Starting phenix.real_space_refine on Wed Mar 20 06:34:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6icz_9645/03_2024/6icz_9645_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 432 5.49 5 Mg 9 5.21 5 S 242 5.16 5 C 58799 2.51 5 N 18300 2.21 5 O 20111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A TYR 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A TYR 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C ARG 785": "NH1" <-> "NH2" Residue "C TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 342": "OE1" <-> "OE2" Residue "T PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 457": "NH1" <-> "NH2" Residue "V ARG 545": "NH1" <-> "NH2" Residue "V ARG 602": "NH1" <-> "NH2" Residue "W PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 266": "NH1" <-> "NH2" Residue "W PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 495": "NH1" <-> "NH2" Residue "X ARG 58": "NH1" <-> "NH2" Residue "X ARG 65": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 92": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "Z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 136": "NH1" <-> "NH2" Residue "Z ARG 139": "NH1" <-> "NH2" Residue "Z TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 97900 Number of models: 1 Model: "" Number of chains: 58 Chain: "v" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 711 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 6, 'TRANS': 137} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 295 Chain: "w" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 445 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 190 Chain: "u" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 1907 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 342} Link IDs: {'PTRANS': 12, 'TRANS': 373} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1244 Unresolved non-hydrogen angles: 1586 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 27, 'PHE:plan': 14, 'GLU:plan': 27, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 682 Chain: "x" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 124 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 17837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2253, 17837 Classifications: {'peptide': 2253} Incomplete info: {'truncation_to_alanine': 241} Link IDs: {'PCIS': 1, 'PTRANS': 125, 'TRANS': 2126} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 12, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 6, 'HIS:plan': 12, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 532 Chain: "B" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2040 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 16, 'rna3p_pur': 34, 'rna3p_pyr': 40} Link IDs: {'rna2p': 22, 'rna3p': 74} Chain: "C" Number of atoms: 7066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7066 Classifications: {'peptide': 894} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 839} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2366 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 10, 'TRANS': 292} Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 45, 'rna3p_pyr': 35} Link IDs: {'rna2p': 17, 'rna3p': 79} Chain: "G" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1549 Classifications: {'RNA': 84} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 38} Link IDs: {'rna2p': 13, 'rna3p': 70} Chain breaks: 3 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {' G%rna3p_pur:plan2': 7, ' C%rna3p_pyr:plan': 6, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 8, ' C%rna3p_pyr:plan2': 6, ' G%rna3p_pur:plan': 7, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 263 Chain: "H" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2966 Classifications: {'RNA': 140} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 12, 'rna3p_pur': 60, 'rna3p_pyr': 62} Link IDs: {'rna2p': 18, 'rna3p': 121} Chain breaks: 6 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: "L" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3064 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 18, 'TRANS': 435} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 716 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 407 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1098 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} 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: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2296 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain: "P" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 929 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 2 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2073 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 22, 'TRANS': 238} Chain breaks: 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: "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: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 2765 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 12, 'TRANS': 439} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 782 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 17, 'TYR:plan': 7, 'ASN:plan1': 22, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 14, 'GLU:plan': 29, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 520 Chain: "W" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4122 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 24, 'TRANS': 483} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 87} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "Z" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1999 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 15, 'TRANS': 226} Chain breaks: 1 Chain: "I" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 2782 Classifications: {'peptide': 564} Incomplete info: {'backbone_only': 15, 'truncation_to_alanine': 473} Link IDs: {'PTRANS': 18, 'TRANS': 545} Chain breaks: 32 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1921 Unresolved non-hydrogen angles: 2467 Unresolved non-hydrogen dihedrals: 1609 Unresolved non-hydrogen chiralities: 153 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': 57, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1179 Chain: "y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "Q" Number of atoms: 6562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 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: 2621 Conformer: "B" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 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: 2621 bond proxies already assigned to first conformer: 6533 Chain: "h" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 398 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "m" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "n" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 339 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "o" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 804 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 272 Chain: "p" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 464 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 163 Chain: "Y" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 2917 Classifications: {'peptide': 713} Incomplete info: {'backbone_only': 639, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 40, 'TRANS': 672} Chain breaks: 1 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 2859 Unresolved non-hydrogen angles: 4110 Unresolved non-hydrogen dihedrals: 1839 Unresolved non-hydrogen chiralities: 847 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 11, 'TYR:plan': 28, 'ASN:plan1': 18, 'TRP:plan': 5, 'ASP:plan': 40, 'PHE:plan': 25, 'GLU:plan': 51, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 1279 Chain: "a" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 399 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 480 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "f" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "g" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 363 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "K" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 757 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 320 Chain: "q" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 659 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "r" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 654 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "s" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "t" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "D" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 8530 Classifications: {'peptide': 1722} Incomplete info: {'truncation_to_alanine': 1541} Link IDs: {'PTRANS': 79, 'TRANS': 1642} Unresolved chain link angles: 79 Unresolved non-hydrogen bonds: 5611 Unresolved non-hydrogen angles: 7189 Unresolved non-hydrogen dihedrals: 4662 Unresolved non-hydrogen chiralities: 532 Planarities with less than four sites: {'GLN:plan1': 83, 'ASP:plan': 89, 'TYR:plan': 61, 'ASN:plan1': 70, 'TRP:plan': 19, 'HIS:plan': 52, 'PHE:plan': 65, 'GLU:plan': 125, 'ARG:plan': 88} Unresolved non-hydrogen planarities: 2997 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: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 47974 SG CYS N 105 66.712 179.199 120.153 1.00 8.96 S ATOM 48068 SG CYS N 117 66.648 176.191 117.929 1.00 14.99 S ATOM 48082 SG CYS N 119 63.481 177.920 118.496 1.00 14.40 S ATOM 48201 SG CYS N 134 65.552 175.893 121.259 1.00 15.26 S ATOM 47943 SG CYS N 101 64.159 181.531 119.103 1.00 11.48 S ATOM 47949 SG CYS N 102 66.948 182.599 121.641 1.00 9.32 S ATOM 47974 SG CYS N 105 66.712 179.199 120.153 1.00 8.96 S ATOM 48224 SG CYS N 137 63.963 181.224 122.576 1.00 14.71 S ATOM 47943 SG CYS N 101 64.159 181.531 119.103 1.00 11.48 S ATOM 48082 SG CYS N 119 63.481 177.920 118.496 1.00 14.40 S ATOM 48234 SG CYS N 139 60.706 179.657 119.583 1.00 17.96 S ATOM 48255 SG CYS N 142 62.110 180.624 116.290 1.00 18.34 S ATOM 48309 SG CYS O 24 74.357 144.798 123.668 1.00 27.56 S ATOM 48331 SG CYS O 27 73.650 148.690 124.528 1.00 23.84 S ATOM 48774 SG CYS O 81 76.958 147.279 124.473 1.00 22.90 S ATOM 48796 SG CYS O 84 72.718 146.359 126.918 1.00 28.74 S ATOM 48480 SG CYS O 45 87.199 151.709 133.523 1.00 17.41 S ATOM 48503 SG CYS O 48 90.336 150.226 133.279 1.00 17.79 S ATOM 48699 SG CYS O 71 88.767 149.876 129.960 1.00 14.03 S ATOM 48721 SG CYS O 74 88.022 147.523 132.088 1.00 21.74 S ATOM 49442 SG CYS O 165 60.003 164.045 136.631 1.00 31.92 S ATOM 49508 SG CYS O 173 57.505 166.676 136.269 1.00 32.96 S ATOM 49556 SG CYS O 179 60.162 165.150 133.154 1.00 39.81 S ATOM 65531 SG CYS Z 120 100.451 234.463 128.162 1.00 43.03 S ATOM 65554 SG CYS Z 123 97.007 234.174 129.167 1.00 37.66 S ATOM 65629 SG CYS Z 133 97.626 230.630 128.320 1.00 22.82 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N MET Q 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB MET Q 79 " occ=0.50 residue: pdb=" N MET Q 326 " occ=0.58 ... (3 atoms not shown) pdb=" CB MET Q 326 " occ=0.58 residue: pdb=" N HIS D1502 " occ=0.92 ... (3 atoms not shown) pdb=" CB HIS D1502 " occ=0.92 Time building chain proxies: 42.46, per 1000 atoms: 0.43 Number of scatterers: 97900 At special positions: 0 Unit cell: (240.84, 330.486, 349.218, 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 242 16.00 P 432 15.00 Mg 9 11.99 O 20111 8.00 N 18300 7.00 C 58799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.29 Conformation dependent library (CDL) restraints added in 16.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 117 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 134 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 119 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 101 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 102 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 137 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 105 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 142 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 139 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 101 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 27 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 24 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 84 " pdb=" ZN O 502 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 74 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 71 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 45 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 48 " pdb=" ZN O 503 " pdb="ZN ZN O 503 " - pdb=" NE2 HIS O 183 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 165 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 179 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 173 " pdb=" ZN Z 601 " pdb="ZN ZN Z 601 " - pdb=" NE2 HIS Z 128 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 120 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 133 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 123 " Number of angles added : 36 27820 Ramachandran restraints generated. 13910 Oldfield, 0 Emsley, 13910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 522 helices and 111 sheets defined 41.5% alpha, 12.5% beta 88 base pairs and 182 stacking pairs defined. Time for finding SS restraints: 36.56 Creating SS restraints... Processing helix chain 'v' and resid 40 through 42 No H-bonds generated for 'chain 'v' and resid 40 through 42' Processing helix chain 'v' and resid 54 through 67 Processing helix chain 'v' and resid 69 through 71 No H-bonds generated for 'chain 'v' and resid 69 through 71' Processing helix chain 'v' and resid 107 through 112 Processing helix chain 'v' and resid 116 through 141 removed outlier: 4.108A pdb=" N VAL v 121 " --> pdb=" O GLU v 117 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 96 removed outlier: 4.766A pdb=" N GLU w 95 " --> pdb=" O ASP w 91 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR w 96 " --> pdb=" O LYS w 92 " (cutoff:3.500A) Processing helix chain 'w' and resid 124 through 134 Processing helix chain 'u' and resid 40 through 42 No H-bonds generated for 'chain 'u' and resid 40 through 42' Processing helix chain 'u' and resid 47 through 56 Processing helix chain 'u' and resid 63 through 74 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 88 through 98 Processing helix chain 'u' and resid 116 through 129 Processing helix chain 'u' and resid 146 through 155 Processing helix chain 'u' and resid 164 through 172 Processing helix chain 'u' and resid 189 through 192 No H-bonds generated for 'chain 'u' and resid 189 through 192' Processing helix chain 'u' and resid 198 through 207 removed outlier: 4.172A pdb=" N TYR u 207 " --> pdb=" O ASP u 203 " (cutoff:3.500A) Processing helix chain 'u' and resid 223 through 231 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: 5.051A pdb=" N ASN u 230 " --> pdb=" O LEU u 226 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS u 231 " --> pdb=" O GLU u 227 " (cutoff:3.500A) Processing helix chain 'u' and resid 243 through 245 No H-bonds generated for 'chain 'u' and resid 243 through 245' Processing helix chain 'u' and resid 261 through 275 removed outlier: 3.611A pdb=" N ASP u 266 " --> pdb=" O TRP u 263 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP u 273 " --> pdb=" O ASP u 270 " (cutoff:3.500A) Processing helix chain 'u' and resid 287 through 300 removed outlier: 3.501A pdb=" N ALA u 300 " --> pdb=" O LYS u 296 " (cutoff:3.500A) Processing helix chain 'u' and resid 313 through 325 Processing helix chain 'u' and resid 335 through 337 No H-bonds generated for 'chain 'u' and resid 335 through 337' Processing helix chain 'u' and resid 358 through 367 removed outlier: 3.578A pdb=" N ILE u 362 " --> pdb=" O ARG u 358 " (cutoff:3.500A) Processing helix chain 'u' and resid 370 through 372 No H-bonds generated for 'chain 'u' and resid 370 through 372' Processing helix chain 'u' and resid 383 through 396 Processing helix chain 'x' and resid 172 through 174 No H-bonds generated for 'chain 'x' and resid 172 through 174' Processing helix chain 'A' and resid 27 through 44 removed outlier: 4.152A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.788A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 removed outlier: 4.388A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 3.507A 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 137 through 157 Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 542 through 565 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 616 removed outlier: 4.219A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 661 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 677 through 696 removed outlier: 3.706A pdb=" N LEU A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A 695 " --> pdb=" O HIS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 removed outlier: 3.937A pdb=" N LYS A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 819 Processing helix chain 'A' and resid 835 through 847 removed outlier: 3.729A pdb=" N LEU A 839 " --> pdb=" O ASP A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 913 through 932 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 990 through 998 Processing helix chain 'A' and resid 1003 through 1013 removed outlier: 4.031A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1053 removed outlier: 4.404A pdb=" N SER A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1044 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1045 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1053 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.835A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1234 through 1249 Processing helix chain 'A' and resid 1256 through 1273 removed outlier: 3.802A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1280 No H-bonds generated for 'chain 'A' and resid 1277 through 1280' Processing helix chain 'A' and resid 1282 through 1302 Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1340 through 1343 No H-bonds generated for 'chain 'A' and resid 1340 through 1343' Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'A' and resid 1375 through 1398 Processing helix chain 'A' and resid 1419 through 1422 Processing helix chain 'A' and resid 1427 through 1430 No H-bonds generated for 'chain 'A' and resid 1427 through 1430' Processing helix chain 'A' and resid 1436 through 1445 removed outlier: 3.800A pdb=" N THR A1440 " --> pdb=" O TRP A1436 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1477 removed outlier: 3.920A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1487 removed outlier: 4.450A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1520 through 1537 removed outlier: 4.200A pdb=" N SER A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A1525 " --> pdb=" O ALA A1521 " (cutoff:3.500A) Proline residue: A1530 - end of helix removed outlier: 3.514A pdb=" N PHE A1534 " --> pdb=" O PRO A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1570 through 1576 Processing helix chain 'A' and resid 1581 through 1599 removed outlier: 3.525A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 Processing helix chain 'A' and resid 1722 through 1736 Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1768 through 1771 removed outlier: 3.643A pdb=" N LEU A1771 " --> pdb=" O TYR A1768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1768 through 1771' Processing helix chain 'A' and resid 1824 through 1826 No H-bonds generated for 'chain 'A' and resid 1824 through 1826' Processing helix chain 'A' and resid 1833 through 1851 removed outlier: 4.563A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1875 Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1893 through 1898 Processing helix chain 'A' and resid 1900 through 1907 Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 removed outlier: 3.876A pdb=" N SER A1934 " --> pdb=" O TYR A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1954 Processing helix chain 'A' and resid 1973 through 1995 Processing helix chain 'A' and resid 1999 through 2001 No H-bonds generated for 'chain 'A' and resid 1999 through 2001' Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2071 through 2088 removed outlier: 3.744A 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: 4.451A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.561A 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) Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2167 through 2171 removed outlier: 4.055A pdb=" N GLU A2171 " --> pdb=" O TYR A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2202 removed outlier: 3.651A pdb=" N ASP A2202 " --> pdb=" O LYS A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2311 through 2314 No H-bonds generated for 'chain 'A' and resid 2311 through 2314' Processing helix chain 'A' and resid 2321 through 2325 Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 174 through 177 No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 209 through 221 removed outlier: 4.898A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 Processing helix chain 'C' and resid 261 through 265 removed outlier: 4.348A pdb=" N LEU C 265 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 292 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.903A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 441 through 452 Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 597 through 613 Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 694 through 701 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 756 through 774 Processing helix chain 'C' and resid 812 through 821 Processing helix chain 'C' and resid 844 through 853 Processing helix chain 'C' and resid 878 through 880 No H-bonds generated for 'chain 'C' and resid 878 through 880' Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 941 removed outlier: 5.805A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG C 931 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 941 " --> pdb=" O ARG C 938 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 217 through 238 removed outlier: 3.784A pdb=" N ASP J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 254 Processing helix chain 'J' and resid 258 through 271 Processing helix chain 'J' and resid 276 through 288 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 310 through 322 Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.542A pdb=" N GLU J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 355 Processing helix chain 'J' and resid 359 through 372 removed outlier: 3.848A pdb=" N LEU J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 388 Processing helix chain 'J' and resid 392 through 406 Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 429 through 440 Processing helix chain 'J' and resid 451 through 466 removed outlier: 3.544A pdb=" N ARG J 466 " --> pdb=" O PHE J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 490 Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 497 through 512 Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 541 through 548 removed outlier: 3.812A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA J 548 " --> pdb=" O GLU J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 550 through 554 Processing helix chain 'J' and resid 560 through 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 593 through 603 removed outlier: 3.949A pdb=" N THR J 598 " --> pdb=" O ARG J 594 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 623 removed outlier: 3.503A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 642 Processing helix chain 'J' and resid 650 through 659 removed outlier: 3.550A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.670A pdb=" N MET J 674 " --> pdb=" O PRO J 670 " (cutoff:3.500A) Proline residue: J 675 - end of helix removed outlier: 3.675A pdb=" N LEU J 678 " --> pdb=" O MET J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 700 through 707 Processing helix chain 'J' and resid 719 through 730 Processing helix chain 'J' and resid 741 through 755 removed outlier: 3.691A pdb=" N LEU J 755 " --> pdb=" O ARG J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 765 through 774 Processing helix chain 'J' and resid 782 through 799 Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 31 through 34 No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 43 through 50 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 107 Processing helix chain 'L' and resid 146 through 159 Processing helix chain 'L' and resid 165 through 193 Processing helix chain 'L' and resid 207 through 212 removed outlier: 4.084A pdb=" N TYR L 210 " --> pdb=" O GLY L 207 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN L 211 " --> pdb=" O VAL L 208 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA L 212 " --> pdb=" O ASP L 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 207 through 212' Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 252 through 269 Processing helix chain 'L' and resid 508 through 525 removed outlier: 3.800A pdb=" N ILE L 525 " --> pdb=" O ARG L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 533 Processing helix chain 'L' and resid 544 through 551 Proline residue: L 548 - end of helix Processing helix chain 'L' and resid 557 through 570 Proline residue: L 563 - end of helix Processing helix chain 'L' and resid 594 through 607 Processing helix chain 'L' and resid 615 through 628 Proline residue: L 620 - end of helix Processing helix chain 'L' and resid 691 through 794 removed outlier: 3.596A pdb=" N ARG L 695 " --> pdb=" O SER L 691 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY L 723 " --> pdb=" O ILE L 719 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR L 724 " --> pdb=" O LEU L 720 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU L 743 " --> pdb=" O TRP L 739 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN L 744 " --> pdb=" O ASP L 740 " (cutoff:3.500A) Proline residue: L 764 - end of helix removed outlier: 3.981A pdb=" N LEU L 767 " --> pdb=" O ILE L 763 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU L 768 " --> pdb=" O PRO L 764 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG L 780 " --> pdb=" O ARG L 776 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN L 785 " --> pdb=" O GLU L 781 " (cutoff:3.500A) removed outlier: 4.511A 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: 3.564A 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) Processing helix chain 'M' and resid 127 through 141 Processing helix chain 'M' and resid 146 through 160 removed outlier: 3.548A pdb=" N LYS M 155 " --> pdb=" O ARG M 151 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE M 160 " --> pdb=" O HIS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 195 removed outlier: 3.591A pdb=" N ARG M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 229 removed outlier: 4.169A pdb=" N LYS M 217 " --> pdb=" O GLU M 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE M 218 " --> pdb=" O ARG M 214 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS M 228 " --> pdb=" O ARG M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'N' and resid 13 through 34 removed outlier: 4.330A pdb=" N GLU N 16 " --> pdb=" O ASP N 13 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU N 19 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Proline residue: N 20 - end of helix removed outlier: 3.621A pdb=" N ASP N 23 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP N 26 " --> pdb=" O ASP N 23 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET N 29 " --> pdb=" O ASP N 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU N 33 " --> pdb=" O ARG N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 65 Proline residue: N 48 - end of helix removed outlier: 3.607A pdb=" N ILE N 52 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS N 54 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS N 56 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR N 57 " --> pdb=" O HIS N 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP N 62 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU N 63 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 80 Processing helix chain 'N' and resid 86 through 92 removed outlier: 3.576A pdb=" N LYS N 91 " --> pdb=" O ASN N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 106 No H-bonds generated for 'chain 'N' and resid 104 through 106' Processing helix chain 'N' and resid 123 through 125 No H-bonds generated for 'chain 'N' and resid 123 through 125' Processing helix chain 'O' and resid 72 through 78 Processing helix chain 'O' and resid 94 through 100 Processing helix chain 'O' and resid 111 through 126 Processing helix chain 'O' and resid 136 through 139 No H-bonds generated for 'chain 'O' and resid 136 through 139' Processing helix chain 'O' and resid 157 through 160 Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 198 through 203 Processing helix chain 'O' and resid 208 through 218 Processing helix chain 'O' and resid 245 through 254 removed outlier: 5.921A pdb=" N GLN O 254 " --> pdb=" O ASN O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 287 Processing helix chain 'P' and resid 51 through 55 Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'R' and resid 99 through 101 No H-bonds generated for 'chain 'R' and resid 99 through 101' Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing helix chain 'R' and resid 139 through 161 removed outlier: 4.027A pdb=" N ALA R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 245 removed outlier: 3.887A pdb=" N TRP R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 267 No H-bonds generated for 'chain 'R' and resid 264 through 267' Processing helix chain 'R' and resid 271 through 274 No H-bonds generated for 'chain 'R' and resid 271 through 274' Processing helix chain 'R' and resid 283 through 314 Processing helix chain 'S' and resid 33 through 45 Processing helix chain 'S' and resid 120 through 122 No H-bonds generated for 'chain 'S' and resid 120 through 122' Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 150 through 172 Processing helix chain 'V' and resid 178 through 187 removed outlier: 3.521A pdb=" N GLN V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 207 Processing helix chain 'V' and resid 209 through 225 removed outlier: 5.184A pdb=" N HIS V 213 " --> pdb=" O ILE V 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 246 Processing helix chain 'V' and resid 250 through 265 Processing helix chain 'V' and resid 272 through 283 Processing helix chain 'V' and resid 287 through 307 removed outlier: 3.552A pdb=" N GLU V 299 " --> pdb=" O GLY V 295 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU V 302 " --> pdb=" O LYS V 298 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS V 303 " --> pdb=" O GLU V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 309 through 324 Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 362 through 364 No H-bonds generated for 'chain 'V' and resid 362 through 364' Processing helix chain 'V' and resid 380 through 383 Processing helix chain 'V' and resid 391 through 405 removed outlier: 3.578A pdb=" N GLU V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 449 through 464 Processing helix chain 'V' and resid 469 through 479 Processing helix chain 'V' and resid 483 through 499 removed outlier: 3.530A pdb=" N LEU V 494 " --> pdb=" O CYS V 490 " (cutoff:3.500A) Processing helix chain 'V' and resid 505 through 517 Processing helix chain 'V' and resid 519 through 534 removed outlier: 3.731A pdb=" N ASP V 534 " --> pdb=" O LYS V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 536 through 538 No H-bonds generated for 'chain 'V' and resid 536 through 538' Processing helix chain 'V' and resid 541 through 556 Processing helix chain 'V' and resid 563 through 567 removed outlier: 4.043A pdb=" N CYS V 567 " --> pdb=" O VAL V 564 " (cutoff:3.500A) Processing helix chain 'V' and resid 577 through 594 Processing helix chain 'V' and resid 598 through 606 removed outlier: 4.012A pdb=" N ASP V 605 " --> pdb=" O ALA V 601 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU V 606 " --> pdb=" O ARG V 602 " (cutoff:3.500A) Processing helix chain 'V' and resid 621 through 634 Processing helix chain 'V' and resid 641 through 647 Processing helix chain 'W' and resid 85 through 88 No H-bonds generated for 'chain 'W' and resid 85 through 88' Processing helix chain 'W' and resid 102 through 105 No H-bonds generated for 'chain 'W' and resid 102 through 105' Processing helix chain 'W' and resid 122 through 134 Processing helix chain 'W' and resid 156 through 161 removed outlier: 4.070A pdb=" N GLU W 160 " --> pdb=" O GLU W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 227 removed outlier: 3.657A pdb=" N LYS W 214 " --> pdb=" O GLU W 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP W 217 " --> pdb=" O GLN W 213 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 141 removed outlier: 4.534A pdb=" N PHE X 79 " --> pdb=" O SER X 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS X 80 " --> pdb=" O GLY X 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG X 87 " --> pdb=" O HIS X 84 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN X 93 " --> pdb=" O TYR X 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP X 94 " --> pdb=" O GLN X 91 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 108 " --> pdb=" O LEU X 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU X 114 " --> pdb=" O LYS X 111 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN X 116 " --> pdb=" O LEU X 113 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS X 129 " --> pdb=" O LYS X 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 163 through 166 No H-bonds generated for 'chain 'Z' and resid 163 through 166' Processing helix chain 'Z' and resid 175 through 194 removed outlier: 3.806A pdb=" N LYS Z 180 " --> pdb=" O GLU Z 177 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 275 No H-bonds generated for 'chain 'Z' and resid 273 through 275' Processing helix chain 'Z' and resid 313 through 316 No H-bonds generated for 'chain 'Z' and resid 313 through 316' Processing helix chain 'Z' and resid 320 through 337 Processing helix chain 'Z' and resid 347 through 368 Processing helix chain 'I' and resid 157 through 165 Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 173 through 182 Proline residue: I 177 - end of helix Processing helix chain 'I' and resid 187 through 200 Processing helix chain 'I' and resid 205 through 217 Processing helix chain 'I' and resid 223 through 232 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 237 through 249 Processing helix chain 'I' and resid 255 through 266 Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.635A pdb=" N ARG I 276 " --> pdb=" O PHE I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 304 through 314 Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 338 through 350 Proline residue: I 342 - end of helix Processing helix chain 'I' and resid 356 through 365 removed outlier: 3.585A pdb=" N ARG I 363 " --> pdb=" O TRP I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 381 Processing helix chain 'I' and resid 388 through 397 Proline residue: I 394 - end of helix Processing helix chain 'I' and resid 404 through 414 Processing helix chain 'I' and resid 422 through 436 Processing helix chain 'I' and resid 441 through 458 removed outlier: 4.256A 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) Processing helix chain 'I' and resid 464 through 482 Proline residue: I 475 - end of helix Processing helix chain 'I' and resid 488 through 500 Processing helix chain 'I' and resid 508 through 523 Proline residue: I 518 - end of helix Processing helix chain 'I' and resid 528 through 541 removed outlier: 3.536A 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 Processing helix chain 'I' and resid 570 through 578 removed outlier: 4.378A pdb=" N ARG I 577 " --> pdb=" O LEU I 573 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 585 through 597 Proline residue: I 589 - end of helix Processing helix chain 'I' and resid 602 through 614 Processing helix chain 'I' and resid 616 through 635 removed outlier: 6.341A pdb=" N ARG I 621 " --> pdb=" O GLU I 617 " (cutoff:3.500A) 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: 3.529A pdb=" N TYR I 635 " --> pdb=" O MET I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 652 Processing helix chain 'I' and resid 664 through 675 removed outlier: 4.048A pdb=" N GLU I 675 " --> pdb=" O PHE I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 688 Processing helix chain 'I' and resid 707 through 719 Processing helix chain 'I' and resid 723 through 733 removed outlier: 3.723A 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: 3.705A pdb=" N GLN I 731 " --> pdb=" O ARG I 727 " (cutoff:3.500A) Processing helix chain 'I' and resid 741 through 755 removed outlier: 4.295A pdb=" N SER I 751 " --> pdb=" O LYS I 747 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 772 Processing helix chain 'I' and resid 780 through 791 Proline residue: I 788 - end of helix Processing helix chain 'I' and resid 798 through 817 Proline residue: I 816 - end of helix Processing helix chain 'y' and resid 19 through 29 Proline residue: y 28 - end of helix Processing helix chain 'y' and resid 57 through 67 Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 43 through 52 Processing helix chain 'Q' and resid 61 through 69 Processing helix chain 'Q' and resid 72 through 75 No H-bonds generated for 'chain 'Q' and resid 72 through 75' Processing helix chain 'Q' and resid 88 through 103 Processing helix chain 'Q' and resid 110 through 114 Processing helix chain 'Q' and resid 116 through 131 Proline residue: Q 120 - end of helix removed outlier: 3.610A pdb=" N LYS Q 128 " --> pdb=" O HIS Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 156 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: 5.339A pdb=" N GLN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU Q 169 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 177 Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 205 removed outlier: 4.000A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 221 through 235 Processing helix chain 'Q' and resid 244 through 261 Processing helix chain 'Q' and resid 264 through 276 removed outlier: 5.204A pdb=" N TRP Q 269 " --> pdb=" O PRO Q 265 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE Q 270 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 5.446A 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 284 Processing helix chain 'Q' and resid 287 through 290 No H-bonds generated for 'chain 'Q' and resid 287 through 290' Processing helix chain 'Q' and resid 296 through 309 Processing helix chain 'Q' and resid 323 through 344 Processing helix chain 'Q' and resid 346 through 353 removed outlier: 5.090A pdb=" N ASP Q 350 " --> pdb=" O GLU Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 359 No H-bonds generated for 'chain 'Q' and resid 356 through 359' Processing helix chain 'Q' and resid 362 through 369 Processing helix chain 'Q' and resid 374 through 384 Processing helix chain 'Q' and resid 400 through 411 Processing helix chain 'Q' and resid 417 through 423 Processing helix chain 'Q' and resid 462 through 491 removed outlier: 3.516A pdb=" N TYR Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU Q 480 " --> pdb=" O GLU Q 476 " (cutoff:3.500A) Processing helix chain 'Q' and resid 547 through 553 Processing helix chain 'Q' and resid 583 through 587 Processing helix chain 'Q' and resid 631 through 644 Processing helix chain 'Q' and resid 649 through 651 No H-bonds generated for 'chain 'Q' and resid 649 through 651' Processing helix chain 'Q' and resid 661 through 663 No H-bonds generated for 'chain 'Q' and resid 661 through 663' Processing helix chain 'Q' and resid 666 through 678 Processing helix chain 'Q' and resid 685 through 692 removed outlier: 4.795A pdb=" N ASP Q 689 " --> pdb=" O ASP Q 685 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE Q 690 " --> pdb=" O TRP Q 686 " (cutoff:3.500A) Processing helix chain 'Q' and resid 702 through 704 No H-bonds generated for 'chain 'Q' and resid 702 through 704' Processing helix chain 'Q' and resid 721 through 727 Processing helix chain 'Q' and resid 791 through 793 No H-bonds generated for 'chain 'Q' and resid 791 through 793' Processing helix chain 'Q' and resid 804 through 814 Processing helix chain 'Q' and resid 829 through 843 Processing helix chain 'Q' and resid 856 through 868 removed outlier: 3.809A pdb=" N ALA Q 868 " --> pdb=" O GLU Q 864 " (cutoff:3.500A) Processing helix chain 'Q' and resid 873 through 875 No H-bonds generated for 'chain 'Q' and resid 873 through 875' Processing helix chain 'Q' and resid 894 through 918 Processing helix chain 'Q' and resid 929 through 938 Processing helix chain 'Q' and resid 940 through 951 Processing helix chain 'Q' and resid 961 through 966 removed outlier: 3.872A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) Processing helix chain 'Q' and resid 987 through 1016 removed outlier: 4.836A pdb=" N ALA Q1013 " --> pdb=" O GLU Q1009 " (cutoff:3.500A) removed outlier: 5.330A 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) Processing helix chain 'Q' and resid 1020 through 1029 Processing helix chain 'Q' and resid 1039 through 1052 removed outlier: 5.524A pdb=" N HIS Q1047 " --> pdb=" O ALA Q1043 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP Q1048 " --> pdb=" O LEU Q1044 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1064 through 1066 No H-bonds generated for 'chain 'Q' and resid 1064 through 1066' Processing helix chain 'Q' and resid 1069 through 1077 Proline residue: Q1075 - end of helix Processing helix chain 'Q' and resid 1108 through 1113 Processing helix chain 'Q' and resid 1119 through 1126 Processing helix chain 'Q' and resid 1141 through 1150 removed outlier: 4.201A pdb=" N LEU Q1146 " --> pdb=" O SER Q1142 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR Q1147 " --> pdb=" O LEU Q1143 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP Q1149 " --> pdb=" O ASN Q1145 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG Q1150 " --> pdb=" O LEU Q1146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1158 through 1162 Processing helix chain 'Q' and resid 1164 through 1166 No H-bonds generated for 'chain 'Q' and resid 1164 through 1166' Processing helix chain 'Q' and resid 1201 through 1217 Processing helix chain 'Q' and resid 1221 through 1223 No H-bonds generated for 'chain 'Q' and resid 1221 through 1223' Processing helix chain 'Q' and resid 1231 through 1244 Processing helix chain 'Q' and resid 1260 through 1262 No H-bonds generated for 'chain 'Q' and resid 1260 through 1262' Processing helix chain 'Q' and resid 1282 through 1285 Processing helix chain 'Q' and resid 1287 through 1295 Processing helix chain 'Q' and resid 1307 through 1311 Processing helix chain 'Q' and resid 1314 through 1325 Proline residue: Q1318 - end of helix removed outlier: 4.546A pdb=" N SER Q1321 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR Q1324 " --> pdb=" O SER Q1321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1358 through 1375 removed outlier: 3.618A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.672A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.958A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.635A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.512A pdb=" N GLN o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 40 Processing helix chain 'o' and resid 83 through 86 No H-bonds generated for 'chain 'o' and resid 83 through 86' Processing helix chain 'o' and resid 103 through 111 Proline residue: o 108 - end of helix removed outlier: 3.566A pdb=" N SER o 111 " --> pdb=" O PRO o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 124 through 127 Processing helix chain 'o' and resid 131 through 138 Processing helix chain 'o' and resid 152 through 160 Processing helix chain 'p' and resid 20 through 34 removed outlier: 4.195A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE p 34 " --> pdb=" O LEU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 68 Processing helix chain 'p' and resid 89 through 95 Processing helix chain 'Y' and resid 397 through 407 Processing helix chain 'Y' and resid 535 through 543 Processing helix chain 'Y' and resid 553 through 564 Processing helix chain 'Y' and resid 566 through 580 removed outlier: 6.310A pdb=" N GLU Y 572 " --> pdb=" O LYS Y 569 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU Y 574 " --> pdb=" O LYS Y 571 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN Y 576 " --> pdb=" O GLN Y 573 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS Y 579 " --> pdb=" O GLN Y 576 " (cutoff:3.500A) Processing helix chain 'Y' and resid 594 through 605 removed outlier: 3.897A pdb=" N THR Y 599 " --> pdb=" O THR Y 595 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN Y 600 " --> pdb=" O THR Y 596 " (cutoff:3.500A) Processing helix chain 'Y' and resid 620 through 633 Processing helix chain 'Y' and resid 665 through 672 Processing helix chain 'Y' and resid 687 through 689 No H-bonds generated for 'chain 'Y' and resid 687 through 689' Processing helix chain 'Y' and resid 692 through 707 Processing helix chain 'Y' and resid 722 through 729 removed outlier: 3.599A pdb=" N GLN Y 727 " --> pdb=" O LYS Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 756 through 770 Processing helix chain 'Y' and resid 783 through 800 Processing helix chain 'Y' and resid 818 through 825 removed outlier: 3.623A pdb=" N ILE Y 824 " --> pdb=" O MET Y 820 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE Y 825 " --> pdb=" O GLN Y 821 " (cutoff:3.500A) Processing helix chain 'Y' and resid 840 through 842 No H-bonds generated for 'chain 'Y' and resid 840 through 842' Processing helix chain 'Y' and resid 881 through 892 removed outlier: 3.991A pdb=" N ALA Y 891 " --> pdb=" O ARG Y 887 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY Y 892 " --> pdb=" O ALA Y 888 " (cutoff:3.500A) Processing helix chain 'Y' and resid 905 through 910 Processing helix chain 'Y' and resid 919 through 922 Processing helix chain 'Y' and resid 926 through 935 Processing helix chain 'Y' and resid 951 through 963 Processing helix chain 'Y' and resid 975 through 982 Processing helix chain 'Y' and resid 987 through 993 Processing helix chain 'Y' and resid 996 through 999 No H-bonds generated for 'chain 'Y' and resid 996 through 999' Processing helix chain 'Y' and resid 1002 through 1013 Processing helix chain 'Y' and resid 1022 through 1035 removed outlier: 3.831A pdb=" N GLN Y1025 " --> pdb=" O LYS Y1022 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA Y1026 " --> pdb=" O ASP Y1023 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU Y1027 " --> pdb=" O LYS Y1024 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA Y1028 " --> pdb=" O GLN Y1025 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP Y1029 " --> pdb=" O ALA Y1026 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS Y1031 " --> pdb=" O ALA Y1028 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1041 through 1052 Processing helix chain 'Y' and resid 1059 through 1064 Processing helix chain 'Y' and resid 1069 through 1088 Processing helix chain 'Y' and resid 1099 through 1113 removed outlier: 6.601A pdb=" N ARG Y1113 " --> pdb=" O SER Y1109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1170 through 1176 Processing helix chain 'Y' and resid 1178 through 1181 No H-bonds generated for 'chain 'Y' and resid 1178 through 1181' Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'b' and resid 7 through 10 No H-bonds generated for 'chain 'b' and resid 7 through 10' Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.960A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'K' and resid 29 through 42 Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 106 through 134 Processing helix chain 'K' and resid 137 through 198 removed outlier: 3.648A pdb=" N ASN K 141 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.572A pdb=" N THR K 173 " --> pdb=" O ASN K 169 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA K 174 " --> pdb=" O MET K 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR K 193 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 36 removed outlier: 3.720A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (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: 3.560A pdb=" N PHE q 90 " --> pdb=" O MET q 86 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.723A pdb=" N GLN q 101 " --> pdb=" O GLN q 97 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG q 115 " --> pdb=" O ASP q 111 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR q 125 " --> pdb=" O THR q 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR q 133 " --> pdb=" O GLU q 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 36 Processing helix chain 'r' and resid 70 through 74 Processing helix chain 'r' and resid 76 through 132 removed outlier: 3.603A pdb=" N HIS r 88 " --> pdb=" O ALA r 84 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN r 97 " --> pdb=" O ARG r 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR r 98 " --> pdb=" O GLN r 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA r 112 " --> pdb=" O TYR r 108 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR r 125 " --> pdb=" O THR r 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA r 126 " --> pdb=" O LYS r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 72 through 133 removed outlier: 3.630A pdb=" N ALA s 84 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR s 91 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN s 95 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU s 102 " --> pdb=" O THR s 98 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.514A 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 '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: 3.687A 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: 3.522A pdb=" N ARG t 93 " --> pdb=" O SER t 89 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.509A 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: 3.547A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA t 118 " --> pdb=" O CYS t 114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG t 119 " --> pdb=" O ARG t 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 494 removed outlier: 5.462A pdb=" N ARG D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA D 491 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.933A pdb=" N LEU D 514 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG D 519 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 521 " --> pdb=" O LEU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 561 removed outlier: 3.674A pdb=" N LYS D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 590 through 599 Processing helix chain 'D' and resid 617 through 621 Processing helix chain 'D' and resid 623 through 642 Proline residue: D 626 - end of helix removed outlier: 3.833A pdb=" N VAL D 632 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 633 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 664 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 697 through 714 removed outlier: 4.104A pdb=" N GLN D 702 " --> pdb=" O ILE D 698 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN D 705 " --> pdb=" O PHE D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 734 removed outlier: 4.185A pdb=" N THR D 734 " --> pdb=" O THR D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 761 through 766 Processing helix chain 'D' and resid 773 through 777 Processing helix chain 'D' and resid 792 through 802 removed outlier: 3.532A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 817 Processing helix chain 'D' and resid 846 through 853 Processing helix chain 'D' and resid 873 through 883 removed outlier: 4.440A pdb=" N GLN D 877 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR D 879 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 882 " --> pdb=" O TYR D 879 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 883 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 906 Proline residue: D 898 - end of helix Processing helix chain 'D' and resid 913 through 922 removed outlier: 3.720A pdb=" N TYR D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 931 Processing helix chain 'D' and resid 933 through 936 No H-bonds generated for 'chain 'D' and resid 933 through 936' Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 950 through 955 Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 983 through 991 Processing helix chain 'D' and resid 995 through 1004 removed outlier: 3.740A pdb=" N GLN D 999 " --> pdb=" O ASN D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1020 removed outlier: 3.853A pdb=" N ARG D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1031 through 1042 removed outlier: 3.867A pdb=" N LEU D1035 " --> pdb=" O GLU D1032 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU D1037 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN D1038 " --> pdb=" O LEU D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1067 Processing helix chain 'D' and resid 1075 through 1102 removed outlier: 3.750A pdb=" N GLY D1089 " --> pdb=" O THR D1085 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1120 Processing helix chain 'D' and resid 1128 through 1131 Processing helix chain 'D' and resid 1137 through 1145 Processing helix chain 'D' and resid 1150 through 1152 No H-bonds generated for 'chain 'D' and resid 1150 through 1152' Processing helix chain 'D' and resid 1158 through 1162 removed outlier: 3.877A pdb=" N GLY D1162 " --> pdb=" O HIS D1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1158 through 1162' Processing helix chain 'D' and resid 1168 through 1180 removed outlier: 4.722A pdb=" N LYS D1172 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE D1174 " --> pdb=" O GLY D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1320 removed outlier: 4.442A pdb=" N LEU D1320 " --> pdb=" O ALA D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1330 through 1339 removed outlier: 4.788A pdb=" N ASN D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR D1338 " --> pdb=" O GLN D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1370 removed outlier: 3.573A pdb=" N ALA D1363 " --> pdb=" O CYS D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1396 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 1412 through 1418 Processing helix chain 'D' and resid 1431 through 1437 removed outlier: 3.664A pdb=" N LEU D1435 " --> pdb=" O LYS D1431 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER D1436 " --> pdb=" O TRP D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1443 through 1446 No H-bonds generated for 'chain 'D' and resid 1443 through 1446' Processing helix chain 'D' and resid 1456 through 1460 Processing helix chain 'D' and resid 1465 through 1480 Processing helix chain 'D' and resid 1497 through 1504 Processing helix chain 'D' and resid 1508 through 1510 No H-bonds generated for 'chain 'D' and resid 1508 through 1510' Processing helix chain 'D' and resid 1535 through 1541 Processing helix chain 'D' and resid 1543 through 1553 removed outlier: 3.626A pdb=" N TYR D1547 " --> pdb=" O ALA D1543 " (cutoff:3.500A) Processing helix chain 'D' and resid 1568 through 1582 removed outlier: 3.832A pdb=" N ALA D1582 " --> pdb=" O THR D1578 " (cutoff:3.500A) Processing helix chain 'D' and resid 1594 through 1603 removed outlier: 3.603A pdb=" N ILE D1598 " --> pdb=" O GLU D1594 " (cutoff:3.500A) Proline residue: D1599 - end of helix removed outlier: 4.736A pdb=" N LYS D1603 " --> pdb=" O PRO D1599 " (cutoff:3.500A) Processing helix chain 'D' and resid 1607 through 1614 removed outlier: 3.542A pdb=" N GLU D1611 " --> pdb=" O SER D1607 " (cutoff:3.500A) Processing helix chain 'D' and resid 1626 through 1638 Processing helix chain 'D' and resid 1648 through 1651 Processing helix chain 'D' and resid 1681 through 1690 Processing helix chain 'D' and resid 1711 through 1717 Processing helix chain 'D' and resid 1733 through 1741 Processing helix chain 'D' and resid 1748 through 1757 removed outlier: 3.620A pdb=" N TRP D1757 " --> pdb=" O ASP D1753 " (cutoff:3.500A) Processing helix chain 'D' and resid 1759 through 1765 removed outlier: 4.505A pdb=" N THR D1765 " --> pdb=" O TYR D1761 " (cutoff:3.500A) Processing helix chain 'D' and resid 1778 through 1798 Processing helix chain 'D' and resid 1814 through 1822 Processing helix chain 'D' and resid 1826 through 1835 Processing helix chain 'D' and resid 1842 through 1850 removed outlier: 3.679A pdb=" N GLU D1847 " --> pdb=" O ARG D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1853 through 1855 No H-bonds generated for 'chain 'D' and resid 1853 through 1855' Processing helix chain 'D' and resid 1867 through 1873 Processing helix chain 'D' and resid 1887 through 1899 Processing helix chain 'D' and resid 1906 through 1933 removed outlier: 3.746A 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: 4.351A 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: 3.755A pdb=" N LEU D1922 " --> pdb=" O LYS D1918 " (cutoff:3.500A) Processing helix chain 'D' and resid 1936 through 1951 Processing helix chain 'D' and resid 1959 through 1962 removed outlier: 3.940A pdb=" N GLN D1962 " --> pdb=" O TYR D1959 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1959 through 1962' Processing helix chain 'D' and resid 1968 through 1977 removed outlier: 3.681A pdb=" N LYS D1972 " --> pdb=" O SER D1968 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG D1973 " --> pdb=" O GLU D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2013 removed outlier: 3.713A pdb=" N PHE D2010 " --> pdb=" O ASP D2006 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'v' and resid 46 through 51 Processing sheet with id= B, first strand: chain 'w' and resid 145 through 148 removed outlier: 3.745A pdb=" N ASN w 101 " --> pdb=" O GLU w 120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'u' and resid 237 through 239 Processing sheet with id= D, first strand: chain 'u' and resid 400 through 402 removed outlier: 8.689A pdb=" N ASP u 401 " --> pdb=" O ILE u 251 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN u 253 " --> pdb=" O ASP u 401 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY u 375 " --> pdb=" O LYS u 252 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE u 254 " --> pdb=" O GLY u 375 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA u 377 " --> pdb=" O PHE u 254 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL u 256 " --> pdb=" O ALA u 377 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN u 379 " --> pdb=" O VAL u 256 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL u 258 " --> pdb=" O ASN u 379 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL u 381 " --> pdb=" O VAL u 258 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLN u 279 " --> pdb=" O SER u 347 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE u 349 " --> pdb=" O GLN u 279 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL u 281 " --> pdb=" O ILE u 349 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN u 351 " --> pdb=" O VAL u 281 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE u 283 " --> pdb=" O ASN u 351 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER u 305 " --> pdb=" O ILE u 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= F, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= G, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= H, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 6.550A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id= J, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 7.025A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id= L, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id= M, first strand: chain 'A' and resid 1711 through 1716 removed outlier: 8.308A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1637 through 1639 Processing sheet with id= O, first strand: chain 'A' and resid 1913 through 1918 removed outlier: 3.609A pdb=" N GLN A1816 " --> pdb=" O ASN A1811 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A1809 " --> pdb=" O PHE A1818 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 1788 through 1792 Processing sheet with id= Q, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.853A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A2126 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N VAL A2146 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A2260 " --> pdb=" O TYR A2104 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU A2106 " --> pdb=" O GLN A2260 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A2262 " --> pdb=" O LEU A2106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.447A pdb=" N PHE A2270 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 2150 through 2152 Processing sheet with id= T, first strand: chain 'A' and resid 2228 through 2230 Processing sheet with id= U, first strand: chain 'C' and resid 316 through 318 removed outlier: 9.516A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ARG C 130 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 347 through 350 Processing sheet with id= W, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.584A pdb=" N THR C 566 " --> pdb=" O LYS C 508 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 565 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= Y, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.567A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 663 through 666 removed outlier: 3.862A pdb=" N HIS C 903 " --> pdb=" O TYR C 831 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 743 through 747 removed outlier: 6.644A pdb=" N VAL C 787 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 746 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE C 789 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 831 through 838 removed outlier: 6.708A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.876A pdb=" N ALA E 103 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 132 through 137 removed outlier: 3.769A pdb=" N THR E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 114 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 154 through 158 removed outlier: 6.634A pdb=" N GLY E 170 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS E 157 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS E 168 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASP E 180 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA E 186 " --> pdb=" O ASP E 180 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.361A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY E 212 " --> pdb=" O ASP E 216 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP E 216 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 217 " --> pdb=" O MET E 231 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR E 229 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 261 through 263 Processing sheet with id= AH, first strand: chain 'E' and resid 299 through 302 removed outlier: 5.950A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 351 through 355 Processing sheet with id= AJ, first strand: chain 'O' and resid 36 through 39 Processing sheet with id= AK, first strand: chain 'O' and resid 299 through 302 Processing sheet with id= AL, first strand: chain 'R' and resid 175 through 180 Processing sheet with id= AM, first strand: chain 'S' and resid 159 through 163 removed outlier: 6.802A pdb=" N GLU S 17 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA S 162 " --> pdb=" O TYR S 15 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR S 15 " --> pdb=" O ALA S 162 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU S 26 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL S 132 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'S' and resid 55 through 57 Processing sheet with id= AO, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.661A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.565A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL T 254 " --> pdb=" O TYR T 260 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR T 260 " --> pdb=" O VAL T 254 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.805A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'T' and resid 333 through 338 removed outlier: 6.875A pdb=" N GLY T 348 " --> pdb=" O ALA T 334 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL T 336 " --> pdb=" O ILE T 346 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE T 346 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP T 358 " --> pdb=" O THR T 364 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR T 364 " --> pdb=" O ASP T 358 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 377 through 380 removed outlier: 3.815A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'T' and resid 416 through 421 removed outlier: 6.875A pdb=" N GLY T 430 " --> pdb=" O ASN T 417 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU T 419 " --> pdb=" O VAL T 428 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL T 428 " --> pdb=" O LEU T 419 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL T 421 " --> pdb=" O VAL T 426 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL T 426 " --> pdb=" O VAL T 421 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP T 440 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN T 446 " --> pdb=" O ASP T 440 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'T' and resid 194 through 200 removed outlier: 6.616A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA T 467 " --> pdb=" O ALA T 480 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'W' and resid 137 through 139 Processing sheet with id= AW, first strand: chain 'W' and resid 239 through 241 removed outlier: 3.870A pdb=" N ILE W 240 " --> pdb=" O THR W 327 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR W 327 " --> pdb=" O ILE W 240 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG W 326 " --> pdb=" O LEU W 315 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'W' and resid 335 through 340 removed outlier: 6.907A pdb=" N ALA W 350 " --> pdb=" O ARG W 336 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE W 338 " --> pdb=" O LEU W 348 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU W 348 " --> pdb=" O ILE W 338 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE W 340 " --> pdb=" O GLN W 346 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN W 346 " --> pdb=" O PHE W 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA W 351 " --> pdb=" O TYR W 355 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR W 355 " --> pdb=" O ALA W 351 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP W 360 " --> pdb=" O CYS W 366 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS W 366 " --> pdb=" O ASP W 360 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'W' and resid 379 through 381 Processing sheet with id= AZ, first strand: chain 'W' and resid 454 through 457 removed outlier: 3.768A pdb=" N LYS W 454 " --> pdb=" O VAL W 444 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER W 441 " --> pdb=" O SER W 437 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER W 437 " --> pdb=" O SER W 441 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR W 423 " --> pdb=" O THR W 436 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 467 through 469 removed outlier: 3.565A pdb=" N GLN W 484 " --> pdb=" O SER W 480 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 522 through 526 removed outlier: 6.693A pdb=" N ASP W 536 " --> pdb=" O LEU W 542 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU W 542 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 556 through 558 Processing sheet with id= BD, first strand: chain 'y' and resid 78 through 81 Processing sheet with id= BE, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id= BF, first strand: chain 'Q' and resid 511 through 513 removed outlier: 6.824A pdb=" N ARG Q 626 " --> pdb=" O GLN Q 598 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET Q 600 " --> pdb=" O THR Q 624 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR Q 624 " --> pdb=" O MET Q 600 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN Q 542 " --> pdb=" O ILE Q 514 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE Q 514 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'Q' and resid 732 through 735 removed outlier: 3.608A pdb=" N PHE Q 747 " --> pdb=" O ASN Q 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Q 715 " --> pdb=" O PHE Q 747 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Q 749 " --> pdb=" O ASP Q 713 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP Q 713 " --> pdb=" O ILE Q 749 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Q' and resid 1131 through 1133 Processing sheet with id= BI, first strand: chain 'Q' and resid 1177 through 1181 removed outlier: 6.782A pdb=" N LEU Q1301 " --> pdb=" O GLN Q1178 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE Q1180 " --> pdb=" O LEU Q1301 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE Q1303 " --> pdb=" O ILE Q1180 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 1330 through 1332 Processing sheet with id= BK, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BL, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.827A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.217A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.686A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BP, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BR, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.583A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= BS, 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) Processing sheet with id= BT, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.672A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.725A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.792A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.922A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.478A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'o' and resid 14 through 16 removed outlier: 7.107A pdb=" N ALA o 46 " --> pdb=" O LEU o 24 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR o 68 " --> pdb=" O ILE o 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'p' and resid 80 through 83 removed outlier: 3.519A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Y' and resid 734 through 737 removed outlier: 8.711A pdb=" N PHE Y 735 " --> pdb=" O ILE Y 583 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE Y 585 " --> pdb=" O PHE Y 735 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE Y 737 " --> pdb=" O ILE Y 585 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE Y 587 " --> pdb=" O ILE Y 737 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU Y 713 " --> pdb=" O LEU Y 584 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL Y 586 " --> pdb=" O LEU Y 713 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL Y 715 " --> pdb=" O VAL Y 586 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY Y 588 " --> pdb=" O VAL Y 715 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N SER Y 717 " --> pdb=" O GLY Y 588 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LYS Y 612 " --> pdb=" O ALA Y 680 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE Y 682 " --> pdb=" O LYS Y 612 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY Y 614 " --> pdb=" O ILE Y 682 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU Y 684 " --> pdb=" O GLY Y 614 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR Y 616 " --> pdb=" O LEU Y 684 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'Y' and resid 744 through 748 removed outlier: 6.903A pdb=" N GLY Y 897 " --> pdb=" O GLU Y 745 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU Y 747 " --> pdb=" O GLY Y 897 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS Y 899 " --> pdb=" O LEU Y 747 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP Y 775 " --> pdb=" O TYR Y 852 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL Y 854 " --> pdb=" O ASP Y 775 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU Y 777 " --> pdb=" O VAL Y 854 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP Y 856 " --> pdb=" O LEU Y 777 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE Y 779 " --> pdb=" O ASP Y 856 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE Y 808 " --> pdb=" O VAL Y 835 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE Y 837 " --> pdb=" O ILE Y 808 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU Y 810 " --> pdb=" O ILE Y 837 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'Y' and resid 859 through 866 Processing sheet with id= CD, first strand: chain 'Y' and resid 1124 through 1126 Processing sheet with id= CE, first strand: chain 'Y' and resid 1153 through 1156 Processing sheet with id= CF, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= CG, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.829A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.214A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.686A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= CK, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.028A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= CM, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.581A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.570A 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) Processing sheet with id= CO, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.670A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.722A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP e 59 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.923A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.473A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'q' and resid 15 through 17 Processing sheet with id= CU, first strand: chain 'r' and resid 15 through 17 Processing sheet with id= CV, first strand: chain 'D' and resid 435 through 438 removed outlier: 7.124A pdb=" N GLY D 865 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR D 688 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY D 867 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL D 690 " --> pdb=" O GLY D 867 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU D 869 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 692 " --> pdb=" O LEU D 869 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR D 871 " --> pdb=" O ILE D 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 826 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'D' and resid 673 through 675 removed outlier: 5.999A pdb=" N LEU D 500 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LYS D 537 " --> pdb=" O ARG D 610 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 612 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 539 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU D 614 " --> pdb=" O ILE D 539 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 541 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE D 586 " --> pdb=" O TYR D 540 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'D' and resid 832 through 835 Processing sheet with id= CY, first strand: chain 'D' and resid 970 through 972 Processing sheet with id= CZ, first strand: chain 'D' and resid 1250 through 1257 removed outlier: 5.936A pdb=" N LYS D1199 " --> pdb=" O PRO D1192 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU D1201 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D1190 " --> pdb=" O GLU D1201 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR D1203 " --> pdb=" O VAL D1188 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL D1188 " --> pdb=" O THR D1203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR D1205 " --> pdb=" O LEU D1186 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU D1186 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'D' and resid 1279 through 1285 Processing sheet with id= DB, first strand: chain 'D' and resid 1511 through 1513 removed outlier: 6.008A pdb=" N PHE D1347 " --> pdb=" O PHE D1512 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'D' and resid 1523 through 1530 removed outlier: 6.606A pdb=" N GLY D1700 " --> pdb=" O GLU D1524 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N HIS D1526 " --> pdb=" O GLY D1700 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS D1702 " --> pdb=" O HIS D1526 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN D1528 " --> pdb=" O CYS D1702 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE D1704 " --> pdb=" O GLN D1528 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE D1530 " --> pdb=" O ILE D1704 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS D1706 " --> pdb=" O PHE D1530 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'D' and resid 1667 through 1670 Processing sheet with id= DE, first strand: chain 'D' and resid 1802 through 1805 Processing sheet with id= DF, first strand: chain 'D' and resid 2017 through 2023 Processing sheet with id= DG, first strand: chain 'D' and resid 2118 through 2124 removed outlier: 3.767A pdb=" N HIS D2102 " --> pdb=" O VAL D2124 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP D2070 " --> pdb=" O LEU D2076 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D2076 " --> pdb=" O ASP D2070 " (cutoff:3.500A) 4539 hydrogen bonds defined for protein. 12319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 182 stacking parallelities Total time for adding SS restraints: 69.68 Time building geometry restraints manager: 34.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 97579 1.54 - 1.90: 2388 1.90 - 2.26: 2 2.26 - 2.62: 0 2.62 - 2.98: 5 Bond restraints: 99974 Sorted by residual: bond pdb=" CB LEU C 104 " pdb=" CG LEU C 104 " ideal model delta sigma weight residual 1.530 2.641 -1.111 2.00e-02 2.50e+03 3.09e+03 bond pdb=" CE1 PHE C 172 " pdb=" CZ PHE C 172 " ideal model delta sigma weight residual 1.382 2.980 -1.598 3.00e-02 1.11e+03 2.84e+03 bond pdb=" CD1 PHE C 172 " pdb=" CE1 PHE C 172 " ideal model delta sigma weight residual 1.382 2.951 -1.569 3.00e-02 1.11e+03 2.73e+03 bond pdb=" CD2 PHE C 172 " pdb=" CE2 PHE C 172 " ideal model delta sigma weight residual 1.382 2.927 -1.545 3.00e-02 1.11e+03 2.65e+03 bond pdb=" CE2 PHE C 172 " pdb=" CZ PHE C 172 " ideal model delta sigma weight residual 1.382 2.886 -1.504 3.00e-02 1.11e+03 2.51e+03 ... (remaining 99969 not shown) Histogram of bond angle deviations from ideal: 82.65 - 97.67: 56 97.67 - 112.69: 54207 112.69 - 127.72: 82589 127.72 - 142.74: 1342 142.74 - 157.76: 1 Bond angle restraints: 138195 Sorted by residual: angle pdb=" PB ATP Q1501 " pdb=" O3B ATP Q1501 " pdb=" PG ATP Q1501 " ideal model delta sigma weight residual 139.87 113.89 25.98 1.00e+00 1.00e+00 6.75e+02 angle pdb=" PA ATP Q1501 " pdb=" O3A ATP Q1501 " pdb=" PB ATP Q1501 " ideal model delta sigma weight residual 136.83 123.97 12.86 1.00e+00 1.00e+00 1.65e+02 angle pdb=" CD1 LEU C 104 " pdb=" CG LEU C 104 " pdb=" CD2 LEU C 104 " ideal model delta sigma weight residual 110.80 82.65 28.15 2.20e+00 2.07e-01 1.64e+02 angle pdb=" O3' U G 131 " pdb=" C3' U G 131 " pdb=" C2' U G 131 " ideal model delta sigma weight residual 113.70 95.51 18.19 1.50e+00 4.44e-01 1.47e+02 angle pdb=" CA LEU C 104 " pdb=" CB LEU C 104 " pdb=" CG LEU C 104 " ideal model delta sigma weight residual 116.30 157.76 -41.46 3.50e+00 8.16e-02 1.40e+02 ... (remaining 138190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 57828 35.36 - 70.71: 1366 70.71 - 106.07: 164 106.07 - 141.43: 23 141.43 - 176.79: 18 Dihedral angle restraints: 59399 sinusoidal: 19492 harmonic: 39907 Sorted by residual: dihedral pdb=" CA PRO Y 811 " pdb=" C PRO Y 811 " pdb=" N VAL Y 812 " pdb=" CA VAL Y 812 " ideal model delta harmonic sigma weight residual 180.00 101.82 78.18 0 5.00e+00 4.00e-02 2.44e+02 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 -104.67 -75.33 0 5.00e+00 4.00e-02 2.27e+02 dihedral pdb=" CA GLY T 457 " pdb=" C GLY T 457 " pdb=" N SER T 458 " pdb=" CA SER T 458 " ideal model delta harmonic sigma weight residual 180.00 113.13 66.87 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 59396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.975: 16465 0.975 - 1.949: 1 1.949 - 2.924: 0 2.924 - 3.899: 0 3.899 - 4.873: 2 Chirality restraints: 16468 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 2.35 -4.87 2.00e-01 2.50e+01 5.94e+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 2.39 -4.73 2.00e-01 2.50e+01 5.59e+02 chirality pdb=" CG LEU C 104 " pdb=" CB LEU C 104 " pdb=" CD1 LEU C 104 " pdb=" CD2 LEU C 104 " both_signs ideal model delta sigma weight residual False -2.59 -1.40 -1.19 2.00e-01 2.50e+01 3.54e+01 ... (remaining 16465 not shown) Planarity restraints: 17240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C H 40 " 0.073 2.00e-02 2.50e+03 8.83e-02 1.76e+02 pdb=" N1 C H 40 " -0.019 2.00e-02 2.50e+03 pdb=" C2 C H 40 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C H 40 " -0.115 2.00e-02 2.50e+03 pdb=" N3 C H 40 " 0.120 2.00e-02 2.50e+03 pdb=" C4 C H 40 " 0.145 2.00e-02 2.50e+03 pdb=" N4 C H 40 " -0.101 2.00e-02 2.50e+03 pdb=" C5 C H 40 " -0.037 2.00e-02 2.50e+03 pdb=" C6 C H 40 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U H 39 " 0.090 2.00e-02 2.50e+03 5.25e-02 6.21e+01 pdb=" N1 U H 39 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U H 39 " -0.076 2.00e-02 2.50e+03 pdb=" O2 U H 39 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U H 39 " 0.016 2.00e-02 2.50e+03 pdb=" C4 U H 39 " 0.069 2.00e-02 2.50e+03 pdb=" O4 U H 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U H 39 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U H 39 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU T 342 " 0.114 5.00e-02 4.00e+02 1.72e-01 4.71e+01 pdb=" N PRO T 343 " -0.296 5.00e-02 4.00e+02 pdb=" CA PRO T 343 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO T 343 " 0.073 5.00e-02 4.00e+02 ... (remaining 17237 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 45 2.22 - 2.89: 37941 2.89 - 3.56: 135791 3.56 - 4.23: 215073 4.23 - 4.90: 349342 Nonbonded interactions: 738192 Sorted by model distance: nonbonded pdb=" P G G 1 " pdb=" O2' A G 144 " model vdw 1.549 3.400 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C1501 " model vdw 1.571 2.170 nonbonded pdb=" O1G GTP C1500 " pdb="MG MG C1501 " model vdw 1.771 2.170 nonbonded pdb=" O GLN K 113 " pdb=" CB GLN K 117 " model vdw 1.873 2.752 nonbonded pdb=" O ALA K 112 " pdb=" CB HIS K 116 " model vdw 1.983 2.752 ... (remaining 738187 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 3 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 85)) selection = chain 'h' } ncs_group { reference = chain 'b' selection = chain 'i' } ncs_group { reference = chain 'c' selection = chain 'j' } 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' and resid 3 through 75) selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 3 through 48 or resid 54 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'q' and resid 3 through 133) selection = chain 'r' } ncs_group { reference = (chain 's' and resid 68 through 133) selection = (chain 't' and resid 68 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.770 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: 0.090 Extract box with map and model: 17.530 Check model and map are aligned: 1.070 Set scattering table: 0.810 Process input model: 273.300 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.670 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 310.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 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 : 0.015 1.598 99974 Z= 0.998 Angle : 1.443 41.461 138195 Z= 0.928 Chirality : 0.096 4.873 16468 Planarity : 0.007 0.172 17240 Dihedral : 15.570 176.787 33784 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.80 % Favored : 93.41 % Rotamer: Outliers : 1.39 % Allowed : 4.22 % Favored : 94.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.15 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.31 % 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: -2.81 (0.06), residues: 13910 helix: -1.89 (0.05), residues: 5960 sheet: -0.82 (0.11), residues: 1849 loop : -2.04 (0.07), residues: 6101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.005 TRP J 336 HIS 0.029 0.004 HIS C 140 PHE 0.055 0.004 PHE A 258 TYR 0.064 0.004 TYR J 282 ARG 0.036 0.002 ARG T 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27820 Ramachandran restraints generated. 13910 Oldfield, 0 Emsley, 13910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27820 Ramachandran restraints generated. 13910 Oldfield, 0 Emsley, 13910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 12613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1593 time to evaluate : 7.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable