Starting phenix.real_space_refine on Tue Mar 19 18:04:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z58_6891/03_2024/5z58_6891_updated.pdb" } resolution = 4.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 399 5.49 5 Mg 6 5.21 5 S 277 5.16 5 C 57739 2.51 5 N 17122 2.21 5 O 19126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A TYR 1695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2072": "OE1" <-> "OE2" Residue "A GLU 2141": "OE1" <-> "OE2" Residue "A GLU 2171": "OE1" <-> "OE2" Residue "A PHE 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2303": "OE1" <-> "OE2" Residue "A ARG 2330": "NH1" <-> "NH2" Residue "A GLU 2331": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "w ARG 430": "NH1" <-> "NH2" Residue "w PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 495": "NH1" <-> "NH2" Residue "1 TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 590": "NH1" <-> "NH2" Residue "1 ARG 684": "NH1" <-> "NH2" Residue "1 ARG 736": "NH1" <-> "NH2" Residue "1 ARG 827": "NH1" <-> "NH2" Residue "1 ARG 939": "NH1" <-> "NH2" Residue "1 ARG 948": "NH1" <-> "NH2" Residue "1 ARG 1027": "NH1" <-> "NH2" Residue "1 ARG 1045": "NH1" <-> "NH2" Residue "1 ARG 1057": "NH1" <-> "NH2" Residue "1 ARG 1075": "NH1" <-> "NH2" Residue "1 ARG 1109": "NH1" <-> "NH2" Residue "1 ARG 1245": "NH1" <-> "NH2" Residue "1 TYR 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 274": "NH1" <-> "NH2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 326": "NH1" <-> "NH2" Residue "3 PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 429": "NH1" <-> "NH2" Residue "3 ARG 464": "NH1" <-> "NH2" Residue "3 ARG 528": "NH1" <-> "NH2" Residue "3 ARG 690": "NH1" <-> "NH2" Residue "3 ARG 718": "NH1" <-> "NH2" Residue "3 PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 815": "NH1" <-> "NH2" Residue "3 ARG 895": "NH1" <-> "NH2" Residue "3 ARG 1013": "NH1" <-> "NH2" Residue "3 PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 19": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "J TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L GLU 229": "OE1" <-> "OE2" Residue "L GLU 230": "OE1" <-> "OE2" Residue "M ARG 223": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "R ASP 131": "OD1" <-> "OD2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 474": "OE1" <-> "OE2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "Y PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 563": "NH1" <-> "NH2" Residue "Z ARG 597": "NH1" <-> "NH2" Residue "z PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 94673 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 18165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2211, 18165 Classifications: {'peptide': 2211} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 124, 'TRANS': 2085} Chain breaks: 5 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1768 Classifications: {'RNA': 84} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 39} Link IDs: {'rna2p': 13, 'rna3p': 70} Chain breaks: 1 Chain: "C" Number of atoms: 6716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6716 Classifications: {'peptide': 860} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 53, 'TRANS': 806} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 8528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 8528 Classifications: {'peptide': 1722} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1539} Link IDs: {'PTRANS': 79, 'TRANS': 1642} Unresolved chain link angles: 79 Unresolved non-hydrogen bonds: 5613 Unresolved non-hydrogen angles: 7193 Unresolved non-hydrogen dihedrals: 4662 Unresolved non-hydrogen chiralities: 534 Planarities with less than four sites: {'GLN:plan1': 83, 'ASP:plan': 89, 'TYR:plan': 61, 'ASN:plan1': 70, 'TRP:plan': 19, 'HIS:plan': 52, 'PHE:plan': 65, 'GLU:plan': 125, 'ARG:plan': 88} Unresolved non-hydrogen planarities: 2997 Chain: "E" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2338 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Chain: "a" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 399 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "b" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 405 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 480 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "f" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "g" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 363 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "F" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1988 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 44, 'rna3p_pyr': 33} Link IDs: {'rna2p': 16, 'rna3p': 76} Chain breaks: 1 Chain: "G" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1545 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 12, 'rna3p_pur': 24, 'rna3p_pyr': 34} Link IDs: {'rna2p': 19, 'rna3p': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {' G%rna3p_pur:plan2': 2, ' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 1, ' U%rna3p_pyr:plan': 3, ' C%rna3p_pyr:plan2': 2, ' G%rna3p_pur:plan': 2, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "H" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2886 Classifications: {'RNA': 136} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 12, 'rna3p_pur': 59, 'rna3p_pyr': 59} Link IDs: {'rna2p': 18, 'rna3p': 117} Chain breaks: 5 Chain: "h" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 393 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 422 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "m" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "n" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 334 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "o" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 804 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 272 Chain: "p" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 813 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 156} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 304 Chain: "w" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 2369 Classifications: {'peptide': 437} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 319} Link IDs: {'PTRANS': 11, 'TRANS': 425} Chain breaks: 8 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1314 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1088 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 26, 'TYR:plan': 16, 'ASN:plan1': 20, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 12, 'GLU:plan': 54, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 828 Chain: "u" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 247 Chain: "v" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 486 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 87} Link IDs: {'PTRANS': 10, 'TRANS': 87} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 349 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 240 Chain: "1" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7702 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 62, 'TRANS': 975} Chain breaks: 7 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 252 Chain: "2" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1252 Classifications: {'peptide': 183} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 32} Link IDs: {'PTRANS': 19, 'TRANS': 163} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 146 Chain: "3" Number of atoms: 9220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9220 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1116} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 527 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "5" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 807 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "6" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "7" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3463 Classifications: {'peptide': 522} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 260} Link IDs: {'PTRANS': 12, 'TRANS': 509} Chain breaks: 19 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1115 Unresolved non-hydrogen angles: 1417 Unresolved non-hydrogen dihedrals: 947 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 44, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 695 Chain: "L" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1077 Classifications: {'peptide': 132} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 267 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 829 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "R" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2314 Classifications: {'peptide': 309} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 30} Link IDs: {'PTRANS': 21, 'TRANS': 287} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 109 Chain: "T" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2457 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 300} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 2238 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 412} Link IDs: {'PTRANS': 12, 'TRANS': 438} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1511 Unresolved non-hydrogen angles: 1911 Unresolved non-hydrogen dihedrals: 1249 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 20, 'TYR:plan': 12, 'ASN:plan1': 25, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 28, 'GLU:plan': 43, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 824 Chain: "X" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1012 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain breaks: 7 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 231 Chain: "Y" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 737 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 102} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "Z" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 755 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 140 Chain: "z" Number of atoms: 1381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 166} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 166} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1397 Chain: "x" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 2882 Classifications: {'peptide': 583} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 499} Link IDs: {'PTRANS': 27, 'TRANS': 555} Chain breaks: 10 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 1847 Unresolved non-hydrogen angles: 2374 Unresolved non-hydrogen dihedrals: 1522 Unresolved non-hydrogen chiralities: 182 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 23, 'TYR:plan': 23, 'ASN:plan1': 14, 'TRP:plan': 4, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 46, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1028 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 74101 SG CYS 6 23 163.306 154.475 197.572 1.00164.15 S ATOM 74125 SG CYS 6 26 164.080 150.214 197.853 1.00166.36 S ATOM 74372 SG CYS 6 58 164.860 153.002 200.273 1.00110.71 S ATOM 74393 SG CYS 6 61 166.599 154.579 197.575 1.00295.48 S ATOM 74277 SG CYS 6 46 169.150 150.226 215.009 1.00161.06 S ATOM 74300 SG CYS 6 49 170.500 149.958 211.705 1.00111.33 S ATOM 74152 SG CYS 6 30 157.864 141.426 203.414 1.00112.93 S ATOM 74173 SG CYS 6 33 158.153 139.039 200.998 1.00122.26 S ATOM 74468 SG CYS 6 72 156.345 138.153 203.601 1.00163.44 S ATOM 74492 SG CYS 6 75 159.492 137.398 204.772 1.00126.61 S ATOM 79804 SG CYS M 202 143.894 154.003 156.450 1.00 31.25 S ATOM 79876 SG CYS M 211 148.037 153.549 156.874 1.00 94.87 S ATOM 79915 SG CYS M 217 146.642 156.210 155.017 1.00120.91 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N HIS D1502 " occ=0.92 ... (3 atoms not shown) pdb=" CB HIS D1502 " occ=0.92 residue: pdb=" N AASP z 136 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP z 136 " occ=0.50 Time building chain proxies: 39.24, per 1000 atoms: 0.41 Number of scatterers: 94673 At special positions: 0 Unit cell: (278.304, 287.67, 306.402, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 277 16.00 P 399 15.00 Mg 6 11.99 O 19126 8.00 N 17122 7.00 C 57739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 308 " distance=2.74 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.57 Conformation dependent library (CDL) restraints added in 14.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 217 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 202 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 211 " Number of angles added : 12 25294 Ramachandran restraints generated. 12647 Oldfield, 0 Emsley, 12647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 474 helices and 123 sheets defined 38.5% alpha, 15.0% beta 84 base pairs and 173 stacking pairs defined. Time for finding SS restraints: 37.50 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.986A pdb=" N TYR A 88 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Proline residue: A 96 - end of helix removed outlier: 3.520A pdb=" N LEU A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.669A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 532 through 538 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 594 No H-bonds generated for 'chain 'A' and resid 591 through 594' Processing helix chain 'A' and resid 597 through 616 removed outlier: 3.779A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 608 " --> pdb=" O CYS A 605 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 616 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 661 removed outlier: 4.050A pdb=" N THR A 645 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.905A pdb=" N LEU A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 653 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 661 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 694 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 removed outlier: 3.960A 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 849 removed outlier: 3.875A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.634A pdb=" N ASP A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 990 through 999 Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1037 through 1053 Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 removed outlier: 3.755A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1126 No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1136 through 1138 No H-bonds generated for 'chain 'A' and resid 1136 through 1138' Processing helix chain 'A' and resid 1145 through 1160 removed outlier: 4.333A pdb=" N LEU A1149 " --> pdb=" O HIS A1145 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1250 Processing helix chain 'A' and resid 1256 through 1279 removed outlier: 3.868A pdb=" N TYR A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A1276 " --> pdb=" O THR A1272 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A1278 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1302 Processing helix chain 'A' and resid 1308 through 1310 No H-bonds generated for 'chain 'A' and resid 1308 through 1310' Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1368 through 1371 No H-bonds generated for 'chain 'A' and resid 1368 through 1371' Processing helix chain 'A' and resid 1375 through 1399 Processing helix chain 'A' and resid 1406 through 1408 No H-bonds generated for 'chain 'A' and resid 1406 through 1408' Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1427 through 1432 removed outlier: 3.564A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1446 removed outlier: 4.302A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A1446 " --> pdb=" O PHE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1461 No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'A' and resid 1468 through 1477 removed outlier: 3.677A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1487 removed outlier: 3.952A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1529 through 1542 removed outlier: 3.861A pdb=" N LEU A1536 " --> pdb=" O ARG A1532 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) Proline residue: A1540 - end of helix Processing helix chain 'A' and resid 1567 through 1576 Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1652 through 1654 No H-bonds generated for 'chain 'A' and resid 1652 through 1654' Processing helix chain 'A' and resid 1676 through 1689 Processing helix chain 'A' and resid 1722 through 1736 removed outlier: 3.693A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1769 through 1772 No H-bonds generated for 'chain 'A' and resid 1769 through 1772' Processing helix chain 'A' and resid 1824 through 1827 Processing helix chain 'A' and resid 1833 through 1851 Processing helix chain 'A' and resid 1854 through 1856 No H-bonds generated for 'chain 'A' and resid 1854 through 1856' Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 4.040A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1895 through 1898 Processing helix chain 'A' and resid 1900 through 1907 Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1947 through 1954 Processing helix chain 'A' and resid 1973 through 1995 Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2071 through 2088 removed outlier: 3.743A pdb=" N ARG A2076 " --> pdb=" O GLU A2072 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.342A 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: 4.059A pdb=" N GLU A2171 " --> pdb=" O TYR A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2202 removed outlier: 3.650A pdb=" N ASP A2202 " --> pdb=" O LYS A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2311 through 2314 No H-bonds generated for 'chain 'A' and resid 2311 through 2314' Processing helix chain 'A' and resid 2321 through 2325 Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.917A pdb=" N TYR C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 73' Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.713A pdb=" N ASP C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) 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: 5.148A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 271 through 292 removed outlier: 3.837A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.676A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 441 through 452 removed outlier: 5.763A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix removed outlier: 3.528A pdb=" N GLU C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 4.195A 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 519 through 521 No H-bonds generated for 'chain 'C' and resid 519 through 521' Processing helix chain 'C' and resid 597 through 613 Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 694 through 702 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 750 through 753 No H-bonds generated for 'chain 'C' and resid 750 through 753' Processing helix chain 'C' and resid 756 through 776 removed outlier: 4.008A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 823 removed outlier: 4.707A pdb=" N ILE C 809 " --> pdb=" O GLY C 805 " (cutoff:3.500A) Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 840 through 852 removed outlier: 4.879A 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: 5.699A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 933 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 936 " --> pdb=" O PHE C 933 " (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: 5.757A pdb=" N ALA D 491 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.931A 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: 3.879A pdb=" N ILE D 521 " --> pdb=" O LEU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 561 removed outlier: 3.672A pdb=" N LYS D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.615A 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: 3.835A 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: 4.499A pdb=" N ASN D 705 " --> pdb=" O PHE D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 734 removed outlier: 4.189A 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: 3.916A 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: 3.721A pdb=" N TYR D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 931 Processing helix chain 'D' and resid 933 through 936 No H-bonds generated for 'chain 'D' and resid 933 through 936' Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 950 through 955 Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 983 through 991 Processing helix chain 'D' and resid 995 through 1004 removed outlier: 3.738A pdb=" N GLN D 999 " --> pdb=" O ASN D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1020 removed outlier: 3.853A pdb=" N ARG D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1031 through 1042 removed outlier: 3.866A pdb=" N LEU D1035 " --> pdb=" O GLU D1032 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D1037 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.749A pdb=" N GLY D1089 " --> pdb=" O THR D1085 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 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: 4.723A pdb=" N LYS D1172 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 4.115A 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: 5.263A pdb=" N THR D1338 " --> pdb=" O GLN D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1370 removed outlier: 3.575A pdb=" N ALA D1363 " --> pdb=" O CYS D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1396 removed outlier: 3.773A pdb=" N ASP D1392 " --> pdb=" O GLN D1388 " (cutoff:3.500A) removed outlier: 3.847A 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: 4.553A pdb=" N SER D1436 " --> pdb=" O TRP D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1443 through 1446 No H-bonds generated for 'chain 'D' and resid 1443 through 1446' Processing helix chain 'D' and resid 1456 through 1460 Processing helix chain 'D' and resid 1465 through 1480 Processing helix chain 'D' and resid 1497 through 1504 Processing helix chain 'D' and resid 1508 through 1510 No H-bonds generated for 'chain 'D' and resid 1508 through 1510' Processing helix chain 'D' and resid 1535 through 1541 Processing helix chain 'D' and resid 1543 through 1553 removed outlier: 3.626A pdb=" N TYR D1547 " --> pdb=" O ALA D1543 " (cutoff:3.500A) Processing helix chain 'D' and resid 1568 through 1582 removed outlier: 3.832A pdb=" N ALA D1582 " --> pdb=" O THR D1578 " (cutoff:3.500A) Processing helix chain 'D' and resid 1594 through 1603 removed outlier: 3.603A pdb=" N ILE D1598 " --> pdb=" O GLU D1594 " (cutoff:3.500A) Proline residue: D1599 - end of helix removed outlier: 4.738A 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: 3.619A 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: 3.739A pdb=" N LYS D1918 " --> pdb=" O GLU D1914 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE D1920 " --> pdb=" O LEU D1916 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG D1921 " --> pdb=" O SER D1917 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D1922 " --> pdb=" O LYS D1918 " (cutoff:3.500A) Processing helix chain 'D' and resid 1936 through 1951 Processing helix chain 'D' and resid 1959 through 1962 removed outlier: 3.940A pdb=" N GLN D1962 " --> pdb=" O TYR D1959 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1959 through 1962' Processing helix chain 'D' and resid 1968 through 1977 removed outlier: 3.682A pdb=" N LYS D1972 " --> pdb=" O SER D1968 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG D1973 " --> pdb=" O GLU D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2013 removed outlier: 3.716A pdb=" N PHE D2010 " --> pdb=" O ASP D2006 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'b' and resid 10 through 12 No H-bonds generated for 'chain 'b' and resid 10 through 12' Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.959A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain '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: 4.671A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.958A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.636A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.530A 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: 3.565A 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 'p' and resid 164 through 172 Processing helix chain 'p' and resid 197 through 206 Processing helix chain 'w' and resid 4 through 28 Processing helix chain 'w' and resid 30 through 43 removed outlier: 4.416A 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 83 through 106 Proline residue: w 99 - end of helix Proline residue: w 105 - end of helix Processing helix chain 'w' and resid 115 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: 3.995A 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 270 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: 3.520A pdb=" N LYS w 398 " --> pdb=" O TYR w 394 " (cutoff:3.500A) Processing helix chain 'w' and resid 419 through 425 Processing helix chain 'w' and resid 429 through 438 Processing helix chain 'w' and resid 444 through 446 No H-bonds generated for 'chain 'w' and resid 444 through 446' Processing helix chain 'w' and resid 454 through 462 Processing helix chain 'w' and resid 484 through 486 No H-bonds generated for 'chain 'w' and resid 484 through 486' Processing helix chain 'w' and resid 489 through 498 Processing helix chain 'u' and resid 161 through 174 Processing helix chain 'u' and resid 181 through 188 removed outlier: 4.100A pdb=" N GLN u 187 " --> pdb=" O THR u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 196 through 198 No H-bonds generated for 'chain 'u' and resid 196 through 198' Processing helix chain 'u' and resid 203 through 218 removed outlier: 4.146A pdb=" N VAL u 212 " --> pdb=" O THR u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 238 through 248 Processing helix chain 'u' and resid 258 through 273 Processing helix chain 'v' and resid 205 through 209 Processing helix chain '1' and resid 83 through 88 Proline residue: 1 87 - end of helix No H-bonds generated for 'chain '1' and resid 83 through 88' Processing helix chain '1' and resid 103 through 110 Proline residue: 1 109 - end of helix Processing helix chain '1' and resid 120 through 125 Processing helix chain '1' and resid 178 through 189 Processing helix chain '1' and resid 208 through 220 Proline residue: 1 212 - end of helix removed outlier: 4.213A pdb=" N SER 1 217 " --> pdb=" O LYS 1 213 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP 1 218 " --> pdb=" O LYS 1 214 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP 1 219 " --> pdb=" O LEU 1 215 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN 1 220 " --> pdb=" O SER 1 216 " (cutoff:3.500A) Processing helix chain '1' and resid 226 through 235 removed outlier: 4.147A pdb=" N ARG 1 231 " --> pdb=" O PRO 1 228 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP 1 232 " --> pdb=" O SER 1 229 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 258 removed outlier: 3.836A pdb=" N SER 1 242 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 3.990A 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 312 through 334 Proline residue: 1 327 - end of helix removed outlier: 3.517A pdb=" N LYS 1 333 " --> pdb=" O PRO 1 329 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 407 Processing helix chain '1' and resid 420 through 434 Proline residue: 1 427 - end of helix removed outlier: 4.412A pdb=" N LYS 1 430 " --> pdb=" O THR 1 426 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 1 433 " --> pdb=" O ARG 1 429 " (cutoff:3.500A) Processing helix chain '1' and resid 471 through 479 removed outlier: 4.250A pdb=" N ASP 1 476 " --> pdb=" O GLN 1 473 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS 1 477 " --> pdb=" O TYR 1 474 " (cutoff:3.500A) Processing helix chain '1' and resid 491 through 505 removed outlier: 3.667A pdb=" N LYS 1 499 " --> pdb=" O ARG 1 495 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU 1 500 " --> pdb=" O LYS 1 496 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU 1 501 " --> pdb=" O ILE 1 497 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU 1 502 " --> pdb=" O MET 1 498 " (cutoff:3.500A) removed outlier: 3.623A 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 526 No H-bonds generated for 'chain '1' and resid 523 through 526' Processing helix chain '1' and resid 528 through 539 Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 547 through 560 Processing helix chain '1' and resid 565 through 582 removed outlier: 3.848A pdb=" N ARG 1 568 " --> pdb=" O ASP 1 565 " (cutoff:3.500A) Proline residue: 1 569 - end of helix removed outlier: 4.961A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL 1 576 " --> pdb=" O LYS 1 573 " (cutoff:3.500A) removed outlier: 4.389A 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 616 Proline residue: 1 615 - end of helix Processing helix chain '1' and resid 622 through 639 Processing helix chain '1' and resid 641 through 651 Proline residue: 1 646 - end of helix Processing helix chain '1' and resid 658 through 693 removed outlier: 6.087A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 5.061A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY 1 693 " --> pdb=" O ILE 1 689 " (cutoff:3.500A) Processing helix chain '1' and resid 700 through 715 Processing helix chain '1' and resid 721 through 737 removed outlier: 4.743A pdb=" N SER 1 726 " --> pdb=" O SER 1 723 " (cutoff:3.500A) removed outlier: 4.495A 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 778 removed outlier: 4.125A pdb=" N LEU 1 771 " --> pdb=" O ARG 1 767 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE 1 772 " --> pdb=" O GLU 1 768 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE 1 777 " --> pdb=" O LEU 1 773 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN 1 778 " --> pdb=" O ILE 1 774 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 796 Processing helix chain '1' and resid 803 through 809 Processing helix chain '1' and resid 811 through 817 Processing helix chain '1' and resid 828 through 844 Processing helix chain '1' and resid 846 through 858 removed outlier: 5.067A pdb=" N ASP 1 855 " --> pdb=" O SER 1 851 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU 1 857 " --> pdb=" O ILE 1 853 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS 1 858 " --> pdb=" O VAL 1 854 " (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 909 through 941 removed outlier: 6.563A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG 1 924 " --> pdb=" O ALA 1 920 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL 1 925 " --> pdb=" O LEU 1 921 " (cutoff:3.500A) removed outlier: 4.916A 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 944 through 964 removed outlier: 4.754A pdb=" N GLN 1 949 " --> pdb=" O ALA 1 945 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 983 removed outlier: 3.536A pdb=" N TYR 1 981 " --> pdb=" O VAL 1 977 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY 1 983 " --> pdb=" O TYR 1 979 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1001 removed outlier: 3.945A 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: 5.541A pdb=" N LYS 11025 " --> pdb=" O THR 11021 " (cutoff:3.500A) Processing helix chain '1' and resid 1029 through 1044 Processing helix chain '1' and resid 1052 through 1067 removed outlier: 4.926A pdb=" N GLU 11064 " --> pdb=" O PHE 11060 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU 11065 " --> pdb=" O GLU 11061 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU 11066 " --> pdb=" O LEU 11062 " (cutoff:3.500A) removed outlier: 5.471A 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 1098 Processing helix chain '1' and resid 1110 through 1122 Processing helix chain '1' and resid 1125 through 1137 Proline residue: 11130 - end of helix removed outlier: 4.267A pdb=" N ARG 11137 " --> pdb=" O MET 11133 " (cutoff:3.500A) Processing helix chain '1' and resid 1141 through 1177 removed outlier: 7.155A pdb=" N GLU 11160 " --> pdb=" O GLU 11156 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET 11161 " --> pdb=" O TYR 11157 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS 11163 " --> pdb=" O GLY 11159 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP 11164 " --> pdb=" O GLU 11160 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR 11165 " --> pdb=" O MET 11161 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR 11167 " --> pdb=" O LYS 11163 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA 11168 " --> pdb=" O ASP 11164 " (cutoff:3.500A) Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1182 through 1198 Processing helix chain '1' and resid 1205 through 1219 removed outlier: 3.685A 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 1281 through 1283 No H-bonds generated for 'chain '1' and resid 1281 through 1283' Processing helix chain '1' and resid 1298 through 1301 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 478 through 481 Processing helix chain '2' and resid 485 through 492 removed outlier: 4.812A pdb=" N HIS 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) Processing helix chain '2' and resid 515 through 517 No H-bonds generated for 'chain '2' and resid 515 through 517' 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 549 through 557 Processing helix chain '2' and resid 574 through 577 No H-bonds generated for 'chain '2' and resid 574 through 577' Processing helix chain '2' and resid 611 through 617 Processing helix chain '2' and resid 631 through 633 No H-bonds generated for 'chain '2' and resid 631 through 633' Processing helix chain '2' and resid 635 through 638 No H-bonds generated for 'chain '2' and resid 635 through 638' 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: 4.089A pdb=" N VAL 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU 3 825 " --> pdb=" O GLU 3 821 " (cutoff:3.500A) removed outlier: 4.446A 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: 3.646A 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 1183 removed outlier: 3.870A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE 31182 " --> pdb=" O LEU 31178 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN 31183 " --> pdb=" O CYS 31179 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1196 Processing helix chain '3' and resid 1201 through 1215 removed outlier: 4.115A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 36 removed outlier: 4.145A pdb=" N ALA 4 36 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 64 through 74 Processing helix chain '5' and resid 32 through 41 removed outlier: 3.910A pdb=" N LYS 5 41 " --> pdb=" O ASP 5 37 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 77 Processing helix chain '5' and resid 106 through 115 Processing helix chain '6' and resid 25 through 28 removed outlier: 4.652A 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: 4.934A pdb=" N LEU 7 73 " --> pdb=" O MET 7 69 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN 7 74 " --> pdb=" O GLU 7 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 238 removed outlier: 3.756A pdb=" N TYR J 223 " --> pdb=" O GLU J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 258 through 271 Processing helix chain 'J' and resid 276 through 288 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 310 through 323 Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.505A pdb=" N GLU J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 355 Processing helix chain 'J' and resid 359 through 372 removed outlier: 4.065A pdb=" N LEU J 371 " --> pdb=" O GLU J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 388 Processing helix chain 'J' and resid 392 through 406 Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 429 through 441 Processing helix chain 'J' and resid 451 through 466 Processing helix chain 'J' and resid 478 through 490 Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 497 through 512 Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 541 through 548 removed outlier: 3.839A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA J 548 " --> pdb=" O GLU J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 560 through 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 595 through 604 Proline residue: J 604 - end of helix Processing helix chain 'J' and resid 611 through 623 removed outlier: 3.517A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 642 Processing helix chain 'J' and resid 650 through 659 removed outlier: 3.566A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.698A pdb=" N MET J 674 " --> pdb=" O PRO J 670 " (cutoff:3.500A) Proline residue: J 675 - end of helix removed outlier: 3.657A pdb=" N LEU J 678 " --> pdb=" O MET J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 700 through 707 Processing helix chain 'J' and resid 719 through 730 Processing helix chain 'J' and resid 742 through 755 removed outlier: 3.692A pdb=" N LEU J 755 " --> pdb=" O ARG J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 765 through 774 Processing helix chain 'J' and resid 782 through 799 removed outlier: 3.501A pdb=" N SER J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 32 through 37 removed outlier: 3.857A pdb=" N LEU L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 52 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 107 Processing helix chain 'L' and resid 208 through 211 No H-bonds generated for 'chain 'L' and resid 208 through 211' Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 51 through 56 removed outlier: 3.519A pdb=" N ASN P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 205 through 207 No H-bonds generated for 'chain 'P' and resid 205 through 207' Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'R' and resid 98 through 105 removed outlier: 4.016A pdb=" N GLY R 105 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 119 No H-bonds generated for 'chain 'R' and resid 116 through 119' Processing helix chain 'R' and resid 137 through 160 Processing helix chain 'R' and resid 243 through 248 Processing helix chain 'R' and resid 287 through 340 removed outlier: 3.828A pdb=" N LYS R 319 " --> pdb=" O LYS R 315 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU R 320 " --> pdb=" O MET R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 433 No H-bonds generated for 'chain 'R' and resid 431 through 433' Processing helix chain 'R' and resid 444 through 447 No H-bonds generated for 'chain 'R' and resid 444 through 447' Processing helix chain 'R' and resid 457 through 463 Processing helix chain 'V' and resid 150 through 172 Processing helix chain 'V' and resid 178 through 187 removed outlier: 3.539A pdb=" N GLN V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 207 Processing helix chain 'V' and resid 209 through 225 removed outlier: 5.213A pdb=" N HIS V 213 " --> pdb=" O ILE V 210 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 246 Processing helix chain 'V' and resid 250 through 265 Processing helix chain 'V' and resid 272 through 283 Processing helix chain 'V' and resid 287 through 307 removed outlier: 3.578A pdb=" N GLU V 299 " --> pdb=" O GLY V 295 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU V 302 " --> pdb=" O LYS V 298 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LYS V 303 " --> pdb=" O GLU V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 309 through 324 Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 362 through 364 No H-bonds generated for 'chain 'V' and resid 362 through 364' Processing helix chain 'V' and resid 380 through 383 Processing helix chain 'V' and resid 391 through 405 removed outlier: 3.571A pdb=" N GLU V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 450 through 465 removed outlier: 3.702A pdb=" N PHE V 455 " --> pdb=" O ASN V 451 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG V 456 " --> pdb=" O LEU V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 479 Processing helix chain 'V' and resid 484 through 486 No H-bonds generated for 'chain 'V' and resid 484 through 486' Processing helix chain 'V' and resid 488 through 499 Processing helix chain 'V' and resid 505 through 517 removed outlier: 3.554A pdb=" N ALA V 511 " --> pdb=" O PHE V 507 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY V 512 " --> pdb=" O GLY V 508 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS V 515 " --> pdb=" O ALA V 511 " (cutoff:3.500A) Processing helix chain 'V' and resid 519 through 535 removed outlier: 3.618A pdb=" N GLU V 523 " --> pdb=" O LYS V 519 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN V 532 " --> pdb=" O ILE V 528 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR V 533 " --> pdb=" O PHE V 529 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP V 534 " --> pdb=" O LYS V 530 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR V 535 " --> pdb=" O GLU V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 556 removed outlier: 4.493A pdb=" N ALA V 548 " --> pdb=" O ARG V 545 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS V 549 " --> pdb=" O ASN V 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE V 551 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS V 553 " --> pdb=" O MET V 550 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR V 556 " --> pdb=" O HIS V 553 " (cutoff:3.500A) Processing helix chain 'V' and resid 563 through 567 removed outlier: 3.880A pdb=" N CYS V 567 " --> pdb=" O VAL V 564 " (cutoff:3.500A) Processing helix chain 'V' and resid 577 through 594 removed outlier: 4.200A pdb=" N GLU V 592 " --> pdb=" O GLN V 588 " (cutoff:3.500A) Processing helix chain 'V' and resid 598 through 604 Processing helix chain 'V' and resid 621 through 633 Processing helix chain 'V' and resid 641 through 647 Processing helix chain 'X' and resid 185 through 191 Processing helix chain 'X' and resid 222 through 228 Processing helix chain 'Y' and resid 9 through 19 Processing helix chain 'Y' and resid 24 through 26 No H-bonds generated for 'chain 'Y' and resid 24 through 26' Processing helix chain 'Y' and resid 49 through 58 removed outlier: 4.584A pdb=" N GLN Y 58 " --> pdb=" O CYS Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 96 Processing helix chain 'Z' and resid 481 through 498 Processing helix chain 'Z' and resid 501 through 519 removed outlier: 3.569A pdb=" N ARG Z 505 " --> pdb=" O LEU Z 501 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN Z 506 " --> pdb=" O ALA Z 502 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN Z 510 " --> pdb=" O GLN Z 506 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL Z 511 " --> pdb=" O GLN Z 507 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET Z 515 " --> pdb=" O VAL Z 511 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN Z 519 " --> pdb=" O MET Z 515 " (cutoff:3.500A) Processing helix chain 'Z' and resid 528 through 534 Processing helix chain 'Z' and resid 593 through 614 removed outlier: 3.613A pdb=" N LYS Z 605 " --> pdb=" O LEU Z 601 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP Z 614 " --> pdb=" O LEU Z 610 " (cutoff:3.500A) Processing helix chain 'z' and resid 34 through 45 Processing helix chain 'z' and resid 135 through 145 removed outlier: 4.413A pdb=" N TYR z 139 " --> pdb=" O GLY z 135 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN z 140 " --> pdb=" O AASP z 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER z 145 " --> pdb=" O MET z 141 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 153 No H-bonds generated for 'chain 'z' and resid 151 through 153' Processing helix chain 'x' and resid 387 through 398 removed outlier: 4.613A pdb=" N SER x 398 " --> pdb=" O ALA x 394 " (cutoff:3.500A) Processing helix chain 'x' and resid 400 through 402 No H-bonds generated for 'chain 'x' and resid 400 through 402' Processing helix chain 'x' and resid 405 through 414 Processing helix chain 'x' and resid 428 through 439 Proline residue: x 433 - end of helix removed outlier: 3.976A pdb=" N GLU x 438 " --> pdb=" O GLN x 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU x 439 " --> pdb=" O TYR x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 455 through 468 removed outlier: 3.517A pdb=" N MET x 459 " --> pdb=" O ARG x 455 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA x 463 " --> pdb=" O MET x 459 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG x 467 " --> pdb=" O ALA x 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 498 through 507 Processing helix chain 'x' and resid 522 through 524 No H-bonds generated for 'chain 'x' and resid 522 through 524' Processing helix chain 'x' and resid 527 through 542 removed outlier: 3.598A pdb=" N ASP x 538 " --> pdb=" O GLY x 534 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG x 541 " --> pdb=" O LYS x 537 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE x 542 " --> pdb=" O ASP x 538 " (cutoff:3.500A) Processing helix chain 'x' and resid 558 through 563 removed outlier: 4.118A pdb=" N PHE x 563 " --> pdb=" O ARG x 559 " (cutoff:3.500A) Processing helix chain 'x' and resid 592 through 605 removed outlier: 3.953A pdb=" N SER x 598 " --> pdb=" O ALA x 594 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU x 600 " --> pdb=" O VAL x 596 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN x 601 " --> pdb=" O VAL x 597 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL x 604 " --> pdb=" O LEU x 600 " (cutoff:3.500A) Processing helix chain 'x' and resid 618 through 635 removed outlier: 3.879A pdb=" N ALA x 623 " --> pdb=" O GLU x 619 " (cutoff:3.500A) Processing helix chain 'x' and resid 653 through 660 removed outlier: 4.335A pdb=" N ARG x 658 " --> pdb=" O ASP x 654 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE x 659 " --> pdb=" O MET x 655 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE x 660 " --> pdb=" O GLN x 656 " (cutoff:3.500A) Processing helix chain 'x' and resid 675 through 679 removed outlier: 4.315A pdb=" N THR x 679 " --> pdb=" O ILE x 676 " (cutoff:3.500A) Processing helix chain 'x' and resid 716 through 727 removed outlier: 3.640A pdb=" N ALA x 723 " --> pdb=" O ALA x 719 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY x 724 " --> pdb=" O ASN x 720 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG x 725 " --> pdb=" O GLN x 721 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA x 726 " --> pdb=" O ARG x 722 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLY x 727 " --> pdb=" O ALA x 723 " (cutoff:3.500A) Processing helix chain 'x' and resid 740 through 744 removed outlier: 3.544A pdb=" N GLN x 744 " --> pdb=" O ALA x 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 740 through 744' Processing helix chain 'x' and resid 754 through 756 No H-bonds generated for 'chain 'x' and resid 754 through 756' Processing helix chain 'x' and resid 761 through 770 Processing helix chain 'x' and resid 786 through 798 Processing helix chain 'x' and resid 810 through 817 removed outlier: 3.570A pdb=" N ALA x 816 " --> pdb=" O GLY x 812 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU x 817 " --> pdb=" O ARG x 813 " (cutoff:3.500A) Processing helix chain 'x' and resid 822 through 830 Processing helix chain 'x' and resid 837 through 847 removed outlier: 3.830A pdb=" N ALA x 845 " --> pdb=" O LEU x 841 " (cutoff:3.500A) Processing helix chain 'x' and resid 866 through 871 removed outlier: 3.968A pdb=" N ASN x 870 " --> pdb=" O ASN x 866 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE x 871 " --> pdb=" O ALA x 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 866 through 871' Processing helix chain 'x' and resid 877 through 888 removed outlier: 3.586A pdb=" N ASN x 883 " --> pdb=" O LEU x 879 " (cutoff:3.500A) Processing helix chain 'x' and resid 905 through 924 Processing helix chain 'x' and resid 937 through 946 Processing helix chain 'x' and resid 1006 through 1011 removed outlier: 3.917A pdb=" N VAL x1011 " --> pdb=" O TRP x1007 " (cutoff:3.500A) Processing helix chain 'x' and resid 1013 through 1016 No H-bonds generated for 'chain 'x' and resid 1013 through 1016' 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: 6.292A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= F, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 7.058A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1501 through 1503 Processing sheet with id= H, first strand: chain 'A' and resid 1711 through 1716 removed outlier: 6.595A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1637 through 1639 Processing sheet with id= J, first strand: chain 'A' and resid 1913 through 1918 removed outlier: 6.891A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1787 through 1792 removed outlier: 4.641A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (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: 5.890A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A2126 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.791A 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: 6.384A 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: 6.882A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.749A 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: 6.746A pdb=" N GLN A2260 " --> pdb=" O TYR A2104 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU A2106 " --> pdb=" O GLN A2260 " (cutoff:3.500A) removed outlier: 6.396A 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: 6.449A 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 'C' and resid 129 through 134 removed outlier: 8.642A pdb=" N ARG C 130 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 224 through 227 removed outlier: 6.175A pdb=" N ALA C 252 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU C 227 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR C 254 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 347 through 349 Processing sheet with id= S, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.924A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 500 through 502 Processing sheet with id= U, first strand: chain 'C' and resid 530 through 534 removed outlier: 4.121A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.633A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 662 through 666 removed outlier: 5.519A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.718A 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: 3.661A pdb=" N ALA C 676 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.145A 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: 6.334A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 435 through 438 removed outlier: 7.125A pdb=" N GLY D 865 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR D 688 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 6.133A 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: 6.628A pdb=" N LEU D 869 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE D 692 " --> pdb=" O LEU D 869 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 871 " --> pdb=" O ILE D 692 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 826 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 673 through 675 removed outlier: 5.999A pdb=" N LEU D 500 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS D 537 " --> pdb=" O ARG D 610 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 612 " --> pdb=" O LYS D 537 " (cutoff:3.500A) removed outlier: 6.589A 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: 6.764A 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= AB, first strand: chain 'D' and resid 832 through 835 Processing sheet with id= AC, first strand: chain 'D' and resid 970 through 972 Processing sheet with id= AD, first strand: chain 'D' and resid 1250 through 1257 removed outlier: 5.935A 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: 5.661A pdb=" N LEU D1190 " --> pdb=" O GLU D1201 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR D1203 " --> pdb=" O VAL D1188 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL D1188 " --> pdb=" O THR D1203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR D1205 " --> pdb=" O LEU D1186 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU D1186 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 1279 through 1285 Processing sheet with id= AF, first strand: chain 'D' and resid 1511 through 1513 removed outlier: 6.011A pdb=" N PHE D1347 " --> pdb=" O PHE D1512 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 1523 through 1530 removed outlier: 6.605A pdb=" N GLY D1700 " --> pdb=" O GLU D1524 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS D1526 " --> pdb=" O GLY D1700 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS D1702 " --> pdb=" O HIS D1526 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN D1528 " --> pdb=" O CYS D1702 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D1704 " --> pdb=" O GLN D1528 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE D1530 " --> pdb=" O ILE D1704 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS D1706 " --> pdb=" O PHE D1530 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1667 through 1670 Processing sheet with id= AI, first strand: chain 'D' and resid 1802 through 1805 Processing sheet with id= AJ, first strand: chain 'D' and resid 2017 through 2023 Processing sheet with id= AK, first strand: chain 'D' and resid 2118 through 2124 removed outlier: 3.766A 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) Processing sheet with id= AL, first strand: chain 'E' and resid 61 through 63 removed outlier: 4.433A pdb=" N ARG E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER E 346 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 90 through 94 Processing sheet with id= AN, 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: 6.128A 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= AO, first strand: chain 'E' and resid 154 through 159 removed outlier: 6.873A pdb=" N GLY E 170 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS E 157 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.401A 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= AP, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.710A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.521A 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: 7.028A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= AQ, 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: 3.783A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 291 through 293 removed outlier: 6.362A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= AT, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.828A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.214A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= AX, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.030A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= AZ, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.582A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= BC, 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: 4.661A 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= BD, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.791A 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= BE, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.921A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.475A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BH, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.829A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= BI, 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: 5.667A 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: 6.013A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BJ, 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: 6.869A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BL, 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: 5.458A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BN, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.582A 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= BO, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.723A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.791A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= BS, 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: 4.525A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= BT, 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= BU, first strand: chain 'o' and resid 14 through 16 removed outlier: 7.235A pdb=" N ALA o 46 " --> pdb=" O LEU o 24 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR o 68 " --> pdb=" O ILE o 47 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= BV, 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= BW, first strand: chain 'p' and resid 152 through 156 Processing sheet with id= BX, first strand: chain 'w' and resid 406 through 408 Processing sheet with id= BY, first strand: chain 'v' and resid 119 through 122 Processing sheet with id= BZ, first strand: chain 'v' and resid 148 through 153 Processing sheet with id= CA, first strand: chain '3' and resid 14 through 20 removed outlier: 6.640A pdb=" N SER 3 33 " --> pdb=" O SER 3 15 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA 3 17 " --> pdb=" O VAL 3 31 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL 3 31 " --> pdb=" O ALA 3 17 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS 3 19 " --> pdb=" O GLU 3 29 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU 3 29 " --> pdb=" O HIS 3 19 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain '3' and resid 62 through 68 removed outlier: 6.950A pdb=" N GLY 3 81 " --> pdb=" O ARG 3 63 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU 3 65 " --> pdb=" O VAL 3 79 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA 3 67 " --> pdb=" O TYR 3 77 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR 3 77 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL 3 88 " --> pdb=" O VAL 3 80 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU 3 91 " --> pdb=" O LYS 3 101 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS 3 101 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN 3 93 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE 3 99 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain '3' and resid 120 through 123 Processing sheet with id= CD, first strand: chain '3' and resid 144 through 146 Processing sheet with id= CE, first strand: chain '3' and resid 165 through 167 removed outlier: 6.174A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain '3' and resid 170 through 172 Processing sheet with id= CG, first strand: chain '3' and resid 267 through 270 removed outlier: 3.917A pdb=" N VAL 3 248 " --> pdb=" O LYS 3 259 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY 3 247 " --> pdb=" O VAL 3 238 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain '3' and resid 301 through 303 removed outlier: 5.777A pdb=" N LYS 3 312 " --> pdb=" O TYR 3 329 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR 3 329 " --> pdb=" O LYS 3 312 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU 3 316 " --> pdb=" O ILE 3 325 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE 3 325 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain '3' and resid 346 through 349 removed outlier: 6.355A pdb=" N GLN 3 360 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU 3 397 " --> pdb=" O GLN 3 360 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain '3' and resid 775 through 780 Processing sheet with id= CK, first strand: chain '3' and resid 458 through 462 Processing sheet with id= CL, first strand: chain '3' and resid 533 through 537 Processing sheet with id= CM, first strand: chain '3' and resid 563 through 567 Processing sheet with id= CN, first strand: chain '3' and resid 605 through 608 removed outlier: 6.169A pdb=" N SER 3 618 " --> pdb=" O PRO 3 627 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain '3' and resid 687 through 689 removed outlier: 3.560A pdb=" N SER 3 687 " --> pdb=" O ARG 3 676 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain '3' and resid 700 through 706 removed outlier: 6.729A pdb=" N GLU 3 710 " --> pdb=" O SER 3 724 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER 3 724 " --> pdb=" O GLU 3 710 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain '3' and resid 741 through 745 removed outlier: 6.463A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain '3' and resid 784 through 791 removed outlier: 7.235A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE 3 790 " --> pdb=" O ASN 3 796 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN 3 796 " --> pdb=" O ILE 3 790 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN 3 870 " --> pdb=" O THR 3 876 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR 3 876 " --> pdb=" O ASN 3 870 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain '3' and resid 890 through 894 removed outlier: 3.685A pdb=" N SER 3 890 " --> pdb=" O GLY 3 908 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS 3 894 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain '3' and resid 949 through 955 removed outlier: 3.842A pdb=" N ALA 3 950 " --> pdb=" O GLY 3 962 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY 3 962 " --> pdb=" O ALA 3 950 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE 3 952 " --> pdb=" O LEU 3 960 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU 3 960 " --> pdb=" O ILE 3 952 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG 3 958 " --> pdb=" O PRO 3 954 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP 3 971 " --> pdb=" O ARG 3 979 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG 3 979 " --> pdb=" O ASP 3 971 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain '3' and resid 990 through 995 removed outlier: 6.893A pdb=" N SER 31003 " --> pdb=" O SER 3 991 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE 31001 " --> pdb=" O ILE 3 993 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA 31025 " --> pdb=" O TRP 31011 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain '3' and resid 1043 through 1047 removed outlier: 6.506A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain '3' and resid 1104 through 1107 removed outlier: 6.208A pdb=" N ILE 31128 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR 3 7 " --> pdb=" O ILE 31128 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL 31130 " --> pdb=" O ASN 3 5 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN 3 5 " --> pdb=" O VAL 31130 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain '4' and resid 41 through 44 Processing sheet with id= CY, first strand: chain '5' and resid 88 through 91 Processing sheet with id= CZ, first strand: chain '6' and resid 8 through 10 Processing sheet with id= DA, first strand: chain 'R' and resid 174 through 180 Processing sheet with id= DB, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.347A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.511A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL T 254 " --> pdb=" O TYR T 260 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR T 260 " --> pdb=" O VAL T 254 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.547A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'T' and resid 333 through 338 removed outlier: 6.879A pdb=" N GLY T 348 " --> pdb=" O ALA T 334 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL T 336 " --> pdb=" O ILE T 346 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE T 346 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL T 366 " --> pdb=" O LEU T 356 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP T 358 " --> pdb=" O THR T 364 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR T 364 " --> pdb=" O ASP T 358 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'T' and resid 395 through 398 removed outlier: 3.710A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'T' and resid 419 through 421 removed outlier: 3.697A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP T 440 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN T 446 " --> pdb=" O ASP T 440 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'T' and resid 194 through 200 removed outlier: 6.660A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'X' and resid 386 through 392 Processing sheet with id= DJ, first strand: chain 'X' and resid 297 through 299 removed outlier: 6.841A pdb=" N ARG X 285 " --> pdb=" O GLN X 307 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN X 307 " --> pdb=" O ARG X 285 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'Y' and resid 108 through 110 removed outlier: 7.664A pdb=" N VAL Y 68 " --> pdb=" O LYS Y 77 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE Y 79 " --> pdb=" O ASN Y 66 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN Y 66 " --> pdb=" O PHE Y 79 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'Y' and resid 100 through 102 removed outlier: 4.014A pdb=" N ILE Y 100 " --> pdb=" O ILE Y 107 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'z' and resid 54 through 58 removed outlier: 6.753A pdb=" N GLN z 64 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL z 57 " --> pdb=" O ILE z 62 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE z 62 " --> pdb=" O VAL z 57 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU z 98 " --> pdb=" O THR z 116 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET z 101 " --> pdb=" O ILE z 129 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE z 129 " --> pdb=" O MET z 101 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU z 16 " --> pdb=" O VAL z 166 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL z 166 " --> pdb=" O LEU z 16 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS z 18 " --> pdb=" O CYS z 164 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N CYS z 164 " --> pdb=" O LYS z 18 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain 'x' and resid 569 through 571 removed outlier: 9.632A pdb=" N PHE x 570 " --> pdb=" O VAL x 417 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE x 419 " --> pdb=" O PHE x 570 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL x 548 " --> pdb=" O LEU x 418 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE x 420 " --> pdb=" O VAL x 548 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL x 550 " --> pdb=" O ILE x 420 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU x 549 " --> pdb=" O VAL x 517 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS x 447 " --> pdb=" O SER x 515 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL x 517 " --> pdb=" O LYS x 447 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA x 449 " --> pdb=" O VAL x 517 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL x 519 " --> pdb=" O ALA x 449 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR x 451 " --> pdb=" O VAL x 519 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG x 494 " --> pdb=" O ILE x 448 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'x' and resid 479 through 481 Processing sheet with id= DP, first strand: chain 'x' and resid 579 through 583 removed outlier: 7.109A pdb=" N GLY x 732 " --> pdb=" O ASP x 580 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE x 582 " --> pdb=" O GLY x 732 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS x 734 " --> pdb=" O PHE x 582 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP x 610 " --> pdb=" O ILE x 687 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL x 689 " --> pdb=" O ASP x 610 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU x 612 " --> pdb=" O VAL x 689 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP x 691 " --> pdb=" O LEU x 612 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE x 614 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'x' and resid 694 through 701 removed outlier: 3.566A pdb=" N CYS x 695 " --> pdb=" O THR x 712 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'x' and resid 984 through 986 Processing sheet with id= DS, first strand: chain 'x' and resid 988 through 991 removed outlier: 3.544A pdb=" N GLU x 988 " --> pdb=" O ARG x 998 " (cutoff:3.500A) 3914 hydrogen bonds defined for protein. 10584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 204 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 173 stacking parallelities Total time for adding SS restraints: 70.81 Time building geometry restraints manager: 39.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 16064 1.31 - 1.45: 29535 1.45 - 1.60: 50481 1.60 - 1.74: 379 1.74 - 1.89: 435 Bond restraints: 96894 Sorted by residual: bond pdb=" CA ASP C 387 " pdb=" C ASP C 387 " ideal model delta sigma weight residual 1.520 1.478 0.041 4.80e-03 4.34e+04 7.41e+01 bond pdb=" C ASN p 156 " pdb=" N ASN p 157 " ideal model delta sigma weight residual 1.332 1.216 0.116 1.40e-02 5.10e+03 6.90e+01 bond pdb=" C PHE A 316 " pdb=" N PRO A 317 " ideal model delta sigma weight residual 1.337 1.246 0.090 1.11e-02 8.12e+03 6.64e+01 bond pdb=" CA GLN A 483 " pdb=" C GLN A 483 " ideal model delta sigma weight residual 1.522 1.427 0.095 1.23e-02 6.61e+03 5.94e+01 bond pdb=" CA THR T 353 " pdb=" C THR T 353 " ideal model delta sigma weight residual 1.522 1.428 0.093 1.22e-02 6.72e+03 5.87e+01 ... (remaining 96889 not shown) Histogram of bond angle deviations from ideal: 88.19 - 98.85: 32 98.85 - 109.52: 17169 109.52 - 120.19: 74204 120.19 - 130.85: 42129 130.85 - 141.52: 458 Bond angle restraints: 133992 Sorted by residual: angle pdb=" C LYS T 187 " pdb=" N PRO T 188 " pdb=" CA PRO T 188 " ideal model delta sigma weight residual 119.76 132.89 -13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" CA PRO 4 83 " pdb=" CB PRO 4 83 " pdb=" CG PRO 4 83 " ideal model delta sigma weight residual 104.50 124.17 -19.67 1.90e+00 2.77e-01 1.07e+02 angle pdb=" O3' C B 104 " pdb=" C3' C B 104 " pdb=" C2' C B 104 " ideal model delta sigma weight residual 109.50 94.61 14.89 1.50e+00 4.44e-01 9.85e+01 angle pdb=" N ASP P 189 " pdb=" CA ASP P 189 " pdb=" C ASP P 189 " ideal model delta sigma weight residual 112.47 100.67 11.80 1.24e+00 6.50e-01 9.05e+01 angle pdb=" C HIS T 191 " pdb=" N PRO T 192 " pdb=" CA PRO T 192 " ideal model delta sigma weight residual 119.66 126.47 -6.81 7.20e-01 1.93e+00 8.96e+01 ... (remaining 133987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 56473 35.69 - 71.38: 1666 71.38 - 107.08: 173 107.08 - 142.77: 24 142.77 - 178.46: 14 Dihedral angle restraints: 58350 sinusoidal: 20895 harmonic: 37455 Sorted by residual: dihedral pdb=" CA PHE T 400 " pdb=" C PHE T 400 " pdb=" N PRO T 401 " pdb=" CA PRO T 401 " ideal model delta harmonic sigma weight residual -180.00 -53.95 -126.05 0 5.00e+00 4.00e-02 6.36e+02 dihedral pdb=" CA PHE A 166 " pdb=" C PHE A 166 " pdb=" N PRO A 167 " pdb=" CA PRO A 167 " ideal model delta harmonic sigma weight residual -180.00 -70.16 -109.84 0 5.00e+00 4.00e-02 4.83e+02 dihedral pdb=" CA GLN 11107 " pdb=" C GLN 11107 " pdb=" N ASN 11108 " pdb=" CA ASN 11108 " ideal model delta harmonic sigma weight residual -180.00 -91.23 -88.77 0 5.00e+00 4.00e-02 3.15e+02 ... (remaining 58347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 16139 0.951 - 1.902: 0 1.902 - 2.853: 0 2.853 - 3.804: 0 3.804 - 4.755: 2 Chirality restraints: 16141 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.24 -4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.15 -4.48 2.00e-01 2.50e+01 5.03e+02 chirality pdb=" CA LEU p 155 " pdb=" N LEU p 155 " pdb=" C LEU p 155 " pdb=" CB LEU p 155 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 ... (remaining 16138 not shown) Planarity restraints: 16348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 180 " 0.121 5.00e-02 4.00e+02 1.88e-01 5.68e+01 pdb=" N PRO R 181 " -0.326 5.00e-02 4.00e+02 pdb=" CA PRO R 181 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO R 181 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 91 " 0.107 5.00e-02 4.00e+02 1.70e-01 4.60e+01 pdb=" N PRO C 92 " -0.293 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Z 572 " 0.113 5.00e-02 4.00e+02 1.58e-01 4.01e+01 pdb=" N PRO Z 573 " -0.273 5.00e-02 4.00e+02 pdb=" CA PRO Z 573 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO Z 573 " 0.077 5.00e-02 4.00e+02 ... (remaining 16345 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 537 2.39 - 3.02: 60769 3.02 - 3.65: 142249 3.65 - 4.27: 205675 4.27 - 4.90: 322824 Nonbonded interactions: 732054 Sorted by model distance: nonbonded pdb=" O1G GTP C1500 " pdb="MG MG C1501 " model vdw 1.766 2.170 nonbonded pdb=" OD1 ASN A 221 " pdb=" OP1 U B 12 " model vdw 1.832 3.040 nonbonded pdb=" N LEU A 530 " pdb=" NE2 GLN M 198 " model vdw 1.843 3.200 nonbonded pdb=" OH TYR A 312 " pdb=" NH2 ARG C 853 " model vdw 1.846 2.520 nonbonded pdb=" O GLU Y 85 " pdb=" N ALA Z 502 " model vdw 1.847 2.520 ... (remaining 732049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 4 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 85)) selection = chain 'h' } ncs_group { reference = (chain 'b' and (resid 8 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 84 or (resid 85 and (name N or name CA or name \ C or name O )) or resid 86 through 89)) selection = (chain 'i' and resid 8 through 89) } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 4 through 48 or resid 54 through 76)) selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 16.950 Check model and map are aligned: 1.030 Set scattering table: 0.700 Process input model: 273.960 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.440 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:3.000 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 302.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 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 0.127 96894 Z= 0.737 Angle : 1.476 20.150 133992 Z= 0.967 Chirality : 0.100 4.755 16141 Planarity : 0.008 0.188 16348 Dihedral : 16.331 178.461 33971 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 1.21 % Allowed : 6.42 % Favored : 92.37 % Rotamer: Outliers : 4.95 % Allowed : 4.09 % Favored : 90.96 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 2.29 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.06), residues: 12647 helix: -2.07 (0.06), residues: 4789 sheet: -0.80 (0.10), residues: 2074 loop : -1.72 (0.07), residues: 5784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.006 TRP A 637 HIS 0.022 0.003 HIS C 139 PHE 0.067 0.005 PHE A 387 TYR 0.053 0.005 TYR C 314 ARG 0.035 0.002 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25294 Ramachandran restraints generated. 12647 Oldfield, 0 Emsley, 12647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25294 Ramachandran restraints generated. 12647 Oldfield, 0 Emsley, 12647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2659 residues out of total 11446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 2335 time to evaluate : 7.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable