71.78 - 107.67: 206 107.67 - 143.56: 28 143.56 - 179.45: 17 Dihedral angle restraints: 56929 sinusoidal: 23472 harmonic: 33457 Sorted by residual: dihedral pdb=" CA PHE T 400 " pdb=" C PHE T 400 " pdb=" N PRO T 401 " pdb=" CA PRO T 401 " ideal model delta harmonic sigma weight residual -180.00 -54.00 -126.00 0 5.00e+00 4.00e-02 6.35e+02 dihedral pdb=" CA GLY 2 187 " pdb=" C GLY 2 187 " pdb=" N SER 2 196 " pdb=" CA SER 2 196 " ideal model delta harmonic sigma weight residual 180.00 62.09 117.91 0 5.00e+00 4.00e-02 5.56e+02 dihedral pdb=" CA PHE A 166 " pdb=" C PHE A 166 " pdb=" N PRO A 167 " pdb=" CA PRO A 167 " ideal model delta harmonic sigma weight residual -180.00 -70.18 -109.82 0 5.00e+00 4.00e-02 4.82e+02 ... (remaining 56926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 13311 0.951 - 1.902: 1 1.902 - 2.853: 0 2.853 - 3.803: 0 3.803 - 4.754: 2 Chirality restraints: 13314 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.24 -4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.14 -4.48 2.00e-01 2.50e+01 5.02e+02 chirality pdb=" CA PRO Y 13 " pdb=" N PRO Y 13 " pdb=" C PRO Y 13 " pdb=" CB PRO Y 13 " both_signs ideal model delta sigma weight residual False 2.72 0.97 1.74 2.00e-01 2.50e+01 7.60e+01 ... (remaining 13311 not shown) Planarity restraints: 18950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY 2 187 " 0.167 2.00e-02 2.50e+03 2.28e-01 5.22e+02 pdb=" C GLY 2 187 " -0.386 2.00e-02 2.50e+03 pdb=" O GLY 2 187 " 0.171 2.00e-02 2.50e+03 pdb=" N SER 2 196 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL s 481 " 0.246 2.00e-02 2.50e+03 1.43e-01 2.04e+02 pdb=" O VAL s 481 " -0.103 2.00e-02 2.50e+03 pdb=" CA BVAL s 481 " -0.057 2.00e-02 2.50e+03 pdb=" N ALA s 482 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL s 481 " 0.235 2.00e-02 2.50e+03 1.37e-01 1.87e+02 pdb=" O VAL s 481 " -0.098 2.00e-02 2.50e+03 pdb=" CA AVAL s 481 " -0.057 2.00e-02 2.50e+03 pdb=" N ALA s 482 " -0.080 2.00e-02 2.50e+03 ... (remaining 18947 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 56 1.88 - 2.64: 2490 2.64 - 3.39: 138816 3.39 - 4.15: 242584 4.15 - 4.90: 408081 Nonbonded interactions: 792027 Sorted by model distance: nonbonded pdb=" CG1 VAL A 852 " pdb=" NZ LYS A1449 " model vdw 1.129 3.540 nonbonded pdb=" O ALA Y 37 " pdb=" O LYS Y 52 " model vdw 1.219 3.040 nonbonded pdb=" OD1 ASP R 99 " pdb=" OG SER R 114 " model vdw 1.345 2.440 nonbonded pdb=" O6 G B 20 " pdb=" OP1 G B 24 " model vdw 1.388 3.040 nonbonded pdb=" OE2 GLU L 150 " pdb=" OH TYR Y 49 " model vdw 1.463 2.440 ... (remaining 792022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 4 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 46 or (resid 47 and (name N or name CA \ or name C or name O or name CB )) or resid 48 through 56 or (resid 57 and (name \ N or name CA or name C or name O )) or resid 58 through 79)) selection = (chain 'h' and resid 4 through 79) } ncs_group { reference = chain 'b' selection = (chain 'i' and resid 7 through 89) } ncs_group { reference = chain 'c' selection = (chain 'j' and resid 1 through 81) } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 4 through 48 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 76)) selection = (chain 'n' and (resid 4 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 76)) } ncs_group { reference = (chain 'q' and (resid 3 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 118 or (resid 119 and (name N or \ name CA or name C or name O or name CB )) or resid 120 through 133)) selection = (chain 'r' and (resid 3 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 133)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 17.920 Check model and map are aligned: 1.200 Set scattering table: 0.760 Process input model: 343.630 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.760 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 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 : 0.016 1.655 106129 Z= 1.001 Angle : 1.804 40.953 143079 Z= 1.185 Chirality : 0.116 4.754 13314 Planarity : 0.010 0.494 18950 Dihedral : 17.727 179.446 38802 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 1.71 % Allowed : 4.84 % Favored : 93.45 % Rotamer: Outliers : 8.31 % Allowed : 7.59 % Favored : 84.10 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 1.50 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.06), residues: 14863 helix: -1.11 (0.06), residues: 6124 sheet: -0.33 (0.10), residues: 2305 loop : -1.46 (0.07), residues: 6434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.010 TRP A 637 HIS 0.033 0.004 HIS A 680 PHE 0.067 0.007 PHE A 387 TYR 0.077 0.008 TYR u 371 ARG 0.056 0.002 ARG S 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29726 Ramachandran restraints generated. 14863 Oldfield, 0 Emsley, 14863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29726 Ramachandran restraints generated. 14863 Oldfield, 0 Emsley, 14863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2639 residues out of total 13490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 596 poor density : 2043 time to evaluate : 9.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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