Starting phenix.real_space_refine on Mon Mar 18 12:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb9_6413/03_2024/3jb9_6413_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 331 5.49 5 Mg 4 5.21 5 S 329 5.16 5 C 53506 2.51 5 N 15241 2.21 5 O 17133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 886": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1103": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ARG 1188": "NH1" <-> "NH2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A GLU 1300": "OE1" <-> "OE2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A GLU 1345": "OE1" <-> "OE2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A GLU 1465": "OE1" <-> "OE2" Residue "A ARG 1547": "NH1" <-> "NH2" Residue "A ARG 1557": "NH1" <-> "NH2" Residue "A ARG 1568": "NH1" <-> "NH2" Residue "A ARG 1602": "NH1" <-> "NH2" Residue "A GLU 1626": "OE1" <-> "OE2" Residue "A ARG 1811": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A GLU 1972": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 744": "NH1" <-> "NH2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B GLU 898": "OE1" <-> "OE2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "K PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M ARG 224": "NH1" <-> "NH2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 299": "OE1" <-> "OE2" Residue "S ARG 17": "NH1" <-> "NH2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "S ARG 122": "NH1" <-> "NH2" Residue "S GLU 124": "OE1" <-> "OE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "T ARG 17": "NH1" <-> "NH2" Residue "T GLU 24": "OE1" <-> "OE2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T ARG 33": "NH1" <-> "NH2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 48": "OE1" <-> "OE2" Residue "T GLU 86": "OE1" <-> "OE2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T GLU 121": "OE1" <-> "OE2" Residue "T GLU 124": "OE1" <-> "OE2" Residue "T GLU 127": "OE1" <-> "OE2" Residue "U ARG 17": "NH1" <-> "NH2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U ARG 26": "NH1" <-> "NH2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "V ARG 17": "NH1" <-> "NH2" Residue "V GLU 24": "OE1" <-> "OE2" Residue "V ARG 26": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V ARG 117": "NH1" <-> "NH2" Residue "V GLU 121": "OE1" <-> "OE2" Residue "V ARG 122": "NH1" <-> "NH2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "W GLU 188": "OE1" <-> "OE2" Residue "W GLU 201": "OE1" <-> "OE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W GLU 715": "OE1" <-> "OE2" Residue "W GLU 721": "OE1" <-> "OE2" Residue "W ARG 752": "NH1" <-> "NH2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 132": "OE1" <-> "OE2" Residue "Y ARG 171": "NH1" <-> "NH2" Residue "Y GLU 188": "OE1" <-> "OE2" Residue "Y GLU 220": "OE1" <-> "OE2" Residue "Y ARG 260": "NH1" <-> "NH2" Residue "Y ARG 261": "NH1" <-> "NH2" Residue "Y GLU 263": "OE1" <-> "OE2" Residue "Y GLU 264": "OE1" <-> "OE2" Residue "a GLU 24": "OE1" <-> "OE2" Residue "a GLU 38": "OE1" <-> "OE2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "c GLU 338": "OE1" <-> "OE2" Residue "c ARG 350": "NH1" <-> "NH2" Residue "c GLU 377": "OE1" <-> "OE2" Residue "c GLU 419": "OE1" <-> "OE2" Residue "c GLU 442": "OE1" <-> "OE2" Residue "c GLU 464": "OE1" <-> "OE2" Residue "c TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 492": "OE1" <-> "OE2" Residue "c ARG 499": "NH1" <-> "NH2" Residue "c GLU 532": "OE1" <-> "OE2" Residue "c ARG 537": "NH1" <-> "NH2" Residue "c GLU 544": "OE1" <-> "OE2" Residue "c GLU 582": "OE1" <-> "OE2" Residue "d GLU 20": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d ARG 62": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 131": "NH1" <-> "NH2" Residue "d ARG 136": "NH1" <-> "NH2" Residue "d ARG 142": "NH1" <-> "NH2" Residue "d GLU 145": "OE1" <-> "OE2" Residue "e ARG 5": "NH1" <-> "NH2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e ARG 58": "NH1" <-> "NH2" Residue "g GLU 61": "OE1" <-> "OE2" Residue "g ARG 91": "NH1" <-> "NH2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g GLU 102": "OE1" <-> "OE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h ARG 59": "NH1" <-> "NH2" Residue "h ARG 223": "NH1" <-> "NH2" Residue "h GLU 254": "OE1" <-> "OE2" Residue "h ARG 262": "NH1" <-> "NH2" Residue "i GLU 19": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i ARG 35": "NH1" <-> "NH2" Residue "i ARG 181": "NH1" <-> "NH2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 80": "OE1" <-> "OE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R GLU 149": "OE1" <-> "OE2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 188": "OE1" <-> "OE2" Residue "R GLU 215": "OE1" <-> "OE2" Residue "R GLU 216": "OE1" <-> "OE2" Residue "R GLU 241": "OE1" <-> "OE2" Residue "R ARG 242": "NH1" <-> "NH2" Residue "R GLU 251": "OE1" <-> "OE2" Residue "R GLU 256": "OE1" <-> "OE2" Residue "R GLU 278": "OE1" <-> "OE2" Residue "R GLU 282": "OE1" <-> "OE2" Residue "r ARG 505": "NH1" <-> "NH2" Residue "r GLU 538": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X ARG 1031": "NH1" <-> "NH2" Residue "X ARG 1038": "NH1" <-> "NH2" Residue "Z GLU 10": "OE1" <-> "OE2" Residue "Z GLU 32": "OE1" <-> "OE2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "b GLU 60": "OE1" <-> "OE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "f GLU 13": "OE1" <-> "OE2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "l GLU 21": "OE1" <-> "OE2" Residue "l GLU 22": "OE1" <-> "OE2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "n GLU 29": "OE1" <-> "OE2" Residue "n GLU 75": "OE1" <-> "OE2" Residue "o GLU 53": "OE1" <-> "OE2" 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: 86551 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 16230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1964, 16230 Classifications: {'peptide': 1964} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 104, 'TRANS': 1858} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 7196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7196 Classifications: {'peptide': 904} Link IDs: {'PTRANS': 52, 'TRANS': 851} Chain: "C" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 2209 Classifications: {'RNA': 105} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 38, 'rna3p_pyr': 47} Link IDs: {'rna2p': 20, 'rna3p': 84} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 730 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "G" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 620 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain breaks: 1 Chain: "J" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 573 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "K" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2730 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'UNK:plan-1': 51, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "L" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2273 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 3 Chain: "M" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1661 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 185} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1928 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 45, 'rna3p_pyr': 24} Link IDs: {'rna2p': 21, 'rna3p': 68} Chain: "O" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "Q" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 11} Chain: "P" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2323 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 12, 'rna3p_pur': 37, 'rna3p_pyr': 59} Link IDs: {'rna2p': 15, 'rna3p': 95} Chain breaks: 4 Chain: "S" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1069 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "U" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2864 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 7 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 413 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 12, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 17, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 300 Chain: "V" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3024 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 417} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 152, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 160 Chain: "Y" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'UNK:plan-1': 23, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1751 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 2, 'UNK:plan-1': 58, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "c" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2425 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 285} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1187 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "e" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1176 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "g" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1013 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 11, 'TRANS': 136} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "h" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 752 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "i" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1218 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 3800 Classifications: {'peptide': 575} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 315} Link IDs: {'PTRANS': 5, 'TRANS': 569} Chain breaks: 22 Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 995 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 325} Unresolved non-hydrogen planarities: 325 Chain: "r" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 3299 Classifications: {'peptide': 573} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 423} Link IDs: {'PTRANS': 2, 'TRANS': 570} Chain breaks: 29 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 899 Unresolved non-hydrogen angles: 1353 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 435} Unresolved non-hydrogen planarities: 439 Chain: "X" Number of atoms: 9764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9764 Classifications: {'peptide': 1195} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 37, 'TRANS': 1152} Chain breaks: 25 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "j" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1108 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 129 Chain: "k" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 618 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "Z" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 639 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "b" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 1 Chain: "f" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "l" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 620 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "n" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain breaks: 1 Chain: "o" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 573 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "x" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 1360 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'TRANS': 271} Chain breaks: 13 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 816 Unresolved non-hydrogen dihedrals: 272 Planarities with less than four sites: {'UNK:plan-1': 272} Unresolved non-hydrogen planarities: 272 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "e" 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: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 51224 SG CYS Y 117 57.287 167.708 162.430 1.00161.65 S ATOM 51289 SG CYS Y 125 57.343 171.044 164.224 1.00140.65 S ATOM 51329 SG CYS Y 131 56.469 170.636 160.764 1.00172.23 S ATOM 52903 SG CYS a 44 84.724 160.301 150.452 1.00 89.03 S ATOM 53114 SG CYS a 70 87.163 159.477 147.343 1.00 84.95 S ATOM 52737 SG CYS a 23 71.080 156.001 143.089 1.00 87.04 S ATOM 52763 SG CYS a 26 71.048 159.252 142.973 1.00138.77 S ATOM 53188 SG CYS a 80 73.283 157.296 144.548 1.00 82.66 S ATOM 53209 SG CYS a 83 70.754 157.472 145.922 1.00 95.87 S ATOM 55056 SG CYS c 412 133.078 197.168 221.105 1.00207.84 S ATOM 55077 SG CYS c 415 130.844 198.779 222.928 1.00235.70 S ATOM 58899 SG CYS e 101 60.455 191.215 139.264 1.00 54.45 S ATOM 58905 SG CYS e 102 63.602 191.889 141.240 1.00 55.38 S ATOM 58930 SG CYS e 105 62.990 189.077 140.007 1.00 58.82 S ATOM 59180 SG CYS e 137 61.951 190.556 142.964 1.00 64.47 S ATOM 59190 SG CYS e 139 60.462 189.154 141.069 1.00 88.36 S ATOM 58899 SG CYS e 101 60.455 191.215 139.264 1.00 54.45 S ATOM 59031 SG CYS e 119 60.128 187.688 138.501 1.00 53.25 S ATOM 59190 SG CYS e 139 60.462 189.154 141.069 1.00 88.36 S ATOM 59208 SG CYS e 142 58.105 189.877 138.782 1.00 55.51 S ATOM 58930 SG CYS e 105 62.990 189.077 140.007 1.00 58.82 S ATOM 59017 SG CYS e 117 62.037 186.199 140.007 1.00 42.49 S ATOM 59031 SG CYS e 119 60.128 187.688 138.501 1.00 53.25 S ATOM 59157 SG CYS e 134 62.667 186.582 142.540 1.00 98.88 S ATOM 59190 SG CYS e 139 60.462 189.154 141.069 1.00 88.36 S Time building chain proxies: 34.28, per 1000 atoms: 0.40 Number of scatterers: 86551 At special positions: 0 Unit cell: (242.88, 275.88, 314.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 329 16.00 P 331 15.00 Mg 4 11.99 O 17133 8.00 N 15241 7.00 C 53506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 47 " - pdb=" SG CYS a 73 " distance=2.97 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 Atom "HETATM86549 O5' ADP X1500 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 27.59 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 125 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 117 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 131 " pdb="ZN ZN Y 501 " - pdb=" NE2 HIS Y 135 " pdb=" ZN a 401 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 70 " pdb="ZN ZN a 401 " - pdb=" SG CYS a 44 " pdb=" ZN a 402 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 83 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 80 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 402 " - pdb=" SG CYS a 26 " pdb=" ZN c 701 " pdb="ZN ZN c 701 " - pdb=" NE2 HIS c 502 " pdb="ZN ZN c 701 " - pdb=" SG CYS c 412 " pdb="ZN ZN c 701 " - pdb=" SG CYS c 415 " pdb=" ZN e 202 " pdb="ZN ZN e 202 " - pdb=" SG CYS e 142 " pdb="ZN ZN e 202 " - pdb=" SG CYS e 101 " pdb="ZN ZN e 202 " - pdb=" SG CYS e 139 " pdb="ZN ZN e 202 " - pdb=" SG CYS e 119 " Number of angles added : 15 18008 Ramachandran restraints generated. 9004 Oldfield, 0 Emsley, 9004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 384 helices and 84 sheets defined 49.3% alpha, 10.3% beta 60 base pairs and 146 stacking pairs defined. Time for finding SS restraints: 33.88 Creating SS restraints... Processing helix chain 'A' and resid 48 through 65 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.726A pdb=" N ILE A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.729A pdb=" N TYR A 109 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 110 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 114 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.512A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 removed outlier: 3.795A pdb=" N ARG A 173 " --> pdb=" O TRP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 251 through 263 removed outlier: 5.524A pdb=" N GLN A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 336 through 339 No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.597A pdb=" N LEU A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.636A pdb=" N LEU A 455 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 456 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 483 removed outlier: 3.666A pdb=" N SER A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 removed outlier: 4.172A pdb=" N LYS A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.797A pdb=" N LEU A 530 " --> pdb=" O MET A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 4.111A pdb=" N LYS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 588 removed outlier: 3.565A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 removed outlier: 5.440A pdb=" N GLY A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'A' and resid 624 through 639 removed outlier: 4.164A pdb=" N LEU A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 4.133A pdb=" N TRP A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) Proline residue: A 669 - end of helix removed outlier: 3.516A pdb=" N ARG A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 removed outlier: 3.576A pdb=" N ASP A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 719 removed outlier: 3.952A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 745 removed outlier: 4.130A pdb=" N HIS A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.512A pdb=" N ASN A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS A 769 " --> pdb=" O TYR A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 792 through 818 removed outlier: 3.952A pdb=" N LEU A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 802 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 842 Processing helix chain 'A' and resid 858 through 874 removed outlier: 4.350A pdb=" N ALA A 872 " --> pdb=" O ARG A 868 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 895 removed outlier: 3.527A pdb=" N ALA A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 936 through 955 Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.620A pdb=" N GLY A 981 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 982 " --> pdb=" O TRP A 978 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 983 " --> pdb=" O CYS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1010 No H-bonds generated for 'chain 'A' and resid 1007 through 1010' Processing helix chain 'A' and resid 1014 through 1023 removed outlier: 3.587A pdb=" N LEU A1022 " --> pdb=" O ARG A1018 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1035 removed outlier: 3.565A pdb=" N TYR A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1072 removed outlier: 3.702A pdb=" N LEU A1071 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1085 removed outlier: 3.543A pdb=" N GLU A1083 " --> pdb=" O GLN A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1126 through 1139 Processing helix chain 'A' and resid 1169 through 1185 removed outlier: 3.571A pdb=" N ASN A1173 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1227 No H-bonds generated for 'chain 'A' and resid 1224 through 1227' Processing helix chain 'A' and resid 1258 through 1274 removed outlier: 3.769A pdb=" N ARG A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1271 " --> pdb=" O ARG A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1295 removed outlier: 3.535A pdb=" N THR A1289 " --> pdb=" O ASN A1285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A1295 " --> pdb=" O LEU A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 3.749A pdb=" N ILE A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1304' 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 1312 through 1327 removed outlier: 3.582A pdb=" N GLU A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1341 No H-bonds generated for 'chain 'A' and resid 1338 through 1341' Processing helix chain 'A' and resid 1344 through 1346 No H-bonds generated for 'chain 'A' and resid 1344 through 1346' Processing helix chain 'A' and resid 1361 through 1363 No H-bonds generated for 'chain 'A' and resid 1361 through 1363' Processing helix chain 'A' and resid 1393 through 1395 No H-bonds generated for 'chain 'A' and resid 1393 through 1395' Processing helix chain 'A' and resid 1399 through 1423 removed outlier: 3.642A pdb=" N GLN A1407 " --> pdb=" O PHE A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1434 removed outlier: 4.596A pdb=" N ASP A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1446 Processing helix chain 'A' and resid 1449 through 1454 removed outlier: 4.467A pdb=" N HIS A1452 " --> pdb=" O LYS A1449 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A1454 " --> pdb=" O ARG A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1470 removed outlier: 3.685A pdb=" N GLU A1465 " --> pdb=" O ARG A1461 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN A1468 " --> pdb=" O THR A1464 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR A1469 " --> pdb=" O GLU A1465 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A1470 " --> pdb=" O PHE A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1502 removed outlier: 3.793A pdb=" N VAL A1496 " --> pdb=" O ASN A1492 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A1497 " --> pdb=" O ASN A1493 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1511 removed outlier: 3.933A pdb=" N HIS A1511 " --> pdb=" O GLY A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1517 No H-bonds generated for 'chain 'A' and resid 1514 through 1517' Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1543 through 1551 removed outlier: 4.018A pdb=" N ARG A1547 " --> pdb=" O THR A1543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1561 removed outlier: 3.736A pdb=" N PHE A1558 " --> pdb=" O PRO A1554 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A1559 " --> pdb=" O ASN A1555 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1560 " --> pdb=" O ARG A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1566 No H-bonds generated for 'chain 'A' and resid 1563 through 1566' Processing helix chain 'A' and resid 1591 through 1598 removed outlier: 3.753A pdb=" N SER A1596 " --> pdb=" O THR A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1621 removed outlier: 4.648A pdb=" N VAL A1620 " --> pdb=" O ASP A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1628 No H-bonds generated for 'chain 'A' and resid 1625 through 1628' Processing helix chain 'A' and resid 1700 through 1713 removed outlier: 4.083A pdb=" N THR A1713 " --> pdb=" O LEU A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1760 removed outlier: 3.583A pdb=" N LYS A1759 " --> pdb=" O ASN A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1775 Processing helix chain 'A' and resid 1790 through 1795 removed outlier: 3.539A pdb=" N GLU A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1851 No H-bonds generated for 'chain 'A' and resid 1848 through 1851' Processing helix chain 'A' and resid 1857 through 1875 removed outlier: 3.725A pdb=" N LYS A1862 " --> pdb=" O GLY A1858 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1866 " --> pdb=" O LYS A1862 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1868 " --> pdb=" O LYS A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 through 1899 removed outlier: 3.599A pdb=" N ASP A1894 " --> pdb=" O GLY A1891 " (cutoff:3.500A) Proline residue: A1895 - end of helix removed outlier: 3.569A pdb=" N VAL A1898 " --> pdb=" O PRO A1895 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1932 Processing helix chain 'A' and resid 1947 through 1950 No H-bonds generated for 'chain 'A' and resid 1947 through 1950' Processing helix chain 'A' and resid 1953 through 1967 removed outlier: 3.514A pdb=" N SER A1958 " --> pdb=" O TYR A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1980 Proline residue: A1980 - end of helix Processing helix chain 'A' and resid 1997 through 2018 removed outlier: 3.563A pdb=" N LEU A2001 " --> pdb=" O ASP A1997 " (cutoff:3.500A) Proline residue: A2005 - end of helix Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.013A pdb=" N TYR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 128 through 137 Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.783A pdb=" N TYR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.710A pdb=" N VAL B 224 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 260 removed outlier: 3.587A pdb=" N HIS B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.510A pdb=" N HIS B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.569A pdb=" N TYR B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 352 No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 401 through 410 removed outlier: 3.673A pdb=" N LYS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.801A pdb=" N LEU B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 453 through 464 removed outlier: 4.072A pdb=" N ALA B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 478 removed outlier: 3.561A pdb=" N LEU B 478 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 627 removed outlier: 3.511A pdb=" N LEU B 614 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix removed outlier: 3.708A pdb=" N THR B 624 " --> pdb=" O LEU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 660 removed outlier: 3.931A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 4.037A pdb=" N ASN B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 713 " --> pdb=" O GLY B 709 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 714 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.667A pdb=" N PHE B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 765 through 768 No H-bonds generated for 'chain 'B' and resid 765 through 768' Processing helix chain 'B' and resid 770 through 773 No H-bonds generated for 'chain 'B' and resid 770 through 773' Processing helix chain 'B' and resid 778 through 783 removed outlier: 3.987A pdb=" N GLY B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 Proline residue: B 824 - end of helix Processing helix chain 'B' and resid 828 through 837 removed outlier: 3.754A pdb=" N LEU B 835 " --> pdb=" O TYR B 831 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Proline residue: B 858 - end of helix removed outlier: 3.549A pdb=" N ASP B 862 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 865 " --> pdb=" O ASP B 862 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 866 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 897 through 904 Processing helix chain 'B' and resid 941 through 955 removed outlier: 3.921A pdb=" N ARG B 945 " --> pdb=" O ASP B 942 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 949 " --> pdb=" O ASP B 946 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 removed outlier: 4.215A pdb=" N LEU D 8 " --> pdb=" O CYS D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'E' and resid 4 through 8 removed outlier: 3.707A pdb=" N SER E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 8' Processing helix chain 'F' and resid 4 through 7 No H-bonds generated for 'chain 'F' and resid 4 through 7' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 76 through 79 No H-bonds generated for 'chain 'F' and resid 76 through 79' Processing helix chain 'G' and resid 21 through 27 removed outlier: 3.653A pdb=" N PHE G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER G 26 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA G 27 " --> pdb=" O TYR G 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 27' Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.769A pdb=" N GLN G 35 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 38 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'H' and resid 12 through 21 removed outlier: 3.663A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 20 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN H 21 " --> pdb=" O PHE H 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 15 Processing helix chain 'J' and resid 10 through 12 No H-bonds generated for 'chain 'J' and resid 10 through 12' Processing helix chain 'K' and resid 79 through 92 removed outlier: 4.083A pdb=" N UNK K 83 " --> pdb=" O UNK K 79 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N UNK K 84 " --> pdb=" O UNK K 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N UNK K 85 " --> pdb=" O UNK K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 114 Processing helix chain 'K' and resid 125 through 143 removed outlier: 3.559A pdb=" N UNK K 142 " --> pdb=" O UNK K 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N UNK K 143 " --> pdb=" O UNK K 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 107 No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'M' and resid 121 through 124 Processing helix chain 'M' and resid 143 through 168 removed outlier: 3.764A pdb=" N GLU M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN M 151 " --> pdb=" O GLN M 147 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS M 163 " --> pdb=" O LYS M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 248 Processing helix chain 'M' and resid 268 through 270 No H-bonds generated for 'chain 'M' and resid 268 through 270' Processing helix chain 'M' and resid 286 through 314 removed outlier: 3.509A pdb=" N THR M 297 " --> pdb=" O GLU M 293 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL M 298 " --> pdb=" O ALA M 294 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 34 removed outlier: 3.722A pdb=" N GLN S 30 " --> pdb=" O ARG S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 131 removed outlier: 3.729A pdb=" N LEU S 85 " --> pdb=" O ASP S 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU S 90 " --> pdb=" O GLU S 86 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN S 93 " --> pdb=" O GLU S 89 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU S 96 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN S 99 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG S 113 " --> pdb=" O ASP S 109 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL S 114 " --> pdb=" O ALA S 110 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP S 123 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS S 131 " --> pdb=" O GLU S 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 34 removed outlier: 3.583A pdb=" N ARG T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 72 Processing helix chain 'T' and resid 74 through 133 removed outlier: 3.603A pdb=" N GLU T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS T 120 " --> pdb=" O SER T 116 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP T 123 " --> pdb=" O THR T 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER T 133 " --> pdb=" O LEU T 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 34 Processing helix chain 'U' and resid 70 through 134 removed outlier: 3.630A pdb=" N SER U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU U 89 " --> pdb=" O LEU U 85 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN U 93 " --> pdb=" O GLU U 89 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL U 114 " --> pdb=" O ALA U 110 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE U 115 " --> pdb=" O ALA U 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS U 120 " --> pdb=" O SER U 116 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU U 127 " --> pdb=" O ASP U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 184 Proline residue: U 184 - end of helix Processing helix chain 'U' and resid 471 through 473 No H-bonds generated for 'chain 'U' and resid 471 through 473' Processing helix chain 'V' and resid 25 through 34 Processing helix chain 'V' and resid 69 through 130 removed outlier: 3.707A pdb=" N SER V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU V 85 " --> pdb=" O ASP V 81 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU V 90 " --> pdb=" O GLU V 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG V 91 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN V 93 " --> pdb=" O GLU V 89 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU V 94 " --> pdb=" O LEU V 90 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER V 107 " --> pdb=" O THR V 103 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU V 112 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG V 113 " --> pdb=" O ASP V 109 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER V 116 " --> pdb=" O LEU V 112 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG V 117 " --> pdb=" O ARG V 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 23 removed outlier: 3.520A pdb=" N ILE W 16 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA W 19 " --> pdb=" O GLU W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 35 removed outlier: 3.817A pdb=" N LEU W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 50 removed outlier: 3.621A pdb=" N TRP W 48 " --> pdb=" O CYS W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 66 No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 71 through 75 removed outlier: 3.564A pdb=" N LEU W 75 " --> pdb=" O HIS W 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 71 through 75' Processing helix chain 'W' and resid 80 through 87 removed outlier: 3.562A pdb=" N ALA W 84 " --> pdb=" O TRP W 80 " (cutoff:3.500A) Proline residue: W 85 - end of helix No H-bonds generated for 'chain 'W' and resid 80 through 87' Processing helix chain 'W' and resid 92 through 108 removed outlier: 3.872A pdb=" N GLN W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA W 107 " --> pdb=" O ASP W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 171 removed outlier: 3.877A pdb=" N ARG W 167 " --> pdb=" O LEU W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 175 through 202 removed outlier: 3.527A pdb=" N SER W 194 " --> pdb=" O THR W 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN W 197 " --> pdb=" O LEU W 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 224 No H-bonds generated for 'chain 'W' and resid 222 through 224' Processing helix chain 'W' and resid 239 through 270 removed outlier: 3.664A pdb=" N UNK W 244 " --> pdb=" O UNK W 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK W 245 " --> pdb=" O UNK W 241 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N UNK W 247 " --> pdb=" O UNK W 243 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK W 248 " --> pdb=" O UNK W 244 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK W 249 " --> pdb=" O UNK W 245 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N UNK W 250 " --> pdb=" O UNK W 246 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N UNK W 254 " --> pdb=" O UNK W 250 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNK W 267 " --> pdb=" O UNK W 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N UNK W 269 " --> pdb=" O UNK W 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK W 270 " --> pdb=" O UNK W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 508 through 525 removed outlier: 3.799A pdb=" N UNK W 525 " --> pdb=" O UNK W 521 " (cutoff:3.500A) Processing helix chain 'W' and resid 529 through 533 Processing helix chain 'W' and resid 544 through 551 Processing helix chain 'W' and resid 555 through 570 removed outlier: 3.633A pdb=" N UNK W 560 " --> pdb=" O UNK W 556 " (cutoff:3.500A) Processing helix chain 'W' and resid 593 through 607 removed outlier: 3.591A pdb=" N UNK W 597 " --> pdb=" O UNK W 593 " (cutoff:3.500A) Processing helix chain 'W' and resid 615 through 638 removed outlier: 3.503A pdb=" N UNK W 620 " --> pdb=" O UNK W 616 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N UNK W 638 " --> pdb=" O UNK W 634 " (cutoff:3.500A) Processing helix chain 'W' and resid 653 through 756 removed outlier: 3.598A pdb=" N TYR W 657 " --> pdb=" O ALA W 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER W 685 " --> pdb=" O ASP W 681 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER W 686 " --> pdb=" O LEU W 682 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS W 696 " --> pdb=" O PHE W 692 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE W 697 " --> pdb=" O LEU W 693 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS W 702 " --> pdb=" O SER W 698 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU W 704 " --> pdb=" O ALA W 700 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR W 706 " --> pdb=" O LYS W 702 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU W 723 " --> pdb=" O ASN W 719 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA W 724 " --> pdb=" O GLN W 720 " (cutoff:3.500A) Proline residue: W 726 - end of helix removed outlier: 3.516A pdb=" N ILE W 742 " --> pdb=" O LYS W 738 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN W 747 " --> pdb=" O GLU W 743 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN W 748 " --> pdb=" O ALA W 744 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP W 749 " --> pdb=" O TYR W 745 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR W 750 " --> pdb=" O ALA W 746 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR W 754 " --> pdb=" O TYR W 750 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY W 755 " --> pdb=" O ALA W 751 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN W 756 " --> pdb=" O ARG W 752 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'Y' and resid 99 through 102 No H-bonds generated for 'chain 'Y' and resid 99 through 102' Processing helix chain 'Y' and resid 107 through 110 No H-bonds generated for 'chain 'Y' and resid 107 through 110' Processing helix chain 'Y' and resid 118 through 122 Processing helix chain 'Y' and resid 128 through 130 No H-bonds generated for 'chain 'Y' and resid 128 through 130' Processing helix chain 'Y' and resid 187 through 198 removed outlier: 3.585A pdb=" N ALA Y 196 " --> pdb=" O SER Y 192 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP Y 198 " --> pdb=" O HIS Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 230 removed outlier: 3.692A pdb=" N GLU Y 228 " --> pdb=" O GLN Y 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 271 Processing helix chain 'Y' and resid 276 through 288 Processing helix chain 'Y' and resid 293 through 303 Processing helix chain 'Y' and resid 316 through 323 Processing helix chain 'a' and resid 24 through 27 No H-bonds generated for 'chain 'a' and resid 24 through 27' Processing helix chain 'a' and resid 71 through 76 removed outlier: 3.719A pdb=" N TYR a 76 " --> pdb=" O GLY a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 99 Processing helix chain 'a' and resid 112 through 126 removed outlier: 3.699A pdb=" N ASN a 126 " --> pdb=" O ARG a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 150 removed outlier: 3.716A pdb=" N GLU a 148 " --> pdb=" O VAL a 144 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS a 149 " --> pdb=" O LYS a 145 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG a 150 " --> pdb=" O LYS a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 163 through 174 Processing helix chain 'a' and resid 225 through 235 removed outlier: 3.537A pdb=" N PHE a 232 " --> pdb=" O ILE a 228 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN a 234 " --> pdb=" O LYS a 230 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR a 235 " --> pdb=" O HIS a 231 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 266 removed outlier: 3.579A pdb=" N ALA a 265 " --> pdb=" O GLU a 261 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 313 removed outlier: 3.611A pdb=" N UNK a 312 " --> pdb=" O UNK a 308 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N UNK a 313 " --> pdb=" O UNK a 309 " (cutoff:3.500A) Processing helix chain 'a' and resid 318 through 336 removed outlier: 3.660A pdb=" N UNK a 331 " --> pdb=" O UNK a 327 " (cutoff:3.500A) Processing helix chain 'c' and resid 336 through 348 removed outlier: 3.911A pdb=" N GLN c 341 " --> pdb=" O ASP c 337 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU c 342 " --> pdb=" O GLU c 338 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS c 348 " --> pdb=" O LYS c 344 " (cutoff:3.500A) Processing helix chain 'c' and resid 354 through 365 removed outlier: 3.581A pdb=" N ILE c 362 " --> pdb=" O TYR c 358 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA c 363 " --> pdb=" O ALA c 359 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 383 removed outlier: 5.553A pdb=" N GLY c 380 " --> pdb=" O ASP c 376 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS c 381 " --> pdb=" O GLU c 377 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU c 382 " --> pdb=" O ASN c 378 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER c 383 " --> pdb=" O ALA c 379 " (cutoff:3.500A) Processing helix chain 'c' and resid 393 through 398 removed outlier: 4.143A pdb=" N SER c 398 " --> pdb=" O ALA c 394 " (cutoff:3.500A) Processing helix chain 'c' and resid 402 through 411 Processing helix chain 'c' and resid 464 through 483 removed outlier: 3.609A pdb=" N ASP c 468 " --> pdb=" O GLU c 464 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU c 469 " --> pdb=" O ASP c 465 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE c 470 " --> pdb=" O GLU c 466 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER c 483 " --> pdb=" O LEU c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 512 through 529 removed outlier: 3.815A pdb=" N LEU c 517 " --> pdb=" O ARG c 513 " (cutoff:3.500A) Proline residue: c 519 - end of helix removed outlier: 3.648A pdb=" N ARG c 523 " --> pdb=" O PRO c 519 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER c 527 " --> pdb=" O ARG c 523 " (cutoff:3.500A) Processing helix chain 'c' and resid 542 through 548 removed outlier: 4.180A pdb=" N LYS c 547 " --> pdb=" O LEU c 543 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS c 548 " --> pdb=" O GLU c 544 " (cutoff:3.500A) Processing helix chain 'c' and resid 554 through 557 No H-bonds generated for 'chain 'c' and resid 554 through 557' Processing helix chain 'c' and resid 582 through 585 No H-bonds generated for 'chain 'c' and resid 582 through 585' Processing helix chain 'c' and resid 591 through 599 removed outlier: 3.688A pdb=" N VAL c 595 " --> pdb=" O VAL c 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 630 removed outlier: 4.493A pdb=" N MET c 623 " --> pdb=" O PRO c 619 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE c 624 " --> pdb=" O ARG c 620 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG c 627 " --> pdb=" O MET c 623 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS c 630 " --> pdb=" O SER c 626 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 35 removed outlier: 3.712A pdb=" N TYR d 30 " --> pdb=" O CYS d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 112 No H-bonds generated for 'chain 'd' and resid 110 through 112' Processing helix chain 'd' and resid 126 through 134 removed outlier: 3.785A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 35 removed outlier: 3.822A pdb=" N ASP e 17 " --> pdb=" O ASP e 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU e 20 " --> pdb=" O ASP e 17 " (cutoff:3.500A) Proline residue: e 21 - end of helix removed outlier: 3.597A pdb=" N ASP e 28 " --> pdb=" O GLU e 25 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG e 31 " --> pdb=" O ASP e 28 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN e 35 " --> pdb=" O GLN e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 65 Proline residue: e 48 - end of helix removed outlier: 4.009A pdb=" N GLN e 51 " --> pdb=" O PRO e 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER e 57 " --> pdb=" O HIS e 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR e 59 " --> pdb=" O ARG e 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR e 64 " --> pdb=" O TYR e 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR e 65 " --> pdb=" O ASP e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 81 Processing helix chain 'e' and resid 86 through 93 removed outlier: 3.815A pdb=" N LYS e 91 " --> pdb=" O ASN e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 106 Processing helix chain 'e' and resid 118 through 120 No H-bonds generated for 'chain 'e' and resid 118 through 120' Processing helix chain 'g' and resid 15 through 29 Proline residue: g 19 - end of helix Proline residue: g 23 - end of helix removed outlier: 4.103A pdb=" N GLU g 28 " --> pdb=" O LEU g 24 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN g 29 " --> pdb=" O LEU g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 32 through 47 Processing helix chain 'g' and resid 59 through 63 removed outlier: 3.803A pdb=" N VAL g 63 " --> pdb=" O VAL g 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 59 through 63' Processing helix chain 'g' and resid 76 through 79 No H-bonds generated for 'chain 'g' and resid 76 through 79' Processing helix chain 'g' and resid 96 through 115 removed outlier: 3.677A pdb=" N ALA g 105 " --> pdb=" O GLN g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 137 removed outlier: 4.270A pdb=" N ARG g 137 " --> pdb=" O LYS g 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 45 through 50 removed outlier: 3.587A pdb=" N ARG h 49 " --> pdb=" O GLU h 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 50 " --> pdb=" O GLU h 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 45 through 50' Processing helix chain 'h' and resid 53 through 69 removed outlier: 3.524A pdb=" N LEU h 58 " --> pdb=" O ARG h 54 " (cutoff:3.500A) Processing helix chain 'h' and resid 242 through 244 No H-bonds generated for 'chain 'h' and resid 242 through 244' Processing helix chain 'h' and resid 255 through 262 Processing helix chain 'i' and resid 19 through 36 Processing helix chain 'i' and resid 59 through 70 Processing helix chain 'i' and resid 89 through 108 removed outlier: 3.571A pdb=" N GLU i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 115 removed outlier: 4.037A pdb=" N HIS i 115 " --> pdb=" O LEU i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 118 through 184 removed outlier: 3.666A pdb=" N SER i 123 " --> pdb=" O ALA i 119 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA i 126 " --> pdb=" O SER i 122 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU i 133 " --> pdb=" O VAL i 129 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU i 134 " --> pdb=" O GLN i 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS i 154 " --> pdb=" O ARG i 150 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA i 161 " --> pdb=" O MET i 157 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE i 178 " --> pdb=" O LEU i 174 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA i 183 " --> pdb=" O GLN i 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 27 removed outlier: 3.508A pdb=" N UNK R 20 " --> pdb=" O UNK R 16 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N UNK R 21 " --> pdb=" O UNK R 17 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK R 22 " --> pdb=" O UNK R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 65 removed outlier: 3.616A pdb=" N GLU R 50 " --> pdb=" O GLU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 83 removed outlier: 3.571A pdb=" N GLN R 83 " --> pdb=" O TRP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.898A pdb=" N GLU R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL R 99 " --> pdb=" O ARG R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 115 removed outlier: 3.766A pdb=" N GLU R 114 " --> pdb=" O TYR R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 133 removed outlier: 3.745A pdb=" N ASN R 125 " --> pdb=" O ASN R 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU R 126 " --> pdb=" O HIS R 122 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA R 130 " --> pdb=" O LEU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 151 removed outlier: 3.751A pdb=" N MET R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 165 removed outlier: 3.539A pdb=" N LEU R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 183 removed outlier: 3.933A pdb=" N SER R 176 " --> pdb=" O ASN R 172 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU R 181 " --> pdb=" O TYR R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 200 Processing helix chain 'R' and resid 204 through 217 removed outlier: 4.060A pdb=" N PHE R 213 " --> pdb=" O ARG R 209 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 234 removed outlier: 3.579A pdb=" N GLN R 225 " --> pdb=" O ALA R 221 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL R 226 " --> pdb=" O ASN R 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 254 removed outlier: 4.032A pdb=" N PHE R 250 " --> pdb=" O ALA R 246 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 271 removed outlier: 3.508A pdb=" N ARG R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR R 262 " --> pdb=" O GLU R 258 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE R 270 " --> pdb=" O TYR R 266 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 289 removed outlier: 3.818A pdb=" N GLU R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN R 289 " --> pdb=" O HIS R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 310 Processing helix chain 'R' and resid 317 through 332 Processing helix chain 'R' and resid 341 through 353 Processing helix chain 'R' and resid 361 through 368 removed outlier: 3.813A pdb=" N UNK R 366 " --> pdb=" O UNK R 362 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N UNK R 367 " --> pdb=" O UNK R 363 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N UNK R 368 " --> pdb=" O UNK R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 370 through 374 Processing helix chain 'R' and resid 380 through 389 Processing helix chain 'R' and resid 394 through 400 Processing helix chain 'R' and resid 413 through 423 removed outlier: 3.951A pdb=" N UNK R 418 " --> pdb=" O UNK R 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 443 removed outlier: 3.501A pdb=" N UNK R 443 " --> pdb=" O UNK R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 462 Processing helix chain 'R' and resid 469 through 479 removed outlier: 3.676A pdb=" N UNK R 473 " --> pdb=" O UNK R 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N UNK R 479 " --> pdb=" O UNK R 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 488 through 498 removed outlier: 3.671A pdb=" N UNK R 494 " --> pdb=" O UNK R 490 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK R 498 " --> pdb=" O UNK R 494 " (cutoff:3.500A) Processing helix chain 'R' and resid 503 through 515 Processing helix chain 'R' and resid 520 through 527 Processing helix chain 'R' and resid 539 through 550 Processing helix chain 'R' and resid 561 through 575 removed outlier: 3.692A pdb=" N UNK R 575 " --> pdb=" O UNK R 571 " (cutoff:3.500A) Processing helix chain 'R' and resid 585 through 594 Processing helix chain 'R' and resid 602 through 619 Processing helix chain 'R' and resid 626 through 640 Processing helix chain 'r' and resid 122 through 135 Processing helix chain 'r' and resid 140 through 152 Processing helix chain 'r' and resid 156 through 167 Processing helix chain 'r' and resid 172 through 184 Processing helix chain 'r' and resid 190 through 201 Processing helix chain 'r' and resid 205 through 217 removed outlier: 3.608A pdb=" N UNK r 211 " --> pdb=" O UNK r 207 " (cutoff:3.500A) Processing helix chain 'r' and resid 221 through 233 Processing helix chain 'r' and resid 237 through 249 Processing helix chain 'r' and resid 255 through 268 Processing helix chain 'r' and resid 273 through 285 Processing helix chain 'r' and resid 291 through 300 removed outlier: 3.585A pdb=" N UNK r 298 " --> pdb=" O UNK r 295 " (cutoff:3.500A) Processing helix chain 'r' and resid 304 through 316 Processing helix chain 'r' and resid 323 through 335 Processing helix chain 'r' and resid 339 through 349 Processing helix chain 'r' and resid 356 through 371 Processing helix chain 'r' and resid 376 through 393 removed outlier: 4.254A pdb=" N UNK r 392 " --> pdb=" O UNK r 388 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N UNK r 393 " --> pdb=" O UNK r 389 " (cutoff:3.500A) Processing helix chain 'r' and resid 399 through 417 Processing helix chain 'r' and resid 423 through 435 Processing helix chain 'r' and resid 440 through 458 Processing helix chain 'r' and resid 463 through 476 removed outlier: 3.538A pdb=" N UNK r 469 " --> pdb=" O UNK r 465 " (cutoff:3.500A) Processing helix chain 'r' and resid 482 through 494 removed outlier: 4.177A pdb=" N UNK r 491 " --> pdb=" O UNK r 488 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N UNK r 492 " --> pdb=" O UNK r 489 " (cutoff:3.500A) Processing helix chain 'r' and resid 499 through 507 removed outlier: 4.380A pdb=" N VAL r 506 " --> pdb=" O LEU r 502 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE r 507 " --> pdb=" O TYR r 503 " (cutoff:3.500A) Processing helix chain 'r' and resid 514 through 526 Processing helix chain 'r' and resid 531 through 564 removed outlier: 3.520A pdb=" N ALA r 542 " --> pdb=" O GLU r 538 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU r 543 " --> pdb=" O ARG r 539 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER r 545 " --> pdb=" O VAL r 541 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TYR r 546 " --> pdb=" O ALA r 542 " (cutoff:3.500A) Proline residue: r 547 - end of helix removed outlier: 6.339A pdb=" N PHE r 550 " --> pdb=" O TYR r 546 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU r 551 " --> pdb=" O PRO r 547 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU r 555 " --> pdb=" O GLU r 551 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR r 564 " --> pdb=" O PHE r 560 " (cutoff:3.500A) Processing helix chain 'r' and resid 569 through 580 Processing helix chain 'r' and resid 590 through 601 removed outlier: 4.047A pdb=" N LYS r 601 " --> pdb=" O ASP r 597 " (cutoff:3.500A) Processing helix chain 'r' and resid 605 through 614 Processing helix chain 'r' and resid 626 through 638 Processing helix chain 'r' and resid 642 through 652 removed outlier: 3.722A pdb=" N THR r 646 " --> pdb=" O LEU r 642 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU r 649 " --> pdb=" O ARG r 645 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS r 650 " --> pdb=" O THR r 646 " (cutoff:3.500A) Processing helix chain 'r' and resid 659 through 673 removed outlier: 4.291A pdb=" N UNK r 669 " --> pdb=" O UNK r 665 " (cutoff:3.500A) Processing helix chain 'r' and resid 678 through 690 Processing helix chain 'r' and resid 698 through 709 Processing helix chain 'r' and resid 716 through 735 Processing helix chain 'X' and resid 8 through 18 Processing helix chain 'X' and resid 29 through 36 Processing helix chain 'X' and resid 46 through 54 Processing helix chain 'X' and resid 57 through 60 No H-bonds generated for 'chain 'X' and resid 57 through 60' Processing helix chain 'X' and resid 68 through 70 No H-bonds generated for 'chain 'X' and resid 68 through 70' Processing helix chain 'X' and resid 75 through 87 Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.756A pdb=" N LYS X 107 " --> pdb=" O LEU X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 132 removed outlier: 3.515A pdb=" N GLN X 125 " --> pdb=" O VAL X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 146 removed outlier: 3.849A pdb=" N GLN X 145 " --> pdb=" O LYS X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 159 through 167 Processing helix chain 'X' and resid 169 through 182 removed outlier: 4.798A pdb=" N LYS X 173 " --> pdb=" O SER X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 207 removed outlier: 4.045A pdb=" N LEU X 191 " --> pdb=" O GLU X 187 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN X 193 " --> pdb=" O PHE X 189 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU X 195 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER X 196 " --> pdb=" O HIS X 192 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG X 197 " --> pdb=" O ASN X 193 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 232 Proline residue: X 221 - end of helix removed outlier: 3.990A pdb=" N LEU X 232 " --> pdb=" O SER X 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 248 removed outlier: 5.469A pdb=" N PHE X 241 " --> pdb=" O PRO X 237 " (cutoff:3.500A) Proline residue: X 244 - end of helix Processing helix chain 'X' and resid 251 through 257 Processing helix chain 'X' and resid 259 through 262 No H-bonds generated for 'chain 'X' and resid 259 through 262' Processing helix chain 'X' and resid 266 through 279 Processing helix chain 'X' and resid 292 through 312 removed outlier: 4.319A pdb=" N SER X 312 " --> pdb=" O LEU X 308 " (cutoff:3.500A) Processing helix chain 'X' and resid 332 through 341 removed outlier: 4.982A pdb=" N SER X 340 " --> pdb=" O GLU X 336 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE X 341 " --> pdb=" O GLU X 337 " (cutoff:3.500A) Processing helix chain 'X' and resid 344 through 354 Processing helix chain 'X' and resid 370 through 380 Processing helix chain 'X' and resid 386 through 391 Processing helix chain 'X' and resid 399 through 405 removed outlier: 3.515A pdb=" N GLY X 403 " --> pdb=" O ASP X 400 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG X 405 " --> pdb=" O LEU X 402 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 460 removed outlier: 3.700A pdb=" N ARG X 447 " --> pdb=" O LYS X 443 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER X 448 " --> pdb=" O LEU X 444 " (cutoff:3.500A) Processing helix chain 'X' and resid 516 through 521 Processing helix chain 'X' and resid 592 through 599 removed outlier: 4.105A pdb=" N GLY X 599 " --> pdb=" O LEU X 595 " (cutoff:3.500A) Processing helix chain 'X' and resid 622 through 634 removed outlier: 4.876A pdb=" N ASN X 633 " --> pdb=" O VAL X 629 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG X 634 " --> pdb=" O SER X 630 " (cutoff:3.500A) Processing helix chain 'X' and resid 640 through 646 removed outlier: 4.598A pdb=" N ASP X 644 " --> pdb=" O LYS X 640 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU X 645 " --> pdb=" O TRP X 641 " (cutoff:3.500A) Processing helix chain 'X' and resid 652 through 655 removed outlier: 4.236A pdb=" N CYS X 655 " --> pdb=" O PRO X 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 652 through 655' Processing helix chain 'X' and resid 668 through 670 No H-bonds generated for 'chain 'X' and resid 668 through 670' Processing helix chain 'X' and resid 674 through 680 Processing helix chain 'X' and resid 729 through 738 Processing helix chain 'X' and resid 754 through 768 Processing helix chain 'X' and resid 781 through 793 removed outlier: 3.590A pdb=" N LYS X 793 " --> pdb=" O THR X 789 " (cutoff:3.500A) Processing helix chain 'X' and resid 816 through 840 Proline residue: X 828 - end of helix Processing helix chain 'X' and resid 851 through 859 Processing helix chain 'X' and resid 863 through 873 Processing helix chain 'X' and resid 878 through 883 Processing helix chain 'X' and resid 904 through 933 Proline residue: X 930 - end of helix Processing helix chain 'X' and resid 937 through 946 Processing helix chain 'X' and resid 956 through 968 removed outlier: 5.872A pdb=" N GLY X 964 " --> pdb=" O SER X 960 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR X 965 " --> pdb=" O THR X 961 " (cutoff:3.500A) Processing helix chain 'X' and resid 981 through 983 No H-bonds generated for 'chain 'X' and resid 981 through 983' Processing helix chain 'X' and resid 986 through 995 Processing helix chain 'X' and resid 1028 through 1035 removed outlier: 4.067A pdb=" N TYR X1034 " --> pdb=" O LYS X1030 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU X1035 " --> pdb=" O ARG X1031 " (cutoff:3.500A) Processing helix chain 'X' and resid 1050 through 1055 removed outlier: 3.834A pdb=" N LEU X1055 " --> pdb=" O SER X1051 " (cutoff:3.500A) Processing helix chain 'X' and resid 1067 through 1069 No H-bonds generated for 'chain 'X' and resid 1067 through 1069' Processing helix chain 'X' and resid 1073 through 1076 No H-bonds generated for 'chain 'X' and resid 1073 through 1076' Processing helix chain 'X' and resid 1110 through 1125 Processing helix chain 'X' and resid 1130 through 1132 No H-bonds generated for 'chain 'X' and resid 1130 through 1132' Processing helix chain 'X' and resid 1140 through 1152 Processing helix chain 'X' and resid 1192 through 1195 Processing helix chain 'X' and resid 1197 through 1201 Processing helix chain 'X' and resid 1220 through 1222 No H-bonds generated for 'chain 'X' and resid 1220 through 1222' Processing helix chain 'X' and resid 1227 through 1235 removed outlier: 3.659A pdb=" N GLU X1232 " --> pdb=" O LYS X1228 " (cutoff:3.500A) Processing helix chain 'X' and resid 1266 through 1282 Processing helix chain 'j' and resid 5 through 10 removed outlier: 3.511A pdb=" N GLN j 10 " --> pdb=" O GLU j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 39 Processing helix chain 'j' and resid 82 through 85 No H-bonds generated for 'chain 'j' and resid 82 through 85' Processing helix chain 'j' and resid 102 through 110 Proline residue: j 107 - end of helix removed outlier: 3.565A pdb=" N SER j 110 " --> pdb=" O PRO j 107 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 126 Processing helix chain 'j' and resid 130 through 137 Processing helix chain 'j' and resid 151 through 159 Processing helix chain 'k' and resid 17 through 31 removed outlier: 4.195A pdb=" N THR k 30 " --> pdb=" O MET k 26 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR k 31 " --> pdb=" O LEU k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 65 Processing helix chain 'k' and resid 86 through 92 Processing helix chain 'Z' and resid 3 through 11 removed outlier: 4.215A pdb=" N LEU Z 8 " --> pdb=" O CYS Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 65 No H-bonds generated for 'chain 'Z' and resid 63 through 65' Processing helix chain 'Z' and resid 73 through 76 Processing helix chain 'b' and resid 4 through 8 removed outlier: 3.707A pdb=" N SER b 8 " --> pdb=" O THR b 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 4 through 8' Processing helix chain 'f' and resid 4 through 7 No H-bonds generated for 'chain 'f' and resid 4 through 7' Processing helix chain 'f' and resid 62 through 64 No H-bonds generated for 'chain 'f' and resid 62 through 64' Processing helix chain 'f' and resid 76 through 79 No H-bonds generated for 'chain 'f' and resid 76 through 79' Processing helix chain 'l' and resid 21 through 27 removed outlier: 3.653A pdb=" N PHE l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER l 26 " --> pdb=" O GLU l 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA l 27 " --> pdb=" O TYR l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 27' Processing helix chain 'l' and resid 29 through 38 removed outlier: 3.769A pdb=" N GLN l 35 " --> pdb=" O VAL l 32 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL l 37 " --> pdb=" O GLN l 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS l 38 " --> pdb=" O GLN l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 103 through 105 No H-bonds generated for 'chain 'l' and resid 103 through 105' Processing helix chain 'm' and resid 12 through 21 removed outlier: 3.663A pdb=" N LEU m 19 " --> pdb=" O PHE m 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN m 21 " --> pdb=" O PHE m 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 15 Processing helix chain 'o' and resid 10 through 12 No H-bonds generated for 'chain 'o' and resid 10 through 12' Processing helix chain 'x' and resid 19 through 34 Processing helix chain 'x' and resid 42 through 51 Processing helix chain 'x' and resid 55 through 73 Processing helix chain 'x' and resid 78 through 96 Processing helix chain 'x' and resid 100 through 115 Processing helix chain 'x' and resid 120 through 132 Processing helix chain 'x' and resid 137 through 148 Processing helix chain 'x' and resid 153 through 178 Processing helix chain 'x' and resid 183 through 216 Processing helix chain 'x' and resid 290 through 310 Processing helix chain 'x' and resid 339 through 358 Processing helix chain 'x' and resid 368 through 379 Processing helix chain 'x' and resid 383 through 397 Processing helix chain 'x' and resid 401 through 411 Processing sheet with id= A, first strand: chain 'A' and resid 505 through 511 Processing sheet with id= B, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.695A pdb=" N LYS A 548 " --> pdb=" O HIS A 540 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 918 through 921 Processing sheet with id= D, first strand: chain 'A' and resid 1201 through 1203 Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1042 Processing sheet with id= F, first strand: chain 'A' and resid 1209 through 1212 removed outlier: 3.851A pdb=" N LEU A1222 " --> pdb=" O GLN A1251 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A1240 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN A1251 " --> pdb=" O TRP A1238 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TRP A1238 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1366 through 1370 removed outlier: 3.550A pdb=" N TRP A1366 " --> pdb=" O PHE A1377 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A1373 " --> pdb=" O THR A1370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1686 through 1691 removed outlier: 7.396A pdb=" N VAL A1725 " --> pdb=" O ASP A1687 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLN A1689 " --> pdb=" O VAL A1725 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A1727 " --> pdb=" O GLN A1689 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG A1691 " --> pdb=" O ILE A1727 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE A1729 " --> pdb=" O ARG A1691 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1832 through 1834 removed outlier: 3.526A pdb=" N PHE A1832 " --> pdb=" O ASP A1805 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN A1884 " --> pdb=" O LEU A1802 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A1804 " --> pdb=" O GLN A1884 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A1886 " --> pdb=" O VAL A1804 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR A1907 " --> pdb=" O ILE A1885 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A1887 " --> pdb=" O THR A1907 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS A1909 " --> pdb=" O VAL A1887 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1812 through 1816 Processing sheet with id= K, first strand: chain 'A' and resid 1840 through 1844 removed outlier: 3.610A pdb=" N PHE A1941 " --> pdb=" O LEU A1841 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 145 through 148 Processing sheet with id= M, first strand: chain 'B' and resid 200 through 202 Processing sheet with id= N, first strand: chain 'B' and resid 360 through 362 removed outlier: 3.727A pdb=" N LYS B 367 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 551 through 555 removed outlier: 4.231A pdb=" N ILE B 544 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LEU B 563 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 494 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG B 509 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL B 492 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 537 through 540 Processing sheet with id= Q, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.594A pdb=" N THR B 642 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 632 " --> pdb=" O PHE B 644 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 606 through 608 removed outlier: 3.831A pdb=" N GLU B 607 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 677 through 680 Processing sheet with id= T, first strand: chain 'B' and resid 701 through 705 removed outlier: 3.856A pdb=" N GLU B 704 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 911 through 916 removed outlier: 3.538A pdb=" N GLN B 912 " --> pdb=" O GLU B 849 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 845 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 882 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 875 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN B 873 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU B 888 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 871 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLY B 869 " --> pdb=" O PRO B 890 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.831A pdb=" N GLU D 19 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU D 69 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 17 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 29 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN D 40 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 44 through 47 removed outlier: 3.636A pdb=" N VAL D 46 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 54 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 13 through 17 removed outlier: 3.557A pdb=" N GLN E 27 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 38 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 37 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.951A pdb=" N GLU F 18 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR F 68 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER F 16 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR F 28 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA F 42 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 72 through 74 Processing sheet with id= AA, first strand: chain 'G' and resid 98 through 101 removed outlier: 3.731A pdb=" N ALA G 59 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU G 69 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL G 57 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 26 through 28 removed outlier: 3.501A pdb=" N SER H 27 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN H 82 " --> pdb=" O SER H 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 36 through 38 removed outlier: 3.901A pdb=" N GLY H 69 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLN H 58 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU H 67 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 71 through 73 removed outlier: 3.927A pdb=" N GLY H 44 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP H 54 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE H 42 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 19 through 23 removed outlier: 3.612A pdb=" N LYS I 31 " --> pdb=" O GLU I 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU I 49 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 16 through 21 removed outlier: 3.788A pdb=" N GLY J 29 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS J 26 " --> pdb=" O GLU J 48 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 60 through 62 removed outlier: 3.689A pdb=" N GLY J 33 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU J 43 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU J 31 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 177 through 179 Processing sheet with id= AI, first strand: chain 'K' and resid 186 through 188 removed outlier: 3.585A pdb=" N ILE K 187 " --> pdb=" O LEU K 201 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 211 through 213 Processing sheet with id= AK, first strand: chain 'K' and resid 250 through 255 removed outlier: 6.101A pdb=" N ALA K 265 " --> pdb=" O TYR K 251 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU K 253 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL K 263 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY K 266 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 270 " --> pdb=" O GLY K 266 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA K 271 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP K 275 " --> pdb=" O ASN K 281 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN K 281 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 354 through 356 removed outlier: 3.557A pdb=" N ILE K 354 " --> pdb=" O PHE K 368 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 387 through 389 removed outlier: 3.753A pdb=" N GLN K 407 " --> pdb=" O PHE K 397 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'K' and resid 155 through 160 removed outlier: 6.539A pdb=" N ILE K 447 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL K 158 " --> pdb=" O VAL K 445 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL K 445 " --> pdb=" O VAL K 158 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER K 444 " --> pdb=" O GLU K 440 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS K 446 " --> pdb=" O THR K 438 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA K 426 " --> pdb=" O CYS K 439 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 292 through 297 removed outlier: 6.577A pdb=" N GLY K 307 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU K 295 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL K 305 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 55 through 58 removed outlier: 3.604A pdb=" N VAL L 55 " --> pdb=" O GLY L 68 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'L' and resid 107 through 109 removed outlier: 3.617A pdb=" N SER L 119 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG L 129 " --> pdb=" O SER L 119 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP L 121 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS L 127 " --> pdb=" O ASP L 121 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.903A pdb=" N ALA L 140 " --> pdb=" O VAL L 154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 154 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS L 172 " --> pdb=" O VAL L 162 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP L 164 " --> pdb=" O CYS L 170 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N CYS L 170 " --> pdb=" O ASP L 164 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 182 through 185 Processing sheet with id= AT, first strand: chain 'L' and resid 225 through 227 Processing sheet with id= AU, first strand: chain 'L' and resid 275 through 277 Processing sheet with id= AV, first strand: chain 'L' and resid 324 through 329 removed outlier: 3.786A pdb=" N SER L 329 " --> pdb=" O THR L 333 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR L 333 " --> pdb=" O SER L 329 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 182 through 185 Processing sheet with id= AX, first strand: chain 'S' and resid 13 through 15 Processing sheet with id= AY, first strand: chain 'T' and resid 13 through 15 Processing sheet with id= AZ, first strand: chain 'U' and resid 13 through 15 Processing sheet with id= BA, first strand: chain 'U' and resid 189 through 191 removed outlier: 3.592A pdb=" N LEU U 466 " --> pdb=" O THR U 479 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'U' and resid 202 through 207 removed outlier: 6.247A pdb=" N SER U 218 " --> pdb=" O ILE U 203 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU U 205 " --> pdb=" O PHE U 216 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE U 216 " --> pdb=" O GLU U 205 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU U 207 " --> pdb=" O SER U 214 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER U 214 " --> pdb=" O LEU U 207 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU U 228 " --> pdb=" O LEU U 234 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU U 234 " --> pdb=" O LEU U 228 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'U' and resid 251 through 256 removed outlier: 6.618A pdb=" N THR U 266 " --> pdb=" O LEU U 252 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS U 254 " --> pdb=" O VAL U 264 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL U 264 " --> pdb=" O CYS U 254 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRP U 256 " --> pdb=" O ILE U 262 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE U 262 " --> pdb=" O TRP U 256 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU U 282 " --> pdb=" O PRO U 276 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'U' and resid 325 through 328 removed outlier: 4.114A pdb=" N CYS U 318 " --> pdb=" O SER U 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE U 300 " --> pdb=" O ALA U 313 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'U' and resid 336 through 341 removed outlier: 6.257A pdb=" N GLY U 351 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU U 339 " --> pdb=" O VAL U 349 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL U 349 " --> pdb=" O LEU U 339 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL U 341 " --> pdb=" O LEU U 347 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU U 347 " --> pdb=" O VAL U 341 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR U 369 " --> pdb=" O PHE U 359 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU U 361 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU U 367 " --> pdb=" O GLU U 361 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'U' and resid 378 through 383 removed outlier: 6.791A pdb=" N THR U 393 " --> pdb=" O LYS U 379 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU U 381 " --> pdb=" O VAL U 391 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL U 391 " --> pdb=" O LEU U 381 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE U 383 " --> pdb=" O TRP U 389 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TRP U 389 " --> pdb=" O PHE U 383 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR U 394 " --> pdb=" O ASP U 399 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP U 399 " --> pdb=" O THR U 394 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN U 412 " --> pdb=" O ILE U 402 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP U 404 " --> pdb=" O LEU U 410 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU U 410 " --> pdb=" O ASP U 404 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'U' and resid 455 through 457 Processing sheet with id= BH, first strand: chain 'V' and resid 13 through 16 removed outlier: 4.180A pdb=" N ASN V 21 " --> pdb=" O SER V 16 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Y' and resid 177 through 179 Processing sheet with id= BJ, first strand: chain 'a' and resid 35 through 38 Processing sheet with id= BK, first strand: chain 'a' and resid 249 through 253 removed outlier: 3.535A pdb=" N ALA a 250 " --> pdb=" O ALA a 182 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'c' and resid 433 through 437 removed outlier: 6.417A pdb=" N ALA c 504 " --> pdb=" O ASN c 493 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN c 493 " --> pdb=" O ALA c 504 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'd' and resid 149 through 154 removed outlier: 6.690A pdb=" N GLN d 7 " --> pdb=" O ILE d 150 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA d 152 " --> pdb=" O GLU d 5 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU d 5 " --> pdb=" O ALA d 152 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU d 16 " --> pdb=" O VAL d 122 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL d 122 " --> pdb=" O GLU d 16 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR d 117 " --> pdb=" O MET d 90 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU d 88 " --> pdb=" O PHE d 119 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'X' and resid 483 through 485 Processing sheet with id= BO, first strand: chain 'X' and resid 699 through 704 Processing sheet with id= BP, first strand: chain 'X' and resid 1039 through 1041 removed outlier: 8.523A pdb=" N ILE X1040 " --> pdb=" O LEU X 743 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N MET X 745 " --> pdb=" O ILE X1040 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU X1005 " --> pdb=" O THR X 744 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL X 746 " --> pdb=" O LEU X1005 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU X1007 " --> pdb=" O VAL X 746 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU X 976 " --> pdb=" O VAL X1006 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU X1008 " --> pdb=" O LEU X 976 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL X 978 " --> pdb=" O LEU X1008 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL X 775 " --> pdb=" O ILE X 977 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'X' and resid 1087 through 1090 Processing sheet with id= BR, first strand: chain 'X' and resid 557 through 562 removed outlier: 7.016A pdb=" N ASN X 584 " --> pdb=" O ALA X 560 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'j' and resid 13 through 15 removed outlier: 7.106A pdb=" N ALA j 45 " --> pdb=" O LEU j 23 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR j 67 " --> pdb=" O ILE j 46 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR j 91 " --> pdb=" O LEU j 68 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN j 116 " --> pdb=" O LEU j 92 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'k' and resid 77 through 80 removed outlier: 3.518A pdb=" N ASP k 36 " --> pdb=" O VAL k 52 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Z' and resid 66 through 70 removed outlier: 6.831A pdb=" N GLU Z 19 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU Z 69 " --> pdb=" O THR Z 17 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR Z 17 " --> pdb=" O LEU Z 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Z 29 " --> pdb=" O ARG Z 42 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN Z 40 " --> pdb=" O ILE Z 31 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'Z' and resid 44 through 47 removed outlier: 3.635A pdb=" N VAL Z 46 " --> pdb=" O SER Z 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER Z 54 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'b' and resid 13 through 17 removed outlier: 3.558A pdb=" N GLN b 27 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL b 38 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU b 37 " --> pdb=" O LEU b 70 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'f' and resid 65 through 69 removed outlier: 6.952A pdb=" N GLU f 18 " --> pdb=" O ARG f 66 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR f 68 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER f 16 " --> pdb=" O TYR f 68 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR f 28 " --> pdb=" O ALA f 42 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA f 42 " --> pdb=" O THR f 28 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'l' and resid 72 through 74 Processing sheet with id= BZ, first strand: chain 'l' and resid 98 through 101 removed outlier: 3.732A pdb=" N ALA l 59 " --> pdb=" O VAL l 67 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU l 69 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL l 57 " --> pdb=" O GLU l 69 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'm' and resid 26 through 28 removed outlier: 3.501A pdb=" N SER m 27 " --> pdb=" O GLN m 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN m 82 " --> pdb=" O SER m 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CA Processing sheet with id= CB, first strand: chain 'm' and resid 36 through 38 removed outlier: 3.901A pdb=" N GLY m 69 " --> pdb=" O ALA m 56 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLN m 58 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU m 67 " --> pdb=" O GLN m 58 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'm' and resid 71 through 73 removed outlier: 3.927A pdb=" N GLY m 44 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP m 54 " --> pdb=" O ILE m 42 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE m 42 " --> pdb=" O ASP m 54 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'n' and resid 19 through 23 removed outlier: 3.611A pdb=" N LYS n 31 " --> pdb=" O GLU n 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU n 49 " --> pdb=" O LYS n 31 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'o' and resid 16 through 21 removed outlier: 3.788A pdb=" N GLY o 29 " --> pdb=" O VAL o 17 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS o 26 " --> pdb=" O GLU o 48 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'o' and resid 60 through 62 removed outlier: 3.689A pdb=" N GLY o 33 " --> pdb=" O VAL o 41 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU o 43 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU o 31 " --> pdb=" O GLU o 43 " (cutoff:3.500A) 3089 hydrogen bonds defined for protein. 8670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 256 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 146 stacking parallelities Total time for adding SS restraints: 48.70 Time building geometry restraints manager: 30.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.55: 87180 1.55 - 1.91: 1547 1.91 - 2.26: 0 2.26 - 2.62: 0 2.62 - 2.98: 1 Bond restraints: 88728 Sorted by residual: bond pdb=" C TYR W 236 " pdb=" N UNK W 238 " ideal model delta sigma weight residual 1.329 2.978 -1.649 1.40e-02 5.10e+03 1.39e+04 bond pdb=" CB THR j 76 " pdb=" OG1 THR j 76 " ideal model delta sigma weight residual 1.433 1.776 -0.343 1.60e-02 3.91e+03 4.60e+02 bond pdb=" CB SER j 118 " pdb=" OG SER j 118 " ideal model delta sigma weight residual 1.417 1.822 -0.405 2.00e-02 2.50e+03 4.10e+02 bond pdb=" CA ASN j 58 " pdb=" CB ASN j 58 " ideal model delta sigma weight residual 1.532 1.381 0.151 1.42e-02 4.96e+03 1.13e+02 bond pdb=" CB CYS U 318 " pdb=" SG CYS U 318 " ideal model delta sigma weight residual 1.808 1.480 0.328 3.30e-02 9.18e+02 9.87e+01 ... (remaining 88723 not shown) Histogram of bond angle deviations from ideal: 53.66 - 73.98: 1 73.98 - 94.29: 21 94.29 - 114.60: 56019 114.60 - 134.92: 65588 134.92 - 155.23: 14 Bond angle restraints: 121643 Sorted by residual: angle pdb=" O TYR W 236 " pdb=" C TYR W 236 " pdb=" N UNK W 238 " ideal model delta sigma weight residual 123.00 53.66 69.34 1.60e+00 3.91e-01 1.88e+03 angle pdb=" CA TYR W 236 " pdb=" C TYR W 236 " pdb=" N UNK W 238 " ideal model delta sigma weight residual 116.20 155.23 -39.03 2.00e+00 2.50e-01 3.81e+02 angle pdb=" CD ARG j 54 " pdb=" NE ARG j 54 " pdb=" CZ ARG j 54 " ideal model delta sigma weight residual 124.40 142.87 -18.47 1.40e+00 5.10e-01 1.74e+02 angle pdb=" C CYS j 70 " pdb=" N GLY j 71 " pdb=" CA GLY j 71 " ideal model delta sigma weight residual 120.10 131.63 -11.53 9.50e-01 1.11e+00 1.47e+02 angle pdb=" CA PHE j 48 " pdb=" CB PHE j 48 " pdb=" CG PHE j 48 " ideal model delta sigma weight residual 113.80 125.24 -11.44 1.00e+00 1.00e+00 1.31e+02 ... (remaining 121638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 51808 35.61 - 71.22: 2121 71.22 - 106.82: 172 106.82 - 142.43: 18 142.43 - 178.04: 16 Dihedral angle restraints: 54135 sinusoidal: 23419 harmonic: 30716 Sorted by residual: dihedral pdb=" C5' C N 21 " pdb=" C4' C N 21 " pdb=" C3' C N 21 " pdb=" O3' C N 21 " ideal model delta sinusoidal sigma weight residual 147.00 77.19 69.81 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" C4' C N 21 " pdb=" C3' C N 21 " pdb=" C2' C N 21 " pdb=" C1' C N 21 " ideal model delta sinusoidal sigma weight residual -35.00 33.66 -68.66 1 8.00e+00 1.56e-02 9.54e+01 dihedral pdb=" C4' C P 14 " pdb=" C3' C P 14 " pdb=" C2' C P 14 " pdb=" C1' C P 14 " ideal model delta sinusoidal sigma weight residual -35.00 32.86 -67.86 1 8.00e+00 1.56e-02 9.35e+01 ... (remaining 54132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 12554 0.115 - 0.231: 1442 0.231 - 0.346: 105 0.346 - 0.462: 15 0.462 - 0.577: 4 Chirality restraints: 14120 Sorted by residual: chirality pdb=" CA PRO j 112 " pdb=" N PRO j 112 " pdb=" C PRO j 112 " pdb=" CB PRO j 112 " both_signs ideal model delta sigma weight residual False 2.72 2.14 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CA HIS A 457 " pdb=" N HIS A 457 " pdb=" C HIS A 457 " pdb=" CB HIS A 457 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CA ALA k 93 " pdb=" N ALA k 93 " pdb=" C ALA k 93 " pdb=" CB ALA k 93 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.49 2.00e-01 2.50e+01 6.03e+00 ... (remaining 14117 not shown) Planarity restraints: 14487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR W 236 " 0.180 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" C TYR W 236 " -0.279 2.00e-02 2.50e+03 pdb=" O TYR W 236 " 0.014 2.00e-02 2.50e+03 pdb=" N UNK W 238 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK Y 303 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK Y 303 " 0.216 2.00e-02 2.50e+03 pdb=" O UNK Y 303 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK Y 304 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK Y 301 " 0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK Y 301 " -0.216 2.00e-02 2.50e+03 pdb=" O UNK Y 301 " 0.080 2.00e-02 2.50e+03 pdb=" N UNK Y 302 " 0.069 2.00e-02 2.50e+03 ... (remaining 14484 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 43 1.98 - 2.71: 4457 2.71 - 3.44: 124408 3.44 - 4.17: 203753 4.17 - 4.90: 349718 Nonbonded interactions: 682379 Sorted by model distance: nonbonded pdb=" SG CYS e 117 " pdb="ZN ZN e 203 " model vdw 1.253 2.590 nonbonded pdb=" N7 G N 75 " pdb=" NH2 ARG R 75 " model vdw 1.342 2.600 nonbonded pdb=" OD1 ASN A1821 " pdb=" CG GLN c 421 " model vdw 1.387 3.440 nonbonded pdb=" O2' C N 79 " pdb=" O5' A N 80 " model vdw 1.440 2.440 nonbonded pdb=" P G O 100 " pdb=" O2' A Q 501 " model vdw 1.497 3.400 ... (remaining 682374 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 'F' selection = chain 'f' } ncs_group { reference = (chain 'G' and (resid 19 through 78 or resid 89 through 115)) selection = chain 'l' } ncs_group { reference = chain 'H' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'o' } ncs_group { reference = (chain 'S' and (resid 1 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 64 or (resid 65 through 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 131)) selection = (chain 'T' and (resid 1 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 64 or (resid 65 throug \ h 66 and (name N or name CA or name C or name O or name CB )) or resid 67 throug \ h 131)) selection = (chain 'V' and (resid 1 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB )) or resid 58 through 131)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 13.220 Check model and map are aligned: 0.960 Set scattering table: 0.590 Process input model: 222.280 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.510 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: 0.030 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 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 : 0.010 1.649 88728 Z= 0.719 Angle : 1.295 69.335 121643 Z= 0.838 Chirality : 0.074 0.577 14120 Planarity : 0.007 0.231 14487 Dihedral : 18.143 178.040 34074 Min Nonbonded Distance : 1.253 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 3.01 % Allowed : 9.06 % Favored : 87.93 % Rotamer: Outliers : 8.06 % Allowed : 10.01 % Favored : 81.93 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.24 % Cis-general : 0.06 % Twisted Proline : 1.21 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.07), residues: 9004 helix: -2.75 (0.07), residues: 3262 sheet: -2.60 (0.13), residues: 1211 loop : -2.51 (0.08), residues: 4531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 169 HIS 0.015 0.002 HIS A 457 PHE 0.035 0.002 PHE U 321 TYR 0.042 0.002 TYR X1122 ARG 0.017 0.001 ARG X1224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18008 Ramachandran restraints generated. 9004 Oldfield, 0 Emsley, 9004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18008 Ramachandran restraints generated. 9004 Oldfield, 0 Emsley, 9004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2415 residues out of total 8214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 638 poor density : 1777 time to evaluate : 6.802 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 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