Starting phenix.real_space_refine on Mon Mar 18 10:10:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahd_9624/03_2024/6ahd_9624_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 540 5.49 5 Mg 1 5.21 5 S 143 5.16 5 C 47287 2.51 5 N 17628 2.21 5 O 19703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1523": "NH1" <-> "NH2" Residue "A ARG 1617": "NH1" <-> "NH2" Residue "A GLU 1795": "OE1" <-> "OE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N ARG 302": "NH1" <-> "NH2" Residue "N ARG 351": "NH1" <-> "NH2" Residue "M ARG 84": "NH1" <-> "NH2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 186": "NH1" <-> "NH2" Residue "L PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 351": "NH1" <-> "NH2" Residue "L ARG 354": "NH1" <-> "NH2" Residue "9 GLU 122": "OE1" <-> "OE2" Residue "9 ARG 127": "NH1" <-> "NH2" Residue "9 GLU 268": "OE1" <-> "OE2" Residue "9 GLU 305": "OE1" <-> "OE2" Residue "9 ARG 307": "NH1" <-> "NH2" Residue "9 ARG 350": "NH1" <-> "NH2" Residue "9 GLU 352": "OE1" <-> "OE2" Residue "J ARG 525": "NH1" <-> "NH2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K ARG 129": "NH1" <-> "NH2" Residue "K ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 85302 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 17290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2209, 17290 Classifications: {'peptide': 2209} Incomplete info: {'backbone_only': 236} Link IDs: {'PTRANS': 127, 'TRANS': 2081} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1096 Unresolved non-hydrogen angles: 1586 Unresolved non-hydrogen dihedrals: 749 Unresolved non-hydrogen chiralities: 299 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 10, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'HIS:plan': 12, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 549 Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2881 Classifications: {'RNA': 136} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 17, 'rna3p_pur': 50, 'rna3p_pyr': 55} Link IDs: {'rna2p': 31, 'rna3p': 104} Chain breaks: 2 Chain: "B" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2420 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 38, 'rna3p_pyr': 59} Link IDs: {'rna2p': 17, 'rna3p': 97} Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1995 Classifications: {'RNA': 94} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 42, 'rna3p_pyr': 35} Link IDs: {'rna2p': 16, 'rna3p': 77} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1612 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 21, 'rna3p_pyr': 29} Link IDs: {'rna2p': 27, 'rna3p': 49} Chain breaks: 1 Chain: "O" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 6440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6440 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 769} Chain breaks: 1 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: "N" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 4518 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 463} Link IDs: {'PTRANS': 35, 'TRANS': 745} Chain breaks: 3 Unresolved non-hydrogen bonds: 1816 Unresolved non-hydrogen angles: 2303 Unresolved non-hydrogen dihedrals: 1546 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 14, 'TYR:plan': 10, 'ASN:plan1': 22, 'TRP:plan': 19, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 59, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1068 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2874 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "9" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1087 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 6, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 139 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1273 Classifications: {'peptide': 227} Incomplete info: {'backbone_only': 120, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 407 Unresolved non-hydrogen chiralities: 159 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 272 Chain: "a" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 344 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 101 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: 155 Chain: "b" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 328 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 113 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: 120 Chain: "c" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 388 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 92} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 399 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 120 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: 163 Chain: "d" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 88 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: 125 Chain: "e" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 316 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 100 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: 168 Chain: "f" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 67} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 88 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: 117 Chain: "g" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 324 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 102 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: 140 Chain: "E" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1196 Classifications: {'peptide': 299} Incomplete info: {'backbone_only': 275} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1197 Unresolved non-hydrogen angles: 1741 Unresolved non-hydrogen dihedrals: 785 Unresolved non-hydrogen chiralities: 355 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 16, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 7, 'ASP:plan': 22, 'PHE:plan': 11, 'GLU:plan': 11, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 589 Chain: "X" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 378 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 144 Chain: "W" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 844 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 158} Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 14, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 262 Chain: "A0" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 581 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "0" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 225 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 44} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 126 Chain: "Z" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 883 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 11, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 18, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 347 Chain: "8" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 277 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "Y" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 2258 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 387} Link IDs: {'PTRANS': 11, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 1374 Unresolved non-hydrogen angles: 1750 Unresolved non-hydrogen dihedrals: 1141 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 14, 'TYR:plan': 11, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 25, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 762 Chain: "H" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2311 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 48, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 94} Chain breaks: 3 Chain: "h" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 320 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 100 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: 140 Chain: "i" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 344 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 101 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: 155 Chain: "j" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 328 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 113 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: 120 Chain: "k" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 340 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 82} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 109 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: 163 Chain: "l" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 88 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: 125 Chain: "m" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 316 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 100 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: 168 Chain: "n" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 272 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 82 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: 113 Chain: "o" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 648 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 156} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 984 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 213 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: 305 Chain: "p" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 376 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 88} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 569 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 112 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: 184 Chain: "u" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 496 Classifications: {'peptide': 124} Incomplete info: {'backbone_only': 122} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 11, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 325 Chain: "v" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 376 Classifications: {'peptide': 94} Incomplete info: {'backbone_only': 92} Link IDs: {'PTRANS': 10, 'TRANS': 83} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 450 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 232 Chain: "w" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 1693 Classifications: {'peptide': 423} Incomplete info: {'backbone_only': 401, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 412} Chain breaks: 4 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1892 Unresolved non-hydrogen angles: 2694 Unresolved non-hydrogen dihedrals: 1262 Unresolved non-hydrogen chiralities: 495 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 23, 'TYR:plan': 20, 'ASN:plan1': 21, 'TRP:plan': 6, 'HIS:plan': 14, 'PHE:plan': 16, 'GLU:plan': 56, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 1033 Chain: "q" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 360 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 87} Link IDs: {'PTRANS': 3, 'TRANS': 86} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 535 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 163 Chain: "r" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 70} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 143 Chain: "s" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 71} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 136 Chain: "t" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 288 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 67} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "x" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 280 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 63} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "y" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 260 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 58} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "z" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 244 Classifications: {'peptide': 61} Incomplete info: {'backbone_only': 55} Link IDs: {'TRANS': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 300 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 69} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "Q" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 292 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 58} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 83 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: 125 Chain: "R" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 314 Classifications: {'peptide': 78} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 99 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: 168 Chain: "S" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 298 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 63} Link IDs: {'PTRANS': 3, 'TRANS': 69} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 87 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: 117 Chain: "T" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 288 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 63} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "U" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 256 Classifications: {'peptide': 64} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "V" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 334 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 114 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: 120 Chain: "K" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 1821 Classifications: {'peptide': 414} Incomplete info: {'backbone_only': 313, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1544 Unresolved non-hydrogen angles: 2227 Unresolved non-hydrogen dihedrals: 1057 Unresolved non-hydrogen chiralities: 415 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 18, 'TYR:plan': 10, 'ASN:plan1': 17, 'TRP:plan': 13, 'ASP:plan': 21, 'PHE:plan': 13, 'GLU:plan': 21, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 804 Chain: "1" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 4192 Classifications: {'peptide': 1048} Incomplete info: {'backbone_only': 982} Link IDs: {'PTRANS': 63, 'TRANS': 984} Chain breaks: 7 Unresolved chain link angles: 63 Unresolved non-hydrogen bonds: 4251 Unresolved non-hydrogen angles: 6148 Unresolved non-hydrogen dihedrals: 2717 Unresolved non-hydrogen chiralities: 1293 Planarities with less than four sites: {'GLN:plan1': 38, 'ARG:plan': 61, 'TYR:plan': 40, 'ASN:plan1': 35, 'TRP:plan': 11, 'ASP:plan': 57, 'PHE:plan': 25, 'GLU:plan': 72, 'HIS:plan': 26} Unresolved non-hydrogen planarities: 1874 Chain: "3" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 4672 Classifications: {'peptide': 1168} Incomplete info: {'backbone_only': 1090} Link IDs: {'PTRANS': 59, 'TRANS': 1108} Chain breaks: 7 Unresolved chain link angles: 59 Unresolved non-hydrogen bonds: 4679 Unresolved non-hydrogen angles: 6798 Unresolved non-hydrogen dihedrals: 2943 Unresolved non-hydrogen chiralities: 1442 Planarities with less than four sites: {'GLN:plan1': 47, 'ASP:plan': 62, 'TYR:plan': 37, 'ASN:plan1': 55, 'TRP:plan': 7, 'HIS:plan': 25, 'PHE:plan': 57, 'GLU:plan': 84, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 2207 Chain: "5" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 432 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 102} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 250 Chain: "6" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 356 Classifications: {'peptide': 89} Incomplete info: {'backbone_only': 79} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 141 Chain: "7" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 264 Classifications: {'peptide': 66} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "2" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 728 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 170} Link IDs: {'PTRANS': 18, 'TRANS': 163} Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 801 Unresolved non-hydrogen angles: 1137 Unresolved non-hydrogen dihedrals: 549 Unresolved non-hydrogen chiralities: 212 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 361 Chain: "4" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 312 Classifications: {'peptide': 78} Incomplete info: {'backbone_only': 71} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "D" Number of atoms: 6796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1699, 6796 Classifications: {'peptide': 1699} Incomplete info: {'backbone_only': 1620} Link IDs: {'PTRANS': 78, 'TRANS': 1620} Unresolved chain link angles: 78 Unresolved non-hydrogen bonds: 7158 Unresolved non-hydrogen angles: 10336 Unresolved non-hydrogen dihedrals: 4602 Unresolved non-hydrogen chiralities: 2146 Planarities with less than four sites: {'GLN:plan1': 81, 'HIS:plan': 51, 'TYR:plan': 61, 'ASN:plan1': 69, 'TRP:plan': 19, 'ASP:plan': 87, 'PHE:plan': 63, 'GLU:plan': 124, 'ARG:plan': 87} Unresolved non-hydrogen planarities: 3304 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS D1502 " occ=0.92 ... (2 atoms not shown) pdb=" O HIS D1502 " occ=0.92 Time building chain proxies: 36.44, per 1000 atoms: 0.43 Number of scatterers: 85302 At special positions: 0 Unit cell: (272.952, 327.81, 347.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 540 15.00 Mg 1 11.99 O 19703 8.00 N 17628 7.00 C 47287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1194 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS O 38 " - pdb=" SG CYS O 79 " distance=2.01 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 308 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.80 Conformation dependent library (CDL) restraints added in 13.6 seconds 27704 Ramachandran restraints generated. 13852 Oldfield, 0 Emsley, 13852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 487 helices and 148 sheets defined 36.5% alpha, 15.9% beta 122 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 33.80 Creating SS restraints... Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 84 through 93 removed outlier: 4.462A pdb=" N GLY A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.923A pdb=" N ASN A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 409 through 412 No H-bonds generated for 'chain 'A' and resid 409 through 412' 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 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.549A pdb=" N ALA A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.270A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' 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: 4.389A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 616 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.907A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.558A pdb=" N GLU A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 696 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 removed outlier: 3.552A pdb=" N LYS A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 819 Processing helix chain 'A' and resid 835 through 850 removed outlier: 4.515A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.655A pdb=" N ILE A 867 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 913 through 932 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 990 through 998 removed outlier: 4.195A pdb=" N ARG A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 Processing helix chain 'A' and resid 1037 through 1061 removed outlier: 7.996A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1124 through 1127 No H-bonds generated for 'chain 'A' and resid 1124 through 1127' Processing helix chain 'A' and resid 1145 through 1160 Processing helix chain 'A' and resid 1234 through 1250 removed outlier: 3.928A pdb=" N PHE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A1241 " --> pdb=" O MET A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1274 Processing helix chain 'A' and resid 1282 through 1303 removed outlier: 4.024A pdb=" N ASP A1286 " --> pdb=" O GLN A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1317 No H-bonds generated for 'chain 'A' and resid 1314 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 1337 through 1340 No H-bonds generated for 'chain 'A' and resid 1337 through 1340' 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 1397 removed outlier: 3.703A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1422 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 4.538A pdb=" N HIS A1428 " --> pdb=" O LYS A1425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1430 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1445 removed outlier: 4.887A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1478 Processing helix chain 'A' and resid 1480 through 1485 Processing helix chain 'A' and resid 1508 through 1515 removed outlier: 5.546A pdb=" N TRP A1515 " --> pdb=" O GLU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1535 Proline residue: A1530 - end of helix 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 1567 through 1576 Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1601 through 1604 No H-bonds generated for 'chain 'A' and resid 1601 through 1604' Processing helix chain 'A' and resid 1676 through 1689 Processing helix chain 'A' and resid 1722 through 1736 Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1824 through 1827 Processing helix chain 'A' and resid 1834 through 1851 removed outlier: 3.569A pdb=" N SER A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1875 Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1894 through 1898 removed outlier: 3.640A pdb=" N LEU A1897 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1908 Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1949 through 1954 Processing helix chain 'A' and resid 1973 through 1994 removed outlier: 4.202A pdb=" N ILE A1977 " --> pdb=" O ASP A1973 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A1978 " --> pdb=" O GLU A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2070 through 2088 removed outlier: 4.251A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A2088 " --> pdb=" O HIS A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2167 through 2171 removed outlier: 4.058A 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 'O' and resid 11 through 20 Processing helix chain 'O' and resid 36 through 49 Processing helix chain 'O' and resid 51 through 54 removed outlier: 4.650A pdb=" N ASN O 54 " --> pdb=" O LYS O 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 51 through 54' Processing helix chain 'O' and resid 70 through 73 No H-bonds generated for 'chain 'O' and resid 70 through 73' Processing helix chain 'O' and resid 109 through 124 removed outlier: 3.889A pdb=" N VAL O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 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: 5.018A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 214 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 264 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 341 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 399 Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 441 through 452 removed outlier: 4.802A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 3.817A pdb=" N GLU C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 467 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 697 through 701 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 756 through 776 removed outlier: 4.763A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 823 removed outlier: 5.280A pdb=" N ILE C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 840 through 852 removed outlier: 5.308A pdb=" N SER C 844 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 940 removed outlier: 5.854A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 933 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS C 936 " --> pdb=" O PHE C 933 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 937 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 22 No H-bonds generated for 'chain 'N' and resid 20 through 22' Processing helix chain 'N' and resid 143 through 151 removed outlier: 4.192A pdb=" N GLU N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 159 removed outlier: 3.657A pdb=" N SER N 159 " --> pdb=" O GLU N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 172 No H-bonds generated for 'chain 'N' and resid 169 through 172' Processing helix chain 'N' and resid 184 through 192 removed outlier: 3.518A pdb=" N ALA N 188 " --> pdb=" O ASP N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 304 Processing helix chain 'N' and resid 310 through 320 Processing helix chain 'N' and resid 325 through 338 Processing helix chain 'N' and resid 343 through 350 removed outlier: 3.543A pdb=" N LEU N 347 " --> pdb=" O GLU N 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 368 removed outlier: 3.560A pdb=" N ALA N 360 " --> pdb=" O THR N 357 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA N 363 " --> pdb=" O ALA N 360 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN N 364 " --> pdb=" O VAL N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 375 through 382 Processing helix chain 'N' and resid 386 through 398 removed outlier: 4.230A pdb=" N ARG N 391 " --> pdb=" O ARG N 387 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL N 392 " --> pdb=" O ALA N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 409 Processing helix chain 'N' and resid 416 through 429 Processing helix chain 'N' and resid 434 through 443 Processing helix chain 'N' and resid 446 through 457 Processing helix chain 'N' and resid 465 through 476 Processing helix chain 'N' and resid 480 through 492 Processing helix chain 'N' and resid 504 through 516 Processing helix chain 'N' and resid 519 through 531 Processing helix chain 'N' and resid 541 through 552 Processing helix chain 'N' and resid 557 through 568 Processing helix chain 'N' and resid 575 through 586 Processing helix chain 'N' and resid 590 through 603 Processing helix chain 'N' and resid 609 through 621 Processing helix chain 'N' and resid 624 through 637 Processing helix chain 'N' and resid 643 through 654 Processing helix chain 'N' and resid 658 through 671 Processing helix chain 'N' and resid 676 through 687 Processing helix chain 'N' and resid 691 through 704 Processing helix chain 'N' and resid 709 through 721 Processing helix chain 'N' and resid 725 through 738 Processing helix chain 'N' and resid 744 through 755 Processing helix chain 'N' and resid 759 through 773 removed outlier: 3.811A pdb=" N ASN N 773 " --> pdb=" O SER N 769 " (cutoff:3.500A) Processing helix chain 'N' and resid 778 through 787 Processing helix chain 'N' and resid 794 through 805 Processing helix chain 'N' and resid 811 through 821 Processing helix chain 'N' and resid 827 through 833 Processing helix chain 'N' and resid 844 through 854 Processing helix chain 'N' and resid 857 through 870 Processing helix chain 'N' and resid 877 through 887 Processing helix chain 'N' and resid 891 through 902 removed outlier: 3.621A pdb=" N ARG N 898 " --> pdb=" O GLU N 895 " (cutoff:3.500A) Processing helix chain 'N' and resid 906 through 916 removed outlier: 3.979A pdb=" N VAL N 915 " --> pdb=" O TRP N 912 " (cutoff:3.500A) Processing helix chain 'N' and resid 924 through 929 Processing helix chain 'N' and resid 934 through 939 Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'M' and resid 39 through 48 Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 67 through 76 removed outlier: 4.098A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 113 through 124 Processing helix chain 'L' and resid 54 through 79 Processing helix chain 'L' and resid 89 through 120 removed outlier: 3.784A pdb=" N THR L 100 " --> pdb=" O ALA L 96 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 101 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 4.262A pdb=" N GLU L 126 " --> pdb=" O PRO L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 153 through 156 No H-bonds generated for 'chain 'L' and resid 153 through 156' Processing helix chain 'L' and resid 161 through 172 removed outlier: 3.713A pdb=" N SER L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 215 removed outlier: 4.622A pdb=" N PHE L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 222 Processing helix chain 'L' and resid 226 through 235 Processing helix chain 'L' and resid 238 through 242 Processing helix chain 'L' and resid 246 through 249 No H-bonds generated for 'chain 'L' and resid 246 through 249' Processing helix chain 'L' and resid 269 through 272 Processing helix chain 'L' and resid 280 through 282 No H-bonds generated for 'chain 'L' and resid 280 through 282' Processing helix chain 'L' and resid 285 through 287 No H-bonds generated for 'chain 'L' and resid 285 through 287' Processing helix chain 'L' and resid 289 through 308 Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 357 through 364 removed outlier: 3.637A pdb=" N LYS L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 373 No H-bonds generated for 'chain 'L' and resid 370 through 373' Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 422 through 431 removed outlier: 3.799A pdb=" N ARG L 426 " --> pdb=" O LYS L 422 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR L 427 " --> pdb=" O THR L 423 " (cutoff:3.500A) Processing helix chain '9' and resid 120 through 129 Processing helix chain '9' and resid 161 through 187 Processing helix chain '9' and resid 202 through 213 Processing helix chain '9' and resid 263 through 265 No H-bonds generated for 'chain '9' and resid 263 through 265' Processing helix chain '9' and resid 292 through 309 Processing helix chain '9' and resid 332 through 335 No H-bonds generated for 'chain '9' and resid 332 through 335' Processing helix chain 'J' and resid 442 through 466 removed outlier: 3.934A pdb=" N LYS J 446 " --> pdb=" O LYS J 442 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS J 447 " --> pdb=" O LYS J 443 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU J 455 " --> pdb=" O GLN J 451 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 456 " --> pdb=" O THR J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 489 removed outlier: 6.944A pdb=" N THR J 487 " --> pdb=" O ARG J 483 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU J 488 " --> pdb=" O VAL J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 519 removed outlier: 3.608A pdb=" N LYS J 519 " --> pdb=" O ASN J 515 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 529 removed outlier: 4.092A pdb=" N VAL J 527 " --> pdb=" O GLU J 523 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS J 528 " --> pdb=" O GLN J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 533 No H-bonds generated for 'chain 'J' and resid 531 through 533' Processing helix chain 'J' and resid 554 through 566 removed outlier: 3.634A pdb=" N GLU J 561 " --> pdb=" O LYS J 557 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA J 564 " --> pdb=" O ILE J 560 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 599 removed outlier: 3.580A pdb=" N LYS J 592 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 593 " --> pdb=" O LYS J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 656 through 664 removed outlier: 3.873A pdb=" N HIS J 664 " --> pdb=" O HIS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 669 No H-bonds generated for 'chain 'J' and resid 667 through 669' Processing helix chain 'a' and resid 7 through 12 removed outlier: 4.670A pdb=" N HIS a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'b' and resid 3 through 10 removed outlier: 3.959A pdb=" N LEU b 10 " --> pdb=" O PHE b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 64 No H-bonds generated for 'chain 'b' and resid 62 through 64' Processing helix chain 'b' and resid 76 through 80 Processing helix chain 'c' and resid 21 through 26 Processing helix chain 'c' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN c 34 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL c 36 " --> pdb=" O THR c 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS c 37 " --> pdb=" O GLN c 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN c 38 " --> pdb=" O SER c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 105 No H-bonds generated for 'chain 'c' and resid 103 through 105' Processing helix chain 'd' and resid 7 through 14 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' 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 'f' and resid 10 through 12 No H-bonds generated for 'chain 'f' and resid 10 through 12' Processing helix chain 'f' and resid 64 through 66 No H-bonds generated for 'chain 'f' and resid 64 through 66' Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 65 through 67 No H-bonds generated for 'chain 'g' and resid 65 through 67' Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 36 through 81 Processing helix chain 'W' and resid 37 through 47 Processing helix chain 'W' and resid 148 through 155 Processing helix chain 'W' and resid 161 through 163 No H-bonds generated for 'chain 'W' and resid 161 through 163' Processing helix chain 'A0' and resid 24 through 35 Processing helix chain 'A0' and resid 57 through 60 No H-bonds generated for 'chain 'A0' and resid 57 through 60' Processing helix chain '0' and resid 271 through 313 Processing helix chain 'Z' and resid 23 through 30 Processing helix chain 'Z' and resid 33 through 40 Processing helix chain 'Z' and resid 44 through 53 Processing helix chain 'Z' and resid 69 through 80 Processing helix chain 'Z' and resid 84 through 92 Processing helix chain 'Z' and resid 97 through 110 Processing helix chain 'Z' and resid 113 through 124 Proline residue: Z 122 - end of helix Processing helix chain 'Z' and resid 144 through 152 Processing helix chain 'Z' and resid 168 through 174 Processing helix chain '8' and resid 92 through 99 Processing helix chain '8' and resid 103 through 108 Processing helix chain '8' and resid 119 through 133 Processing helix chain 'Y' and resid 7 through 20 Processing helix chain 'Y' and resid 24 through 34 Processing helix chain 'Y' and resid 44 through 52 Processing helix chain 'Y' and resid 56 through 64 Processing helix chain 'Y' and resid 70 through 86 Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 101 through 109 Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Y' and resid 128 through 130 No H-bonds generated for 'chain 'Y' and resid 128 through 130' Processing helix chain 'Y' and resid 139 through 151 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: 3.957A 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: 3.636A 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: 3.634A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.699A 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 'l' and resid 7 through 14 Processing helix chain 'l' and resid 66 through 68 No H-bonds generated for 'chain 'l' and resid 66 through 68' Processing helix chain 'm' and resid 17 through 27 Processing helix chain 'm' and resid 81 through 83 No H-bonds generated for 'chain 'm' 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: 3.511A 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: 4.193A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) removed outlier: 5.286A 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 'u' and resid 161 through 176 removed outlier: 3.719A pdb=" N ARG u 176 " --> pdb=" O GLN u 172 " (cutoff:3.500A) Processing helix chain 'u' and resid 179 through 189 removed outlier: 4.007A pdb=" N GLN u 184 " --> pdb=" O GLN u 180 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN u 187 " --> pdb=" O THR u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 192 through 198 Processing helix chain 'u' and resid 203 through 218 removed outlier: 4.145A pdb=" N VAL u 212 " --> pdb=" O THR u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 241 through 273 Processing helix chain 'v' and resid 205 through 209 Processing helix chain 'w' and resid 4 through 28 Processing helix chain 'w' and resid 30 through 43 removed outlier: 4.414A pdb=" N ASP w 35 " --> pdb=" O THR w 32 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 57 Processing helix chain 'w' and resid 70 through 97 Proline residue: w 78 - end of helix Processing helix chain 'w' and resid 111 through 122 Proline residue: w 120 - end of helix Processing helix chain 'w' and resid 135 through 142 Processing helix chain 'w' and resid 159 through 161 No H-bonds generated for 'chain 'w' and resid 159 through 161' Processing helix chain 'w' and resid 166 through 168 No H-bonds generated for 'chain 'w' and resid 166 through 168' Processing helix chain 'w' and resid 175 through 177 No H-bonds generated for 'chain 'w' and resid 175 through 177' Processing helix chain 'w' and resid 183 through 193 Processing helix chain 'w' and resid 200 through 209 removed outlier: 3.997A pdb=" N LEU w 209 " --> pdb=" O ASP w 205 " (cutoff:3.500A) Processing helix chain 'w' and resid 219 through 222 No H-bonds generated for 'chain 'w' and resid 219 through 222' Processing helix chain 'w' and resid 231 through 251 Processing helix chain 'w' and resid 257 through 275 removed outlier: 3.765A pdb=" N LEU w 272 " --> pdb=" O LEU w 268 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS w 273 " --> pdb=" O ALA w 269 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N CYS w 274 " --> pdb=" O LEU w 270 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY w 275 " --> pdb=" O GLY w 271 " (cutoff:3.500A) Processing helix chain 'w' and resid 298 through 302 Processing helix chain 'w' and resid 308 through 316 Processing helix chain 'w' and resid 318 through 333 Processing helix chain 'w' and resid 335 through 350 Processing helix chain 'w' and resid 353 through 367 Processing helix chain 'w' and resid 394 through 400 removed outlier: 4.089A pdb=" N LEU w 399 " --> pdb=" O TRP w 395 " (cutoff:3.500A) Processing helix chain 'w' and resid 419 through 426 removed outlier: 4.094A pdb=" N GLN w 423 " --> pdb=" O PRO w 419 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG w 424 " --> pdb=" O LYS w 420 " (cutoff:3.500A) Processing helix chain 'w' and resid 429 through 438 Processing helix chain 'w' and resid 454 through 462 Processing helix chain 'q' and resid 2 through 10 Processing helix chain 'q' and resid 64 through 66 No H-bonds generated for 'chain 'q' and resid 64 through 66' Processing helix chain 'q' and resid 74 through 76 No H-bonds generated for 'chain 'q' and resid 74 through 76' Processing helix chain 'q' and resid 79 through 88 Processing helix chain 'r' and resid 19 through 24 removed outlier: 4.525A pdb=" N SER r 24 " --> pdb=" O LEU r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 3 through 9 Processing helix chain 's' and resid 63 through 65 No H-bonds generated for 'chain 's' and resid 63 through 65' Processing helix chain 's' and resid 73 through 79 removed outlier: 4.305A pdb=" N ILE s 76 " --> pdb=" O ASP s 73 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL s 79 " --> pdb=" O ILE s 76 " (cutoff:3.500A) Processing helix chain 't' and resid 14 through 20 Processing helix chain 't' and resid 76 through 78 No H-bonds generated for 'chain 't' and resid 76 through 78' Processing helix chain 'x' and resid 8 through 14 Processing helix chain 'y' and resid 78 through 80 No H-bonds generated for 'chain 'y' and resid 78 through 80' Processing helix chain 'z' and resid 6 through 8 No H-bonds generated for 'chain 'z' and resid 6 through 8' Processing helix chain 'z' and resid 64 through 66 No H-bonds generated for 'chain 'z' and resid 64 through 66' Processing helix chain 'P' and resid 27 through 37 Processing helix chain 'Q' and resid 6 through 13 removed outlier: 3.621A pdb=" N PHE Q 10 " --> pdb=" O ASN Q 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 26 Processing helix chain 'S' and resid 5 through 12 removed outlier: 3.756A pdb=" N LYS S 11 " --> pdb=" O PRO S 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE S 12 " --> pdb=" O GLU S 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 12 Processing helix chain 'V' and resid 3 through 9 removed outlier: 3.666A pdb=" N LYS V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 98 removed outlier: 4.167A pdb=" N LEU K 87 " --> pdb=" O GLN K 83 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 114 removed outlier: 5.573A pdb=" N CYS K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 139 removed outlier: 4.214A pdb=" N ARG K 130 " --> pdb=" O PRO K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 194 Proline residue: K 187 - end of helix removed outlier: 4.756A pdb=" N MET K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS K 191 " --> pdb=" O PRO K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 219 removed outlier: 3.599A pdb=" N GLN K 210 " --> pdb=" O THR K 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET K 211 " --> pdb=" O ARG K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 439 No H-bonds generated for 'chain 'K' and resid 437 through 439' Processing helix chain '1' and resid 83 through 90 Proline residue: 1 87 - end of helix Processing helix chain '1' and resid 94 through 97 No H-bonds generated for 'chain '1' and resid 94 through 97' Processing helix chain '1' and resid 104 through 110 Proline residue: 1 109 - end of helix Processing helix chain '1' and resid 119 through 125 removed outlier: 3.774A pdb=" N HIS 1 122 " --> pdb=" O TYR 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 174 through 189 Processing helix chain '1' and resid 208 through 217 Proline residue: 1 212 - end of helix removed outlier: 4.170A pdb=" N SER 1 217 " --> pdb=" O LYS 1 213 " (cutoff:3.500A) Processing helix chain '1' and resid 226 through 235 removed outlier: 3.713A pdb=" N ARG 1 231 " --> pdb=" O PRO 1 228 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP 1 232 " --> pdb=" O SER 1 229 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 258 removed outlier: 3.933A pdb=" N SER 1 242 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU 1 243 " --> pdb=" O ALA 1 239 " (cutoff:3.500A) Proline residue: 1 245 - end of helix Proline residue: 1 249 - end of helix Proline residue: 1 256 - end of helix Processing helix chain '1' and resid 301 through 324 Proline residue: 1 314 - end of helix Processing helix chain '1' and resid 401 through 404 No H-bonds generated for 'chain '1' and resid 401 through 404' Processing helix chain '1' and resid 421 through 428 Proline residue: 1 427 - end of helix Processing helix chain '1' and resid 430 through 434 Processing helix chain '1' and resid 470 through 478 removed outlier: 4.376A pdb=" N ASP 1 476 " --> pdb=" O GLN 1 473 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS 1 477 " --> pdb=" O TYR 1 474 " (cutoff:3.500A) Processing helix chain '1' and resid 491 through 505 removed outlier: 3.589A pdb=" N LYS 1 499 " --> pdb=" O ARG 1 495 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU 1 500 " --> pdb=" O LYS 1 496 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU 1 501 " --> pdb=" O ILE 1 497 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU 1 502 " --> pdb=" O MET 1 498 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS 1 503 " --> pdb=" O LYS 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 509 through 521 Processing helix chain '1' and resid 523 through 540 removed outlier: 5.891A pdb=" N ALA 1 528 " --> pdb=" O ARG 1 524 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY 1 529 " --> pdb=" O GLU 1 525 " (cutoff:3.500A) Proline residue: 1 530 - end of helix Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 546 through 562 removed outlier: 3.826A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 565 through 582 removed outlier: 3.677A pdb=" N ARG 1 568 " --> pdb=" O ASP 1 565 " (cutoff:3.500A) Proline residue: 1 569 - end of helix removed outlier: 5.241A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL 1 576 " --> pdb=" O LYS 1 573 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU 1 579 " --> pdb=" O VAL 1 576 " (cutoff:3.500A) Proline residue: 1 580 - end of helix Processing helix chain '1' and resid 587 through 603 Processing helix chain '1' and resid 606 through 613 Processing helix chain '1' and resid 615 through 617 No H-bonds generated for 'chain '1' and resid 615 through 617' Processing helix chain '1' and resid 622 through 639 Processing helix chain '1' and resid 641 through 653 Proline residue: 1 646 - end of helix removed outlier: 3.665A pdb=" N LYS 1 653 " --> pdb=" O LYS 1 649 " (cutoff:3.500A) Processing helix chain '1' and resid 658 through 694 removed outlier: 5.921A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 4.861A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY 1 693 " --> pdb=" O ILE 1 689 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU 1 694 " --> pdb=" O ILE 1 690 " (cutoff:3.500A) Processing helix chain '1' and resid 699 through 716 Processing helix chain '1' and resid 721 through 737 removed outlier: 4.516A pdb=" N SER 1 726 " --> pdb=" O SER 1 723 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS 1 729 " --> pdb=" O SER 1 726 " (cutoff:3.500A) Proline residue: 1 730 - end of helix Processing helix chain '1' and resid 741 through 756 Proline residue: 1 755 - end of helix Processing helix chain '1' and resid 761 through 776 removed outlier: 4.600A pdb=" N LEU 1 771 " --> pdb=" O ARG 1 767 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE 1 772 " --> pdb=" O GLU 1 768 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 795 Processing helix chain '1' and resid 803 through 817 removed outlier: 4.515A pdb=" N LEU 1 811 " --> pdb=" O LYS 1 807 " (cutoff:3.500A) Proline residue: 1 812 - end of helix Processing helix chain '1' and resid 821 through 825 removed outlier: 3.768A pdb=" N LEU 1 825 " --> pdb=" O HIS 1 821 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 821 through 825' Processing helix chain '1' and resid 827 through 844 Processing helix chain '1' and resid 847 through 856 removed outlier: 4.803A pdb=" N ASP 1 855 " --> pdb=" O SER 1 851 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) Processing helix chain '1' and resid 862 through 878 Processing helix chain '1' and resid 881 through 883 No H-bonds generated for 'chain '1' and resid 881 through 883' Processing helix chain '1' and resid 887 through 901 Processing helix chain '1' and resid 908 through 941 removed outlier: 7.041A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG 1 924 " --> pdb=" O ALA 1 920 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL 1 925 " --> pdb=" O LEU 1 921 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS 1 926 " --> pdb=" O GLY 1 922 " (cutoff:3.500A) Proline residue: 1 927 - end of helix Proline residue: 1 930 - end of helix Processing helix chain '1' and resid 948 through 964 removed outlier: 5.478A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 983 removed outlier: 3.582A pdb=" N TYR 1 981 " --> pdb=" O VAL 1 977 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLY 1 983 " --> pdb=" O TYR 1 979 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1001 removed outlier: 4.302A pdb=" N SER 1 992 " --> pdb=" O GLU 1 988 " (cutoff:3.500A) Processing helix chain '1' and resid 1013 through 1025 Proline residue: 11018 - end of helix Proline residue: 11022 - end of helix removed outlier: 5.566A pdb=" N LYS 11025 " --> pdb=" O THR 11021 " (cutoff:3.500A) Processing helix chain '1' and resid 1029 through 1045 Processing helix chain '1' and resid 1052 through 1067 removed outlier: 5.257A pdb=" N GLU 11064 " --> pdb=" O PHE 11060 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU 11065 " --> pdb=" O GLU 11061 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU 11066 " --> pdb=" O LEU 11062 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS 11067 " --> pdb=" O LEU 11063 " (cutoff:3.500A) Processing helix chain '1' and resid 1071 through 1088 Processing helix chain '1' and resid 1090 through 1099 Processing helix chain '1' and resid 1109 through 1122 removed outlier: 3.971A pdb=" N VAL 11119 " --> pdb=" O ILE 11116 " (cutoff:3.500A) Processing helix chain '1' and resid 1125 through 1137 Proline residue: 11130 - end of helix removed outlier: 4.009A pdb=" N ARG 11137 " --> pdb=" O MET 11133 " (cutoff:3.500A) Processing helix chain '1' and resid 1141 through 1163 removed outlier: 7.439A pdb=" N GLU 11160 " --> pdb=" O GLU 11156 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET 11161 " --> pdb=" O TYR 11157 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS 11163 " --> pdb=" O GLY 11159 " (cutoff:3.500A) Processing helix chain '1' and resid 1165 through 1177 Proline residue: 11171 - end of helix removed outlier: 3.799A pdb=" N ALA 11176 " --> pdb=" O LEU 11173 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 11177 " --> pdb=" O GLU 11174 " (cutoff:3.500A) Processing helix chain '1' and resid 1182 through 1198 Processing helix chain '1' and resid 1205 through 1219 removed outlier: 4.009A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Proline residue: 11217 - end of helix Processing helix chain '1' and resid 1224 through 1241 Processing helix chain '1' and resid 1243 through 1250 Processing helix chain '1' and resid 1259 through 1274 Processing helix chain '1' and resid 1280 through 1283 Processing helix chain '1' and resid 1298 through 1301 Processing helix chain '3' and resid 190 through 193 No H-bonds generated for 'chain '3' and resid 190 through 193' Processing helix chain '3' and resid 430 through 432 No H-bonds generated for 'chain '3' and resid 430 through 432' Processing helix chain '3' and resid 809 through 826 removed outlier: 3.792A pdb=" N VAL 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU 3 825 " --> pdb=" O GLU 3 821 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALA 3 826 " --> pdb=" O GLU 3 822 " (cutoff:3.500A) Processing helix chain '3' and resid 839 through 844 Processing helix chain '3' and resid 1135 through 1151 removed outlier: 3.975A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1160 through 1164 Processing helix chain '3' and resid 1176 through 1182 removed outlier: 4.350A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE 31182 " --> pdb=" O LEU 31178 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1196 Processing helix chain '3' and resid 1201 through 1215 removed outlier: 4.231A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 41 removed outlier: 3.735A pdb=" N LYS 5 41 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 76 Processing helix chain '5' and resid 106 through 115 Processing helix chain '6' and resid 25 through 28 removed outlier: 4.523A pdb=" N GLY 6 28 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 25 through 28' Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 74 through 77 No H-bonds generated for 'chain '6' and resid 74 through 77' Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '7' and resid 28 through 45 Processing helix chain '7' and resid 47 through 56 Processing helix chain '7' and resid 61 through 74 removed outlier: 5.334A pdb=" N LEU 7 73 " --> pdb=" O MET 7 69 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN 7 74 " --> pdb=" O GLU 7 70 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 467 Processing helix chain '2' and resid 472 through 474 No H-bonds generated for 'chain '2' and resid 472 through 474' Processing helix chain '2' and resid 477 through 480 No H-bonds generated for 'chain '2' and resid 477 through 480' Processing helix chain '2' and resid 485 through 492 removed outlier: 4.843A pdb=" N HIS 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) Processing helix chain '2' and resid 526 through 529 No H-bonds generated for 'chain '2' and resid 526 through 529' Processing helix chain '2' and resid 533 through 536 No H-bonds generated for 'chain '2' and resid 533 through 536' Processing helix chain '2' and resid 552 through 555 No H-bonds generated for 'chain '2' and resid 552 through 555' Processing helix chain '2' and resid 568 through 577 removed outlier: 5.608A pdb=" N PHE 2 575 " --> pdb=" O LEU 2 571 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE 2 576 " --> pdb=" O HIS 2 572 " (cutoff:3.500A) Processing helix chain '2' and resid 611 through 617 Processing helix chain '2' and resid 633 through 639 Processing helix chain '4' and resid 26 through 35 removed outlier: 3.716A pdb=" N GLN 4 35 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 64 through 74 removed outlier: 3.590A pdb=" N LYS 4 72 " --> pdb=" O ASP 4 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 494 removed outlier: 5.460A 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: 3.930A pdb=" N LEU D 514 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 519 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 521 " --> pdb=" O LEU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 561 removed outlier: 3.672A pdb=" N LYS D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.616A 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: 3.834A pdb=" N VAL D 632 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 633 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.618A 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: 4.103A pdb=" N GLN D 702 " --> pdb=" O ILE D 698 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN D 705 " --> pdb=" O PHE D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 734 removed outlier: 4.188A 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: 3.536A 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: 4.439A pdb=" N GLN D 877 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 3.764A 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 Processing helix chain 'D' and resid 1011 through 1020 removed outlier: 3.852A pdb=" N ARG D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1031 through 1042 removed outlier: 3.868A pdb=" N LEU D1035 " --> pdb=" O GLU D1032 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D1037 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.747A 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: 4.720A pdb=" N LYS D1172 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE D1174 " --> pdb=" O GLY D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1320 removed outlier: 4.446A pdb=" N LEU D1320 " --> pdb=" O ALA D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1330 through 1339 removed outlier: 4.789A pdb=" N ASN D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 5.265A 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: 3.774A pdb=" N ASP D1392 " --> pdb=" O GLN D1388 " (cutoff:3.500A) removed outlier: 3.845A 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: 3.665A pdb=" N LEU D1435 " --> pdb=" O LYS D1431 " (cutoff:3.500A) removed outlier: 4.552A 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: 3.627A pdb=" N TYR D1547 " --> pdb=" O ALA D1543 " (cutoff:3.500A) Processing helix chain 'D' and resid 1568 through 1582 removed outlier: 3.833A pdb=" N ALA D1582 " --> pdb=" O THR D1578 " (cutoff:3.500A) Processing helix chain 'D' and resid 1594 through 1603 removed outlier: 3.604A pdb=" N ILE D1598 " --> pdb=" O GLU D1594 " (cutoff:3.500A) Proline residue: D1599 - end of helix removed outlier: 4.738A pdb=" N LYS D1603 " --> pdb=" O PRO D1599 " (cutoff:3.500A) 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: 4.504A pdb=" N THR D1765 " --> pdb=" O TYR D1761 " (cutoff:3.500A) Processing helix chain 'D' and resid 1768 through 1770 No H-bonds generated for 'chain 'D' and resid 1768 through 1770' 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: 3.678A 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: 3.744A 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: 3.753A pdb=" N LEU D1922 " --> pdb=" O LYS D1918 " (cutoff:3.500A) Processing helix chain 'D' and resid 1936 through 1951 removed outlier: 3.658A pdb=" N LEU D1940 " --> pdb=" O LEU D1936 " (cutoff:3.500A) 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: 4.093A pdb=" N ARG D1973 " --> pdb=" O GLU D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2013 removed outlier: 3.717A pdb=" N PHE D2010 " --> pdb=" O ASP D2006 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= C, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= D, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 7.171A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id= F, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 3.850A pdb=" N GLU A1223 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1342 through 1345 Processing sheet with id= H, first strand: chain 'A' and resid 1711 through 1716 removed outlier: 8.406A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1637 through 1639 removed outlier: 3.531A pdb=" N THR A1657 " --> pdb=" O TRP A1637 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A1655 " --> pdb=" O VAL A1639 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1913 through 1918 removed outlier: 7.169A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1787 through 1791 removed outlier: 4.364A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A1791 " --> pdb=" O THR A1799 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.852A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.481A 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: 5.195A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 11.656A pdb=" N VAL A2146 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN A2260 " --> pdb=" O TYR A2104 " (cutoff:3.500A) removed outlier: 7.848A 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= M, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.448A pdb=" N PHE A2270 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2150 through 2152 Processing sheet with id= O, first strand: chain 'A' and resid 2228 through 2230 Processing sheet with id= P, first strand: chain 'O' and resid 56 through 61 removed outlier: 6.106A pdb=" N VAL O 25 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR O 59 " --> pdb=" O VAL O 25 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL O 27 " --> pdb=" O TYR O 59 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL O 61 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG O 29 " --> pdb=" O VAL O 61 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'O' and resid 91 through 93 Processing sheet with id= R, first strand: chain 'C' and resid 316 through 318 removed outlier: 10.026A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 348 through 350 removed outlier: 4.309A pdb=" N ASN C 350 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 523 through 526 removed outlier: 6.892A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 531 through 534 Processing sheet with id= V, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.810A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.036A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 675 through 677 removed outlier: 3.635A pdb=" N ALA C 676 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 684 " --> pdb=" O VAL C 795 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 795 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 793 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 831 through 838 removed outlier: 6.454A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 252 through 254 Processing sheet with id= AA, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.509A pdb=" N PHE M 53 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N MET M 56 " --> pdb=" O PRO M 79 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL M 81 " --> pdb=" O MET M 56 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 630 through 632 removed outlier: 3.678A pdb=" N VAL J 584 " --> pdb=" O SER J 544 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'a' and resid 64 through 68 removed outlier: 6.214A pdb=" N CYS a 45 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG a 18 " --> pdb=" O VAL a 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL a 82 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE a 20 " --> pdb=" O MET a 80 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET a 80 " --> pdb=" O ILE a 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'a' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA a 33 " --> pdb=" O ILE a 41 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS a 43 " --> pdb=" O PHE a 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE a 31 " --> pdb=" O CYS a 43 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'b' and resid 53 through 55 Processing sheet with id= AF, first strand: chain 'b' and resid 57 through 60 removed outlier: 6.030A pdb=" N LYS b 41 " --> pdb=" O ILE b 29 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE b 29 " --> pdb=" O LYS b 41 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'c' and resid 89 through 96 Processing sheet with id= AH, first strand: chain 'c' and resid 98 through 101 removed outlier: 6.580A pdb=" N GLU c 68 " --> pdb=" O VAL c 56 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL c 56 " --> pdb=" O GLU c 68 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'd' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY d 57 " --> pdb=" O GLU d 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR d 47 " --> pdb=" O LEU d 59 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'd' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER d 35 " --> pdb=" O GLN d 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA d 45 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU d 33 " --> pdb=" O ALA d 45 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.723A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.792A 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: 5.802A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'f' and resid 67 through 72 removed outlier: 6.921A pdb=" N LYS f 20 " --> pdb=" O ILE f 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU f 70 " --> pdb=" O SER f 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER f 18 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA f 72 " --> pdb=" O LYS f 16 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS f 16 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL f 41 " --> pdb=" O ARG f 32 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'f' and resid 45 through 48 removed outlier: 6.475A pdb=" N GLU f 47 " --> pdb=" O ASN f 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN f 56 " --> pdb=" O GLU f 47 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'g' and resid 55 through 58 Processing sheet with id= AP, first strand: chain 'g' and resid 60 through 63 removed outlier: 6.829A pdb=" N SER g 44 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU g 32 " --> pdb=" O SER g 44 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 61 through 63 removed outlier: 4.432A pdb=" N ARG E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER E 346 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 90 through 94 Processing sheet with id= AS, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.574A pdb=" N ALA E 127 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU E 115 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 125 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR E 117 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET E 123 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 145 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP E 137 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG E 143 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 154 through 159 removed outlier: 6.874A pdb=" N GLY E 170 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS E 157 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS E 168 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 188 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.709A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 275 through 277 removed outlier: 3.597A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 291 through 293 removed outlier: 6.363A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'W' and resid 67 through 69 removed outlier: 4.708A pdb=" N LEU W 109 " --> pdb=" O THR W 127 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET W 112 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL W 140 " --> pdb=" O MET W 112 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS W 28 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL W 17 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG W 26 " --> pdb=" O PHE W 15 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE W 15 " --> pdb=" O ARG W 26 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS W 28 " --> pdb=" O VAL W 13 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL W 13 " --> pdb=" O LYS W 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN W 173 " --> pdb=" O ASP W 16 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER W 18 " --> pdb=" O ILE W 171 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE W 171 " --> pdb=" O SER W 18 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'A0' and resid 12 through 18 removed outlier: 4.018A pdb=" N ASNA0 7 " --> pdb=" O LEUA0 68 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Z' and resid 129 through 133 Processing sheet with id= BA, first strand: chain 'Y' and resid 228 through 232 removed outlier: 3.682A pdb=" N GLU Y 239 " --> pdb=" O THR Y 231 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN Y 242 " --> pdb=" O ILE Y 248 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE Y 248 " --> pdb=" O ASN Y 242 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Y' and resid 270 through 272 removed outlier: 3.554A pdb=" N ARG Y 300 " --> pdb=" O VAL Y 290 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS Y 292 " --> pdb=" O CYS Y 298 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS Y 298 " --> pdb=" O LYS Y 292 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Y' and resid 310 through 315 removed outlier: 6.502A pdb=" N ALA Y 325 " --> pdb=" O THR Y 311 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU Y 313 " --> pdb=" O LEU Y 323 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU Y 323 " --> pdb=" O LEU Y 313 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE Y 315 " --> pdb=" O GLN Y 321 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN Y 321 " --> pdb=" O PHE Y 315 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY Y 335 " --> pdb=" O THR Y 341 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR Y 341 " --> pdb=" O GLY Y 335 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Y' and resid 385 through 387 removed outlier: 4.057A pdb=" N ASN Y 385 " --> pdb=" O ILE Y 375 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Y 354 " --> pdb=" O ALA Y 367 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Y' and resid 412 through 416 removed outlier: 6.223A pdb=" N ASN Y 426 " --> pdb=" O ILE Y 431 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE Y 431 " --> pdb=" O ASN Y 426 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 447 through 449 removed outlier: 6.242A pdb=" N SER Y 470 " --> pdb=" O LEU Y 476 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU Y 476 " --> pdb=" O SER Y 470 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'Y' and resid 208 through 214 removed outlier: 3.965A pdb=" N HIS Y 208 " --> pdb=" O LYS Y 512 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU Y 510 " --> pdb=" O LYS Y 210 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY Y 212 " --> pdb=" O LEU Y 508 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU Y 508 " --> pdb=" O GLY Y 212 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU Y 507 " --> pdb=" O SER Y 503 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER Y 503 " --> pdb=" O LEU Y 507 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BI, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.828A 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= BJ, 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: 5.610A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.868A 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= BL, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BM, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.030A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BO, 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= BP, first strand: chain 'l' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY l 57 " --> pdb=" O GLU l 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR l 47 " --> pdb=" O LEU l 59 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'l' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER l 35 " --> pdb=" O GLN l 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA l 45 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU l 33 " --> pdb=" O ALA l 45 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'm' and resid 70 through 75 removed outlier: 5.724A pdb=" N ALA m 61 " --> pdb=" O LEU m 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET m 41 " --> pdb=" O LEU m 35 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU m 35 " --> pdb=" O MET m 41 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG m 30 " --> pdb=" O VAL m 90 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'm' and resid 77 through 79 removed outlier: 3.793A pdb=" N GLY m 49 " --> pdb=" O VAL m 57 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP m 59 " --> pdb=" O ILE m 47 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE m 47 " --> pdb=" O ASP m 59 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.921A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.144A 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: 6.068A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.477A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= BV, 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: 6.728A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'p' and resid 80 through 83 removed outlier: 3.517A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'v' and resid 119 through 122 Processing sheet with id= BY, first strand: chain 'v' and resid 148 through 153 Processing sheet with id= BZ, first strand: chain 'w' and resid 406 through 408 Processing sheet with id= CA, first strand: chain 'q' and resid 67 through 71 removed outlier: 6.800A pdb=" N GLU q 18 " --> pdb=" O ARG q 68 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL q 70 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL q 16 " --> pdb=" O VAL q 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU q 23 " --> pdb=" O LEU q 19 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS q 39 " --> pdb=" O HIS q 30 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'r' and resid 75 through 81 removed outlier: 3.616A pdb=" N ARG r 37 " --> pdb=" O MET r 33 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'r' and resid 85 through 87 removed outlier: 6.434A pdb=" N GLY r 55 " --> pdb=" O LEU r 43 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU r 43 " --> pdb=" O GLY r 55 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 's' and resid 44 through 46 removed outlier: 3.672A pdb=" N TYR s 68 " --> pdb=" O GLU s 18 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 's' and resid 58 through 61 removed outlier: 5.780A pdb=" N ARG s 41 " --> pdb=" O LEU s 29 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU s 29 " --> pdb=" O ARG s 41 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 't' and resid 55 through 58 removed outlier: 5.394A pdb=" N LYS t 34 " --> pdb=" O MET t 30 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 't' and resid 71 through 74 removed outlier: 3.562A pdb=" N GLY t 42 " --> pdb=" O VAL t 50 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU t 52 " --> pdb=" O LEU t 40 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU t 40 " --> pdb=" O GLU t 52 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'x' and resid 29 through 33 Processing sheet with id= CI, first strand: chain 'y' and resid 52 through 54 removed outlier: 3.559A pdb=" N ARG y 31 " --> pdb=" O PHE y 27 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'y' and resid 74 through 76 removed outlier: 6.611A pdb=" N ASP y 49 " --> pdb=" O LEU y 37 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU y 37 " --> pdb=" O ASP y 49 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'z' and resid 67 through 72 removed outlier: 6.681A pdb=" N ILE z 16 " --> pdb=" O ALA z 68 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE z 70 " --> pdb=" O ALA z 14 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA z 14 " --> pdb=" O ILE z 70 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU z 72 " --> pdb=" O THR z 12 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR z 12 " --> pdb=" O GLU z 72 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE z 37 " --> pdb=" O LYS z 28 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'P' and resid 93 through 96 removed outlier: 3.567A pdb=" N ASN P 45 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL P 108 " --> pdb=" O ASN P 45 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'P' and resid 98 through 100 removed outlier: 6.417A pdb=" N GLU P 68 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL P 56 " --> pdb=" O GLU P 68 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'Q' and resid 54 through 58 removed outlier: 7.132A pdb=" N GLU Q 49 " --> pdb=" O SER Q 56 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS Q 17 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'Q' and resid 43 through 45 Processing sheet with id= CP, first strand: chain 'R' and resid 86 through 89 removed outlier: 6.822A pdb=" N VAL R 57 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'S' and resid 26 through 30 Processing sheet with id= CR, first strand: chain 'S' and resid 41 through 43 Processing sheet with id= CS, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.995A pdb=" N ASN S 55 " --> pdb=" O GLU S 47 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'T' and resid 55 through 58 removed outlier: 3.962A pdb=" N VAL T 27 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR T 19 " --> pdb=" O ILE T 72 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'T' and resid 60 through 63 removed outlier: 3.725A pdb=" N GLU T 34 " --> pdb=" O GLN T 42 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER T 44 " --> pdb=" O LEU T 32 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU T 32 " --> pdb=" O SER T 44 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'U' and resid 77 through 82 removed outlier: 6.534A pdb=" N ILE U 20 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET U 80 " --> pdb=" O ARG U 18 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG U 18 " --> pdb=" O MET U 80 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL U 82 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG U 16 " --> pdb=" O VAL U 82 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR U 15 " --> pdb=" O PHE U 31 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE U 41 " --> pdb=" O LYS U 32 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'V' and resid 24 through 27 Processing sheet with id= CX, first strand: chain 'V' and resid 38 through 41 Processing sheet with id= CY, first strand: chain 'V' and resid 43 through 46 Processing sheet with id= CZ, first strand: chain 'K' and resid 236 through 239 Processing sheet with id= DA, first strand: chain 'K' and resid 278 through 281 Processing sheet with id= DB, first strand: chain 'K' and resid 328 through 331 removed outlier: 3.623A pdb=" N TRP K 347 " --> pdb=" O GLN K 361 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP K 351 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU K 357 " --> pdb=" O ASP K 351 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'K' and resid 390 through 393 Processing sheet with id= DD, first strand: chain 'K' and resid 412 through 415 Processing sheet with id= DE, first strand: chain 'K' and resid 474 through 477 Processing sheet with id= DF, first strand: chain 'K' and resid 497 through 500 Processing sheet with id= DG, first strand: chain '3' and resid 14 through 20 removed outlier: 6.229A pdb=" N SER 3 33 " --> pdb=" O SER 3 15 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA 3 17 " --> pdb=" O VAL 3 31 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL 3 31 " --> pdb=" O ALA 3 17 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS 3 19 " --> pdb=" O GLU 3 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU 3 29 " --> pdb=" O HIS 3 19 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain '3' and resid 62 through 67 removed outlier: 6.872A pdb=" N GLY 3 81 " --> pdb=" O ARG 3 63 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU 3 65 " --> pdb=" O VAL 3 79 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL 3 88 " --> pdb=" O VAL 3 80 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU 3 91 " --> pdb=" O LYS 3 101 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LYS 3 101 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 3 93 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE 3 99 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain '3' and resid 120 through 123 Processing sheet with id= DJ, first strand: chain '3' and resid 144 through 146 Processing sheet with id= DK, first strand: chain '3' and resid 165 through 167 removed outlier: 6.216A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain '3' and resid 170 through 172 removed outlier: 3.666A pdb=" N VAL 3 171 " --> pdb=" O ALA 3 183 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 3 183 " --> pdb=" O VAL 3 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= DL Processing sheet with id= DM, first strand: chain '3' and resid 267 through 270 removed outlier: 3.517A pdb=" N LYS 3 259 " --> pdb=" O VAL 3 248 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 3 248 " --> pdb=" O LYS 3 259 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY 3 247 " --> pdb=" O VAL 3 238 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain '3' and resid 301 through 304 removed outlier: 5.724A pdb=" N LYS 3 312 " --> pdb=" O TYR 3 329 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR 3 329 " --> pdb=" O LYS 3 312 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU 3 316 " --> pdb=" O ILE 3 325 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE 3 325 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain '3' and resid 346 through 349 removed outlier: 6.768A pdb=" N GLN 3 360 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU 3 397 " --> pdb=" O GLN 3 360 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain '3' and resid 775 through 780 Processing sheet with id= DQ, first strand: chain '3' and resid 458 through 462 Processing sheet with id= DR, first strand: chain '3' and resid 532 through 534 removed outlier: 4.078A pdb=" N ARG 3 532 " --> pdb=" O ARG 3 528 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain '3' and resid 562 through 567 Processing sheet with id= DT, first strand: chain '3' and resid 605 through 608 Processing sheet with id= DU, first strand: chain '3' and resid 674 through 676 Processing sheet with id= DV, first strand: chain '3' and resid 700 through 706 removed outlier: 6.703A pdb=" N GLU 3 710 " --> pdb=" O SER 3 724 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER 3 724 " --> pdb=" O GLU 3 710 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain '3' and resid 741 through 745 removed outlier: 6.417A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain '3' and resid 785 through 791 removed outlier: 7.019A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE 3 790 " --> pdb=" O ASN 3 796 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN 3 796 " --> pdb=" O ILE 3 790 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN 3 870 " --> pdb=" O THR 3 876 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR 3 876 " --> pdb=" O ASN 3 870 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain '3' and resid 890 through 892 removed outlier: 3.553A pdb=" N SER 3 890 " --> pdb=" O GLY 3 908 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY 3 922 " --> pdb=" O LYS 3 911 " (cutoff:3.500A) Processing sheet with id= DZ, first strand: chain '3' and resid 951 through 955 removed outlier: 4.646A pdb=" N ALA 3 951 " --> pdb=" O GLY 3 962 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY 3 962 " --> pdb=" O ALA 3 951 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP 3 971 " --> pdb=" O ARG 3 979 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ARG 3 979 " --> pdb=" O ASP 3 971 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain '3' and resid 990 through 995 removed outlier: 6.704A pdb=" N SER 31003 " --> pdb=" O SER 3 991 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE 31001 " --> pdb=" O ILE 3 993 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR 3 995 " --> pdb=" O ARG 3 999 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG 3 999 " --> pdb=" O THR 3 995 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA 31025 " --> pdb=" O TRP 31011 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS 31015 " --> pdb=" O LEU 31021 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU 31021 " --> pdb=" O LYS 31015 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain '3' and resid 1043 through 1047 removed outlier: 6.820A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain '3' and resid 1104 through 1107 removed outlier: 6.115A pdb=" N ILE 31128 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR 3 7 " --> pdb=" O ILE 31128 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL 31130 " --> pdb=" O ASN 3 5 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN 3 5 " --> pdb=" O VAL 31130 " (cutoff:3.500A) Processing sheet with id= ., first strand: chain '5' and resid 88 through 91 Processing sheet with id= /, first strand: chain '2' and resid 648 through 650 Processing sheet with id= 0, first strand: chain '4' and resid 85 through 88 Processing sheet with id= 1, first strand: chain '4' and resid 77 through 79 removed outlier: 4.165A pdb=" N ILE 4 77 " --> pdb=" O ILE 4 84 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 435 through 438 removed outlier: 7.126A pdb=" N GLY D 865 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR D 688 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 6.134A 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: 6.630A 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: 7.518A pdb=" N THR D 871 " --> pdb=" O ILE D 692 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 826 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 673 through 675 removed outlier: 6.001A pdb=" N LEU D 500 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS D 537 " --> pdb=" O ARG D 610 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE D 612 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 6.590A 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= 4, first strand: chain 'D' and resid 832 through 835 Processing sheet with id= 5, first strand: chain 'D' and resid 1250 through 1257 removed outlier: 5.934A pdb=" N LYS D1199 " --> pdb=" O PRO D1192 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU D1201 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU D1190 " --> pdb=" O GLU D1201 " (cutoff:3.500A) removed outlier: 6.992A 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: 5.427A pdb=" N LEU D1186 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 1279 through 1284 Processing sheet with id= 7, first strand: chain 'D' and resid 1511 through 1513 removed outlier: 6.009A pdb=" N PHE D1347 " --> pdb=" O PHE D1512 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 1522 through 1528 Processing sheet with id= 9, first strand: chain 'D' and resid 1667 through 1670 Processing sheet with id= :, first strand: chain 'D' and resid 1802 through 1805 Processing sheet with id= ;, first strand: chain 'D' and resid 2017 through 2023 Processing sheet with id= <, 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: 6.580A pdb=" N ASP D2070 " --> pdb=" O LEU D2076 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU D2076 " --> pdb=" O ASP D2070 " (cutoff:3.500A) 4306 hydrogen bonds defined for protein. 11718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 87.68 Time building geometry restraints manager: 32.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 15933 1.28 - 1.42: 24434 1.42 - 1.56: 45524 1.56 - 1.70: 1139 1.70 - 1.84: 238 Bond restraints: 87268 Sorted by residual: bond pdb=" N MET 1 407 " pdb=" CA MET 1 407 " ideal model delta sigma weight residual 1.463 1.706 -0.243 1.08e-02 8.57e+03 5.07e+02 bond pdb=" C ALA 1 406 " pdb=" N MET 1 407 " ideal model delta sigma weight residual 1.333 1.520 -0.186 1.24e-02 6.50e+03 2.26e+02 bond pdb=" N PRO 11243 " pdb=" CA PRO 11243 " ideal model delta sigma weight residual 1.469 1.347 0.122 1.28e-02 6.10e+03 9.02e+01 bond pdb=" N SER 1 944 " pdb=" CA SER 1 944 " ideal model delta sigma weight residual 1.461 1.345 0.116 1.38e-02 5.25e+03 7.02e+01 bond pdb=" CA SER 3 84 " pdb=" C SER 3 84 " ideal model delta sigma weight residual 1.528 1.420 0.107 1.37e-02 5.33e+03 6.15e+01 ... (remaining 87263 not shown) Histogram of bond angle deviations from ideal: 91.03 - 102.29: 872 102.29 - 113.56: 40775 113.56 - 124.83: 72677 124.83 - 136.09: 3037 136.09 - 147.36: 5 Bond angle restraints: 117366 Sorted by residual: angle pdb=" C MET v 146 " pdb=" N PRO v 147 " pdb=" CA PRO v 147 " ideal model delta sigma weight residual 119.84 146.19 -26.35 1.25e+00 6.40e-01 4.44e+02 angle pdb=" C ASP D 946 " pdb=" N PRO D 947 " pdb=" CA PRO D 947 " ideal model delta sigma weight residual 118.85 140.60 -21.75 1.09e+00 8.42e-01 3.98e+02 angle pdb=" C ALA 1 406 " pdb=" N MET 1 407 " pdb=" CA MET 1 407 " ideal model delta sigma weight residual 120.89 147.36 -26.47 1.50e+00 4.44e-01 3.11e+02 angle pdb=" CA ALA 1 406 " pdb=" C ALA 1 406 " pdb=" O ALA 1 406 " ideal model delta sigma weight residual 120.24 105.80 14.44 1.11e+00 8.12e-01 1.69e+02 angle pdb=" C ARG 1 108 " pdb=" N PRO 1 109 " pdb=" CA PRO 1 109 " ideal model delta sigma weight residual 120.38 132.88 -12.50 1.03e+00 9.43e-01 1.47e+02 ... (remaining 117361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 39515 35.89 - 71.77: 1546 71.77 - 107.66: 200 107.66 - 143.54: 18 143.54 - 179.43: 22 Dihedral angle restraints: 41301 sinusoidal: 16613 harmonic: 24688 Sorted by residual: dihedral pdb=" CA ARG 2 558 " pdb=" C ARG 2 558 " pdb=" N PRO 2 559 " pdb=" CA PRO 2 559 " ideal model delta harmonic sigma weight residual -180.00 -124.11 -55.89 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO C 473 " pdb=" C PRO C 473 " pdb=" N LEU C 474 " pdb=" CA LEU C 474 " ideal model delta harmonic sigma weight residual -180.00 -124.37 -55.63 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA PRO N 841 " pdb=" C PRO N 841 " pdb=" N HIS N 842 " pdb=" CA HIS N 842 " ideal model delta harmonic sigma weight residual 180.00 127.50 52.50 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 41298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.986: 9065 0.986 - 1.972: 0 1.972 - 2.958: 0 2.958 - 3.944: 0 3.944 - 4.930: 4 Chirality restraints: 9069 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 2.41 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C1 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C6 IHP A3000 " pdb=" O11 IHP A3000 " both_signs ideal model delta sigma weight residual False 2.32 -2.44 4.76 2.00e-01 2.50e+01 5.66e+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 2.42 -4.75 2.00e-01 2.50e+01 5.65e+02 ... (remaining 9066 not shown) Planarity restraints: 16289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 415 " 0.043 2.00e-02 2.50e+03 7.86e-02 6.18e+01 pdb=" C LEU 1 415 " -0.136 2.00e-02 2.50e+03 pdb=" O LEU 1 415 " 0.050 2.00e-02 2.50e+03 pdb=" N PRO 1 416 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U H 103 " 0.072 2.00e-02 2.50e+03 3.48e-02 2.72e+01 pdb=" N1 U H 103 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U H 103 " -0.011 2.00e-02 2.50e+03 pdb=" O2 U H 103 " -0.017 2.00e-02 2.50e+03 pdb=" N3 U H 103 " -0.012 2.00e-02 2.50e+03 pdb=" C4 U H 103 " 0.013 2.00e-02 2.50e+03 pdb=" O4 U H 103 " 0.034 2.00e-02 2.50e+03 pdb=" C5 U H 103 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U H 103 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G H 105 " -0.048 2.00e-02 2.50e+03 2.76e-02 2.29e+01 pdb=" N9 G H 105 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G H 105 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G H 105 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G H 105 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G H 105 " -0.023 2.00e-02 2.50e+03 pdb=" O6 G H 105 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G H 105 " -0.032 2.00e-02 2.50e+03 pdb=" C2 G H 105 " 0.061 2.00e-02 2.50e+03 pdb=" N2 G H 105 " -0.014 2.00e-02 2.50e+03 pdb=" N3 G H 105 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G H 105 " 0.024 2.00e-02 2.50e+03 ... (remaining 16286 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 414 2.42 - 3.04: 55269 3.04 - 3.66: 119415 3.66 - 4.28: 164573 4.28 - 4.90: 252870 Nonbonded interactions: 592541 Sorted by model distance: nonbonded pdb=" O ILE D1824 " pdb=" O ASN D1825 " model vdw 1.805 3.040 nonbonded pdb=" O2' U G 155 " pdb=" OP2 U G 156 " model vdw 1.890 2.440 nonbonded pdb=" O SER 6 93 " pdb=" N LYS 6 95 " model vdw 1.901 2.520 nonbonded pdb=" OH TYR O 73 " pdb=" OG1 THR N 29 " model vdw 1.901 2.440 nonbonded pdb=" O4' U B 80 " pdb=" O GLY a 4 " model vdw 1.916 3.040 ... (remaining 592536 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 'P' and (name N or name CA or name C or name O )) selection = (chain 'k' and (resid 26 through 75 or resid 91 through 114)) } ncs_group { reference = (chain 'Q' and (name N or name CA or name C or name O )) selection = (chain 'd' and resid 4 through 74) selection = (chain 'l' and resid 4 through 74) } ncs_group { reference = (chain 'R' and (name N or name CA or name C or name O )) selection = (chain 'e' and resid 15 through 92) selection = (chain 'm' and resid 15 through 92) } ncs_group { reference = (chain 'S' and ((resid 4 through 48 and (name N or name CA or name C or name O ) \ ) or resid 54 through 76)) selection = (chain 'f' and (resid 4 through 48 or resid 54 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'T' and (name N or name CA or name C or name O )) selection = (chain 'g' and resid 4 through 74) selection = (chain 'h' and resid 4 through 74) } ncs_group { reference = (chain 'V' and (resid 2 through 82 and (name N or name CA or name C or name O )) \ ) selection = (chain 'b' and resid 2 through 82) selection = (chain 'j' and resid 2 through 82) } ncs_group { reference = chain 'a' selection = chain 'i' } 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=0.92 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 16.730 Check model and map are aligned: 0.930 Set scattering table: 0.580 Process input model: 256.320 Find NCS groups from input model: 3.790 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 285.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4974 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 : 0.011 0.243 87268 Z= 0.745 Angle : 1.379 26.470 117366 Z= 0.911 Chirality : 0.120 4.930 9069 Planarity : 0.007 0.110 16289 Dihedral : 17.052 179.430 30708 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.39 % Favored : 91.69 % Rotamer: Outliers : 2.52 % Allowed : 5.35 % Favored : 92.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.06), residues: 13852 helix: -2.89 (0.05), residues: 5111 sheet: -1.25 (0.10), residues: 2294 loop : -2.21 (0.07), residues: 6447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP N 312 HIS 0.019 0.003 HIS C 477 PHE 0.051 0.004 PHE 9 266 TYR 0.042 0.004 TYR A 94 ARG 0.030 0.002 ARG 9 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27704 Ramachandran restraints generated. 13852 Oldfield, 0 Emsley, 13852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27704 Ramachandran restraints generated. 13852 Oldfield, 0 Emsley, 13852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 12448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 939 time to evaluate : 6.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 28 " (corrupted residue). Skipping it. 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