Starting phenix.real_space_refine on Sun Mar 17 15:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6id1_9647/03_2024/6id1_9647_updated.pdb" } resolution = 2.86 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= 0.009 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 410 5.49 5 Mg 7 5.21 5 S 222 5.16 5 C 48270 2.51 5 N 14595 2.21 5 O 16371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 861": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A ARG 1201": "NH1" <-> "NH2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1402": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1437": "NH1" <-> "NH2" Residue "A ARG 1439": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A GLU 1510": "OE1" <-> "OE2" Residue "A ARG 1544": "NH1" <-> "NH2" Residue "A ARG 1681": "NH1" <-> "NH2" Residue "A ARG 1744": "NH1" <-> "NH2" Residue "A ARG 1746": "NH1" <-> "NH2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A TYR 1930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L GLU 753": "OE1" <-> "OE2" Residue "L GLU 759": "OE1" <-> "OE2" Residue "M ARG 181": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ASP 224": "OD1" <-> "OD2" Residue "O GLU 257": "OE1" <-> "OE2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 273": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "U ARG 550": "NH1" <-> "NH2" Residue "U ARG 556": "NH1" <-> "NH2" Residue "U ARG 585": "NH1" <-> "NH2" Residue "U TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 649": "NH1" <-> "NH2" Residue "U ARG 666": "NH1" <-> "NH2" Residue "U ARG 704": "NH1" <-> "NH2" Residue "U TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 862": "NH1" <-> "NH2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "I ASP 386": "OD1" <-> "OD2" Residue "I ARG 543": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79882 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 16477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1981, 16477 Classifications: {'peptide': 1981} Link IDs: {'PTRANS': 106, 'TRANS': 1874} Chain breaks: 1 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2060 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 31, 'rna3p_pyr': 42} Link IDs: {'rna2p': 24, 'rna3p': 73} Chain: "C" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 888, 7022 Classifications: {'peptide': 888} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 833} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2366 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 10, 'TRANS': 292} Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2075 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 45, 'rna3p_pyr': 35} Link IDs: {'rna2p': 17, 'rna3p': 79} Chain: "J" Number of atoms: 3817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 3817 Classifications: {'peptide': 568} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 265} Link IDs: {'PTRANS': 17, 'TRANS': 550} Chain breaks: 15 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1135 Unresolved non-hydrogen angles: 1440 Unresolved non-hydrogen dihedrals: 962 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 15, 'PHE:plan': 15, 'GLU:plan': 44, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 706 Chain: "L" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3369 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 7 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 339 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1098 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "O" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2340 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain: "P" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 985 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain breaks: 1 Chain: "R" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2165 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 22, 'TRANS': 249} Chain: "S" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "T" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2496 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain: "W" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1276 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 10, 'TRANS': 147} Chain: "G" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1201 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 27} Link IDs: {'rna2p': 19, 'rna3p': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {' G%rna3p_pur:plan2': 8, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 5, ' U%rna3p_pyr:plan': 8, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 8, ' A%rna3p_pur:plan': 5} Unresolved non-hydrogen planarities: 268 Chain: "H" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2884 Classifications: {'RNA': 136} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 23, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 35, 'rna3p': 100} Chain breaks: 6 Chain: "U" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2864 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 334} Chain breaks: 1 Chain: "a" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 399 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 480 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "f" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "g" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 363 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "q" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 659 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 10, 'TRANS': 121} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "r" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 654 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 10, 'TRANS': 120} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 516 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 212 Chain: "s" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "t" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 335 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 980 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "I" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 2875 Classifications: {'peptide': 576} Incomplete info: {'backbone_only': 14, 'truncation_to_alanine': 471} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 18 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1914 Unresolved non-hydrogen angles: 2454 Unresolved non-hydrogen dihedrals: 1602 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 13, 'TYR:plan': 26, 'ASN:plan1': 16, 'TRP:plan': 9, 'ASP:plan': 36, 'PHE:plan': 22, 'GLU:plan': 56, 'ARG:plan': 47} Unresolved non-hydrogen planarities: 1183 Chain: "Q" Number of atoms: 6554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 6554 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 67, 'TRANS': 1254} Chain breaks: 8 Unresolved chain link angles: 67 Unresolved non-hydrogen bonds: 4578 Unresolved non-hydrogen angles: 5873 Unresolved non-hydrogen dihedrals: 3847 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'GLN:plan1': 63, 'ARG:plan': 84, 'TYR:plan': 52, 'ASN:plan1': 70, 'TRP:plan': 15, 'HIS:plan': 42, 'PHE:plan': 76, 'GLU:plan': 97, 'ASP:plan': 62} Unresolved non-hydrogen planarities: 2621 Chain: "y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Chain: "h" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 393 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 424 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "m" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "n" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 329 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "o" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 804 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 528 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 272 Chain: "p" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 464 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 163 Chain: "V" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 3285 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 591} Link IDs: {'CIS': 1, 'PTRANS': 39, 'TRANS': 622} Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2152 Unresolved non-hydrogen angles: 2756 Unresolved non-hydrogen dihedrals: 1782 Unresolved non-hydrogen chiralities: 195 Planarities with less than four sites: {'GLN:plan1': 32, 'HIS:plan': 14, 'TYR:plan': 28, 'ASN:plan1': 24, 'TRP:plan': 5, 'ASP:plan': 43, 'PHE:plan': 24, 'GLU:plan': 43, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1171 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39181 SG CYS N 105 72.320 173.435 113.344 1.00 2.14 S ATOM 39275 SG CYS N 117 72.448 170.256 111.314 1.00 9.28 S ATOM 39289 SG CYS N 119 69.206 171.852 111.699 1.00 7.98 S ATOM 39408 SG CYS N 134 71.350 170.168 114.605 1.00 11.73 S ATOM 39150 SG CYS N 101 68.994 175.041 112.794 1.00 8.39 S ATOM 39156 SG CYS N 102 72.086 176.737 114.893 1.00 3.20 S ATOM 39181 SG CYS N 105 72.320 173.435 113.344 1.00 2.14 S ATOM 39431 SG CYS N 137 69.500 174.852 116.062 1.00 10.15 S ATOM 39150 SG CYS N 101 68.994 175.041 112.794 1.00 8.39 S ATOM 39289 SG CYS N 119 69.206 171.852 111.699 1.00 7.98 S ATOM 39441 SG CYS N 139 65.891 173.016 112.911 1.00 14.14 S ATOM 39462 SG CYS N 142 67.514 174.659 109.770 1.00 12.88 S ATOM 39560 SG CYS O 24 79.288 139.526 114.618 1.00 19.98 S ATOM 39582 SG CYS O 27 78.329 142.067 116.946 1.00 18.96 S ATOM 40025 SG CYS O 81 82.684 141.112 116.271 1.00 13.08 S ATOM 40047 SG CYS O 84 80.002 139.166 118.571 1.00 27.32 S ATOM 39731 SG CYS O 45 91.838 144.046 124.998 1.00 22.06 S ATOM 39950 SG CYS O 71 94.437 145.381 122.171 1.00 15.95 S ATOM 39972 SG CYS O 74 93.544 140.759 124.086 1.00 20.11 S ATOM 40693 SG CYS O 165 65.517 157.328 129.393 1.00 22.66 S ATOM 40759 SG CYS O 173 62.863 159.633 128.379 1.00 23.20 S ATOM 40807 SG CYS O 179 65.689 158.438 125.842 1.00 21.72 S ATOM 55097 SG CYS U 675 134.626 177.759 198.343 1.00 34.30 S ATOM 55123 SG CYS U 678 130.534 179.619 200.720 1.00 38.05 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N MET Q 79 " occ=0.50 ... (3 atoms not shown) pdb=" CB MET Q 79 " occ=0.50 residue: pdb=" N MET Q 326 " occ=0.58 ... (3 atoms not shown) pdb=" CB MET Q 326 " occ=0.58 Time building chain proxies: 32.63, per 1000 atoms: 0.41 Number of scatterers: 79882 At special positions: 0 Unit cell: (246.192, 262.248, 268.938, 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 222 16.00 P 410 15.00 Mg 7 11.99 O 16371 8.00 N 14595 7.00 C 48270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.28 Conformation dependent library (CDL) restraints added in 11.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 117 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 134 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 119 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 137 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 102 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 101 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 101 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 119 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 142 " pdb="ZN ZN N 203 " - pdb=" SG CYS N 139 " pdb=" ZN O 501 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 81 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 84 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 27 " pdb="ZN ZN O 501 " - pdb=" SG CYS O 24 " pdb=" ZN O 502 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 74 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 45 " pdb="ZN ZN O 502 " - pdb=" SG CYS O 71 " pdb=" ZN O 503 " pdb="ZN ZN O 503 " - pdb=" NE2 HIS O 183 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 179 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 173 " pdb="ZN ZN O 503 " - pdb=" SG CYS O 165 " pdb=" ZN U 900 " pdb="ZN ZN U 900 " - pdb=" ND1 HIS U 765 " pdb="ZN ZN U 900 " - pdb=" NE2 HIS U 718 " pdb="ZN ZN U 900 " - pdb=" SG CYS U 678 " pdb="ZN ZN U 900 " - pdb=" SG CYS U 675 " Number of angles added : 29 21040 Ramachandran restraints generated. 10520 Oldfield, 0 Emsley, 10520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 380 helices and 91 sheets defined 40.9% alpha, 12.0% beta 57 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 28.70 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 5.299A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.814A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 removed outlier: 4.074A pdb=" N ARG A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 88 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Proline residue: A 96 - end of helix removed outlier: 4.207A pdb=" N LYS A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 542 through 565 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 616 removed outlier: 4.340A pdb=" N ARG A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 612 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 661 removed outlier: 3.745A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 677 through 696 removed outlier: 3.834A pdb=" N ARG A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 733 through 763 Processing helix chain 'A' and resid 769 through 797 removed outlier: 3.561A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 819 Processing helix chain 'A' and resid 835 through 847 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 913 through 932 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 990 through 1000 Processing helix chain 'A' and resid 1003 through 1013 removed outlier: 3.685A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1053 Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1123 through 1125 No H-bonds generated for 'chain 'A' and resid 1123 through 1125' Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.717A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1248 Processing helix chain 'A' and resid 1258 through 1273 Processing helix chain 'A' and resid 1282 through 1303 Processing helix chain 'A' and resid 1313 through 1317 removed outlier: 4.068A pdb=" N TYR A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1375 through 1398 removed outlier: 4.120A pdb=" N GLN A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1411 removed outlier: 4.172A pdb=" N SER A1411 " --> pdb=" O ASP A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1423 Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1436 through 1441 Processing helix chain 'A' and resid 1469 through 1478 Processing helix chain 'A' and resid 1480 through 1487 removed outlier: 3.532A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1512 through 1515 No H-bonds generated for 'chain 'A' and resid 1512 through 1515' Processing helix chain 'A' and resid 1520 through 1522 No H-bonds generated for 'chain 'A' and resid 1520 through 1522' Processing helix chain 'A' and resid 1529 through 1537 removed outlier: 3.822A pdb=" N ARG A1532 " --> pdb=" O ILE A1529 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG A1533 " --> pdb=" O PRO A1530 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A1534 " --> pdb=" O ASN A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1569 through 1576 Processing helix chain 'A' and resid 1581 through 1597 Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1723 through 1735 removed outlier: 3.744A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1768 through 1772 removed outlier: 3.763A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1851 Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 4.170A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1895 through 1898 Processing helix chain 'A' and resid 1900 through 1907 Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1947 through 1954 removed outlier: 3.659A pdb=" N LYS A1951 " --> pdb=" O ASP A1948 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1954 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1995 Processing helix chain 'A' and resid 2004 through 2011 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 117 through 125 removed outlier: 3.919A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 174 through 177 No H-bonds generated for 'chain 'C' and resid 174 through 177' Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.544A pdb=" N SER C 212 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 261 through 264 No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 271 through 292 removed outlier: 3.696A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 368 through 386 Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 435 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.653A pdb=" N LYS C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 467 Processing helix chain 'C' and resid 600 through 613 Processing helix chain 'C' and resid 634 through 647 Processing helix chain 'C' and resid 694 through 700 Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 756 through 776 removed outlier: 3.737A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 821 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 840 through 853 removed outlier: 3.887A pdb=" N SER C 844 " --> pdb=" O ALA C 840 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 890 Processing helix chain 'C' and resid 926 through 940 removed outlier: 3.630A pdb=" N LEU C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 199 Processing helix chain 'J' and resid 217 through 238 Processing helix chain 'J' and resid 243 through 253 Processing helix chain 'J' and resid 258 through 271 Processing helix chain 'J' and resid 276 through 288 Processing helix chain 'J' and resid 292 through 305 Processing helix chain 'J' and resid 310 through 322 Processing helix chain 'J' and resid 326 through 337 Processing helix chain 'J' and resid 343 through 356 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 376 through 388 Processing helix chain 'J' and resid 392 through 406 removed outlier: 3.849A pdb=" N GLU J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 430 through 439 Processing helix chain 'J' and resid 452 through 466 Processing helix chain 'J' and resid 478 through 490 Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 497 through 512 Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 541 through 554 removed outlier: 3.795A pdb=" N LEU J 546 " --> pdb=" O LEU J 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU J 547 " --> pdb=" O TYR J 543 " (cutoff:3.500A) Proline residue: J 551 - end of helix Processing helix chain 'J' and resid 560 through 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 594 through 596 No H-bonds generated for 'chain 'J' and resid 594 through 596' Processing helix chain 'J' and resid 599 through 604 Proline residue: J 604 - end of helix Processing helix chain 'J' and resid 610 through 623 removed outlier: 3.502A pdb=" N ASP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 642 Processing helix chain 'J' and resid 649 through 659 removed outlier: 3.678A pdb=" N LEU J 653 " --> pdb=" O LEU J 649 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 659 " --> pdb=" O ASP J 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 678 Proline residue: J 670 - end of helix Proline residue: J 675 - end of helix Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 700 through 707 Processing helix chain 'J' and resid 719 through 730 Processing helix chain 'J' and resid 742 through 754 Processing helix chain 'J' and resid 765 through 774 Processing helix chain 'J' and resid 782 through 799 Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 31 through 34 No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 43 through 53 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 111 removed outlier: 4.476A pdb=" N ARG L 110 " --> pdb=" O LYS L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 146 through 160 Processing helix chain 'L' and resid 165 through 194 Processing helix chain 'L' and resid 244 through 248 removed outlier: 3.734A pdb=" N ASP L 248 " --> pdb=" O GLN L 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 244 through 248' Processing helix chain 'L' and resid 252 through 269 Processing helix chain 'L' and resid 508 through 525 removed outlier: 3.799A pdb=" N ILE L 525 " --> pdb=" O ARG L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 533 Processing helix chain 'L' and resid 544 through 551 Proline residue: L 548 - end of helix Processing helix chain 'L' and resid 557 through 570 Proline residue: L 563 - end of helix Processing helix chain 'L' and resid 594 through 607 Processing helix chain 'L' and resid 615 through 628 Proline residue: L 620 - end of helix Processing helix chain 'L' and resid 691 through 794 removed outlier: 3.597A pdb=" N ARG L 695 " --> pdb=" O SER L 691 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY L 723 " --> pdb=" O ILE L 719 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 724 " --> pdb=" O LEU L 720 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU L 743 " --> pdb=" O TRP L 739 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN L 744 " --> pdb=" O ASP L 740 " (cutoff:3.500A) Proline residue: L 764 - end of helix removed outlier: 3.980A pdb=" N LEU L 767 " --> pdb=" O ILE L 763 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU L 768 " --> pdb=" O PRO L 764 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG L 780 " --> pdb=" O ARG L 776 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 785 " --> pdb=" O GLU L 781 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS L 786 " --> pdb=" O LYS L 782 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG L 787 " --> pdb=" O GLU L 783 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR L 788 " --> pdb=" O LEU L 784 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU L 792 " --> pdb=" O TYR L 788 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU L 793 " --> pdb=" O ALA L 789 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU L 794 " --> pdb=" O ASP L 790 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 141 removed outlier: 3.575A pdb=" N GLN M 131 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 160 removed outlier: 7.131A pdb=" N GLU M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU M 159 " --> pdb=" O LYS M 155 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE M 160 " --> pdb=" O HIS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 194 Processing helix chain 'M' and resid 214 through 225 Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'N' and resid 13 through 17 removed outlier: 4.400A pdb=" N GLU N 16 " --> pdb=" O ASP N 13 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 13 through 17' Processing helix chain 'N' and resid 19 through 34 removed outlier: 3.732A pdb=" N THR N 34 " --> pdb=" O ARG N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 65 Proline residue: N 48 - end of helix removed outlier: 3.571A pdb=" N ILE N 52 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS N 53 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS N 56 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE N 60 " --> pdb=" O THR N 57 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE N 64 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 80 Processing helix chain 'N' and resid 86 through 92 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 123 through 126 No H-bonds generated for 'chain 'N' and resid 123 through 126' Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 94 through 99 Processing helix chain 'O' and resid 111 through 126 Processing helix chain 'O' and resid 138 through 141 No H-bonds generated for 'chain 'O' and resid 138 through 141' Processing helix chain 'O' and resid 146 through 148 No H-bonds generated for 'chain 'O' and resid 146 through 148' Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 198 through 203 Processing helix chain 'O' and resid 208 through 219 removed outlier: 3.506A pdb=" N THR O 219 " --> pdb=" O LYS O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 255 removed outlier: 3.916A pdb=" N ARG O 249 " --> pdb=" O GLU O 245 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN O 250 " --> pdb=" O THR O 246 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN O 254 " --> pdb=" O ASN O 250 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE O 255 " --> pdb=" O HIS O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 287 Processing helix chain 'P' and resid 23 through 26 No H-bonds generated for 'chain 'P' and resid 23 through 26' Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 51 through 55 Processing helix chain 'P' and resid 59 through 77 Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing helix chain 'R' and resid 137 through 161 removed outlier: 3.521A pdb=" N LYS R 153 " --> pdb=" O VAL R 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 244 Processing helix chain 'R' and resid 264 through 267 No H-bonds generated for 'chain 'R' and resid 264 through 267' Processing helix chain 'R' and resid 283 through 316 removed outlier: 3.968A pdb=" N ALA R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN R 307 " --> pdb=" O GLU R 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 45 Processing helix chain 'S' and resid 121 through 125 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'W' and resid 102 through 105 No H-bonds generated for 'chain 'W' and resid 102 through 105' Processing helix chain 'W' and resid 122 through 134 Processing helix chain 'W' and resid 156 through 161 removed outlier: 3.513A pdb=" N GLU W 160 " --> pdb=" O VAL W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 224 Processing helix chain 'U' and resid 599 through 608 Processing helix chain 'U' and resid 615 through 621 removed outlier: 3.881A pdb=" N ARG U 620 " --> pdb=" O LYS U 616 " (cutoff:3.500A) Processing helix chain 'U' and resid 636 through 643 Processing helix chain 'U' and resid 651 through 673 removed outlier: 3.831A pdb=" N GLU U 664 " --> pdb=" O LYS U 660 " (cutoff:3.500A) Processing helix chain 'U' and resid 727 through 746 Processing helix chain 'U' and resid 775 through 778 No H-bonds generated for 'chain 'U' and resid 775 through 778' Processing helix chain 'U' and resid 781 through 790 removed outlier: 3.817A pdb=" N MET U 790 " --> pdb=" O LYS U 786 " (cutoff:3.500A) Processing helix chain 'U' and resid 846 through 853 Processing helix chain 'U' and resid 876 through 882 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'b' and resid 7 through 10 No H-bonds generated for 'chain 'b' and resid 7 through 10' Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.960A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'q' and resid 27 through 36 removed outlier: 3.720A pdb=" N LYS q 32 " --> pdb=" O ARG q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 133 removed outlier: 3.728A pdb=" N LEU q 87 " --> pdb=" O ASP q 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE q 90 " --> pdb=" O MET q 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU q 92 " --> pdb=" O HIS q 88 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN q 95 " --> pdb=" O THR q 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR q 98 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN q 101 " --> pdb=" O GLN q 97 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG q 115 " --> pdb=" O ASP q 111 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL q 116 " --> pdb=" O ALA q 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR q 125 " --> pdb=" O THR q 121 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR q 133 " --> pdb=" O GLU q 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 36 Processing helix chain 'r' and resid 70 through 74 Processing helix chain 'r' and resid 76 through 132 removed outlier: 3.602A pdb=" N HIS r 88 " --> pdb=" O ALA r 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS r 122 " --> pdb=" O ALA r 118 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR r 125 " --> pdb=" O THR r 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA r 126 " --> pdb=" O LYS r 122 " (cutoff:3.500A) Processing helix chain 's' and resid 72 through 133 removed outlier: 3.629A pdb=" N ALA s 84 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR s 91 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN s 95 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU s 102 " --> pdb=" O THR s 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE s 117 " --> pdb=" O ALA s 113 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS s 122 " --> pdb=" O ALA s 118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU s 129 " --> pdb=" O THR s 125 " (cutoff:3.500A) Processing helix chain 't' and resid 71 through 132 removed outlier: 3.704A pdb=" N LYS t 76 " --> pdb=" O PRO t 72 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU t 87 " --> pdb=" O ASP t 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU t 92 " --> pdb=" O HIS t 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG t 93 " --> pdb=" O SER t 89 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN t 95 " --> pdb=" O THR t 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN t 109 " --> pdb=" O HIS t 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS t 114 " --> pdb=" O HIS t 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG t 115 " --> pdb=" O ASP t 111 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA t 118 " --> pdb=" O CYS t 114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG t 119 " --> pdb=" O ARG t 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 42 Processing helix chain 'K' and resid 66 through 77 Processing helix chain 'K' and resid 106 through 134 removed outlier: 3.687A pdb=" N ASN K 133 " --> pdb=" O GLN K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 198 removed outlier: 3.544A pdb=" N HIS K 144 " --> pdb=" O GLU K 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS K 148 " --> pdb=" O HIS K 144 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR K 173 " --> pdb=" O ASN K 169 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA K 174 " --> pdb=" O MET K 170 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR K 193 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 165 Proline residue: I 162 - end of helix Processing helix chain 'I' and resid 173 through 182 Proline residue: I 177 - end of helix Processing helix chain 'I' and resid 187 through 200 Processing helix chain 'I' and resid 206 through 217 Processing helix chain 'I' and resid 224 through 233 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 235 through 249 removed outlier: 3.799A pdb=" N ASN I 239 " --> pdb=" O VAL I 235 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL I 240 " --> pdb=" O GLN I 236 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 264 Processing helix chain 'I' and resid 271 through 283 removed outlier: 3.747A pdb=" N LYS I 274 " --> pdb=" O HIS I 271 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU I 280 " --> pdb=" O ASP I 277 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE I 283 " --> pdb=" O GLU I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 removed outlier: 3.901A pdb=" N ARG I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 314 Processing helix chain 'I' and resid 322 through 333 Processing helix chain 'I' and resid 338 through 350 Proline residue: I 342 - end of helix Processing helix chain 'I' and resid 354 through 365 Processing helix chain 'I' and resid 370 through 382 Processing helix chain 'I' and resid 388 through 397 removed outlier: 3.521A pdb=" N GLY I 392 " --> pdb=" O PHE I 388 " (cutoff:3.500A) Proline residue: I 394 - end of helix Processing helix chain 'I' and resid 405 through 417 Processing helix chain 'I' and resid 424 through 438 removed outlier: 3.815A pdb=" N LEU I 432 " --> pdb=" O GLN I 428 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA I 433 " --> pdb=" O VAL I 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 457 removed outlier: 4.709A pdb=" N ARG I 457 " --> pdb=" O LEU I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 476 Proline residue: I 475 - end of helix Processing helix chain 'I' and resid 487 through 498 Processing helix chain 'I' and resid 508 through 523 Proline residue: I 518 - end of helix Processing helix chain 'I' and resid 528 through 541 Processing helix chain 'I' and resid 545 through 557 removed outlier: 5.957A pdb=" N TRP I 550 " --> pdb=" O SER I 546 " (cutoff:3.500A) Proline residue: I 551 - end of helix Processing helix chain 'I' and resid 570 through 579 removed outlier: 4.381A pdb=" N ARG I 577 " --> pdb=" O LEU I 573 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 578 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 585 through 597 Proline residue: I 589 - end of helix Processing helix chain 'I' and resid 602 through 635 removed outlier: 3.522A pdb=" N MET I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA I 614 " --> pdb=" O ARG I 610 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR I 616 " --> pdb=" O ALA I 612 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLU I 617 " --> pdb=" O MET I 613 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ARG I 618 " --> pdb=" O ALA I 614 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA I 619 " --> pdb=" O VAL I 615 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG I 621 " --> pdb=" O GLU I 617 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 622 " --> pdb=" O ARG I 618 " (cutoff:3.500A) Proline residue: I 625 - end of helix removed outlier: 3.531A pdb=" N TYR I 635 " --> pdb=" O MET I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 652 Processing helix chain 'I' and resid 664 through 675 removed outlier: 4.045A pdb=" N GLU I 675 " --> pdb=" O PHE I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 688 Processing helix chain 'I' and resid 707 through 719 Processing helix chain 'I' and resid 723 through 733 removed outlier: 3.722A pdb=" N ARG I 727 " --> pdb=" O MET I 723 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL I 730 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN I 731 " --> pdb=" O ARG I 727 " (cutoff:3.500A) Processing helix chain 'I' and resid 741 through 755 Processing helix chain 'I' and resid 761 through 772 Processing helix chain 'I' and resid 780 through 791 Proline residue: I 788 - end of helix Processing helix chain 'I' and resid 799 through 817 Proline residue: I 816 - end of helix Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 43 through 52 Processing helix chain 'Q' and resid 61 through 69 Processing helix chain 'Q' and resid 72 through 75 No H-bonds generated for 'chain 'Q' and resid 72 through 75' Processing helix chain 'Q' and resid 88 through 103 Processing helix chain 'Q' and resid 110 through 114 Processing helix chain 'Q' and resid 116 through 131 Proline residue: Q 120 - end of helix removed outlier: 3.613A pdb=" N LYS Q 128 " --> pdb=" O HIS Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 156 Processing helix chain 'Q' and resid 160 through 170 removed outlier: 3.938A pdb=" N GLN Q 165 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU Q 169 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 177 Processing helix chain 'Q' and resid 180 through 189 Processing helix chain 'Q' and resid 191 through 205 removed outlier: 3.999A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 221 through 235 Processing helix chain 'Q' and resid 244 through 261 Processing helix chain 'Q' and resid 264 through 276 removed outlier: 5.204A pdb=" N TRP Q 269 " --> pdb=" O PRO Q 265 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE Q 270 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR Q 272 " --> pdb=" O ARG Q 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE Q 273 " --> pdb=" O TRP Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 284 Processing helix chain 'Q' and resid 287 through 290 No H-bonds generated for 'chain 'Q' and resid 287 through 290' Processing helix chain 'Q' and resid 296 through 309 Processing helix chain 'Q' and resid 323 through 344 Processing helix chain 'Q' and resid 349 through 352 No H-bonds generated for 'chain 'Q' and resid 349 through 352' Processing helix chain 'Q' and resid 356 through 360 Processing helix chain 'Q' and resid 362 through 369 Processing helix chain 'Q' and resid 374 through 384 Processing helix chain 'Q' and resid 400 through 411 Processing helix chain 'Q' and resid 417 through 423 Processing helix chain 'Q' and resid 462 through 492 removed outlier: 3.608A pdb=" N ARG Q 491 " --> pdb=" O ASP Q 487 " (cutoff:3.500A) Processing helix chain 'Q' and resid 547 through 553 Processing helix chain 'Q' and resid 583 through 587 Processing helix chain 'Q' and resid 631 through 644 Processing helix chain 'Q' and resid 649 through 651 No H-bonds generated for 'chain 'Q' and resid 649 through 651' Processing helix chain 'Q' and resid 661 through 663 No H-bonds generated for 'chain 'Q' and resid 661 through 663' Processing helix chain 'Q' and resid 666 through 678 Processing helix chain 'Q' and resid 685 through 692 removed outlier: 4.791A pdb=" N ASP Q 689 " --> pdb=" O ASP Q 685 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE Q 690 " --> pdb=" O TRP Q 686 " (cutoff:3.500A) Processing helix chain 'Q' and resid 702 through 704 No H-bonds generated for 'chain 'Q' and resid 702 through 704' Processing helix chain 'Q' and resid 721 through 727 Processing helix chain 'Q' and resid 791 through 793 No H-bonds generated for 'chain 'Q' and resid 791 through 793' Processing helix chain 'Q' and resid 804 through 814 Processing helix chain 'Q' and resid 829 through 843 Processing helix chain 'Q' and resid 856 through 868 removed outlier: 3.809A pdb=" N ALA Q 868 " --> pdb=" O GLU Q 864 " (cutoff:3.500A) Processing helix chain 'Q' and resid 873 through 875 No H-bonds generated for 'chain 'Q' and resid 873 through 875' Processing helix chain 'Q' and resid 894 through 919 Processing helix chain 'Q' and resid 929 through 938 Processing helix chain 'Q' and resid 940 through 951 Processing helix chain 'Q' and resid 961 through 966 removed outlier: 3.870A pdb=" N SER Q 965 " --> pdb=" O VAL Q 961 " (cutoff:3.500A) Processing helix chain 'Q' and resid 987 through 1016 removed outlier: 4.838A pdb=" N ALA Q1013 " --> pdb=" O GLU Q1009 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER Q1014 " --> pdb=" O GLU Q1010 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU Q1015 " --> pdb=" O PHE Q1011 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1020 through 1029 Processing helix chain 'Q' and resid 1039 through 1052 removed outlier: 5.528A pdb=" N HIS Q1047 " --> pdb=" O ALA Q1043 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP Q1048 " --> pdb=" O LEU Q1044 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1064 through 1066 No H-bonds generated for 'chain 'Q' and resid 1064 through 1066' Processing helix chain 'Q' and resid 1069 through 1077 Proline residue: Q1075 - end of helix Processing helix chain 'Q' and resid 1108 through 1113 Processing helix chain 'Q' and resid 1119 through 1126 Processing helix chain 'Q' and resid 1141 through 1150 removed outlier: 4.201A pdb=" N LEU Q1146 " --> pdb=" O SER Q1142 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR Q1147 " --> pdb=" O LEU Q1143 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP Q1149 " --> pdb=" O ASN Q1145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG Q1150 " --> pdb=" O LEU Q1146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1158 through 1162 Processing helix chain 'Q' and resid 1164 through 1166 No H-bonds generated for 'chain 'Q' and resid 1164 through 1166' Processing helix chain 'Q' and resid 1201 through 1217 Processing helix chain 'Q' and resid 1221 through 1223 No H-bonds generated for 'chain 'Q' and resid 1221 through 1223' Processing helix chain 'Q' and resid 1231 through 1244 Processing helix chain 'Q' and resid 1260 through 1263 Processing helix chain 'Q' and resid 1282 through 1285 Processing helix chain 'Q' and resid 1287 through 1295 Processing helix chain 'Q' and resid 1307 through 1311 Processing helix chain 'Q' and resid 1314 through 1325 Proline residue: Q1318 - end of helix removed outlier: 4.550A pdb=" N SER Q1321 " --> pdb=" O PRO Q1318 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR Q1324 " --> pdb=" O SER Q1321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1358 through 1375 removed outlier: 3.616A pdb=" N GLN Q1374 " --> pdb=" O MET Q1370 " (cutoff:3.500A) Processing helix chain 'y' and resid 19 through 29 Proline residue: y 28 - end of helix Processing helix chain 'y' and resid 57 through 67 Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.672A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.959A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.637A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.510A pdb=" N GLN o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 40 Processing helix chain 'o' and resid 83 through 86 No H-bonds generated for 'chain 'o' and resid 83 through 86' Processing helix chain 'o' and resid 103 through 111 Proline residue: o 108 - end of helix removed outlier: 3.566A pdb=" N SER o 111 " --> pdb=" O PRO o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 124 through 127 Processing helix chain 'o' and resid 131 through 138 Processing helix chain 'o' and resid 152 through 160 Processing helix chain 'p' and resid 20 through 34 removed outlier: 4.195A pdb=" N GLN p 33 " --> pdb=" O ALA p 29 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE p 34 " --> pdb=" O LEU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 68 Processing helix chain 'p' and resid 89 through 95 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.691A pdb=" N LYS V 133 " --> pdb=" O ASP V 129 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN V 136 " --> pdb=" O LYS V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 150 removed outlier: 3.740A pdb=" N GLU V 141 " --> pdb=" O PRO V 138 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP V 144 " --> pdb=" O GLU V 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 166 through 180 Proline residue: V 171 - end of helix Processing helix chain 'V' and resid 195 through 208 Processing helix chain 'V' and resid 238 through 247 removed outlier: 4.152A pdb=" N ASN V 247 " --> pdb=" O ARG V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 264 No H-bonds generated for 'chain 'V' and resid 262 through 264' Processing helix chain 'V' and resid 267 through 282 removed outlier: 4.226A pdb=" N ARG V 281 " --> pdb=" O LYS V 277 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN V 282 " --> pdb=" O GLU V 278 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 345 removed outlier: 3.749A pdb=" N THR V 338 " --> pdb=" O ALA V 334 " (cutoff:3.500A) Processing helix chain 'V' and resid 361 through 367 Processing helix chain 'V' and resid 394 through 399 removed outlier: 5.377A pdb=" N ARG V 399 " --> pdb=" O GLN V 395 " (cutoff:3.500A) Processing helix chain 'V' and resid 423 through 426 No H-bonds generated for 'chain 'V' and resid 423 through 426' Processing helix chain 'V' and resid 463 through 474 removed outlier: 3.524A pdb=" N ARG V 472 " --> pdb=" O GLN V 468 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA V 473 " --> pdb=" O ARG V 469 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY V 474 " --> pdb=" O ALA V 470 " (cutoff:3.500A) Processing helix chain 'V' and resid 488 through 491 No H-bonds generated for 'chain 'V' and resid 488 through 491' Processing helix chain 'V' and resid 501 through 503 No H-bonds generated for 'chain 'V' and resid 501 through 503' Processing helix chain 'V' and resid 508 through 516 Processing helix chain 'V' and resid 533 through 545 Processing helix chain 'V' and resid 557 through 564 removed outlier: 3.862A pdb=" N GLU V 564 " --> pdb=" O SER V 560 " (cutoff:3.500A) Processing helix chain 'V' and resid 569 through 581 removed outlier: 3.901A pdb=" N CYS V 579 " --> pdb=" O VAL V 575 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP V 580 " --> pdb=" O ILE V 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR V 581 " --> pdb=" O ALA V 577 " (cutoff:3.500A) Processing helix chain 'V' and resid 584 through 595 Processing helix chain 'V' and resid 604 through 617 removed outlier: 4.298A pdb=" N LYS V 607 " --> pdb=" O THR V 604 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS V 608 " --> pdb=" O GLU V 605 " (cutoff:3.500A) Processing helix chain 'V' and resid 623 through 636 Processing helix chain 'V' and resid 641 through 646 Processing helix chain 'V' and resid 651 through 670 Processing helix chain 'V' and resid 683 through 697 removed outlier: 3.794A pdb=" N ASN V 688 " --> pdb=" O TYR V 685 " (cutoff:3.500A) Processing helix chain 'V' and resid 755 through 761 Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= C, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= D, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= E, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 6.674A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= G, first strand: chain 'A' and resid 1185 through 1188 removed outlier: 4.058A pdb=" N LEU A1185 " --> pdb=" O ILE A1196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1196 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A1225 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id= I, first strand: chain 'A' and resid 1629 through 1631 removed outlier: 6.758A pdb=" N VAL A1701 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLN A1665 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A1703 " --> pdb=" O GLN A1665 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG A1667 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A1705 " --> pdb=" O ARG A1667 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1702 " --> pdb=" O TYR A1715 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1914 through 1918 removed outlier: 6.864A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1788 through 1792 Processing sheet with id= L, first strand: chain 'C' and resid 308 through 310 removed outlier: 3.540A pdb=" N VAL C 225 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 254 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 199 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL C 132 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN C 201 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU C 134 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET C 203 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLY C 136 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 198 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 190 " --> pdb=" O TYR C 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.508A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= O, first strand: chain 'C' and resid 523 through 526 removed outlier: 3.587A pdb=" N GLN C 523 " --> pdb=" O VAL C 509 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 531 through 533 Processing sheet with id= Q, first strand: chain 'C' and resid 653 through 655 Processing sheet with id= R, first strand: chain 'C' and resid 663 through 666 removed outlier: 3.598A pdb=" N HIS C 903 " --> pdb=" O TYR C 831 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 674 through 677 removed outlier: 4.665A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET C 687 " --> pdb=" O CYS C 674 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 676 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 685 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 795 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP C 793 " --> pdb=" O THR C 686 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 744 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 831 through 838 Processing sheet with id= U, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.511A pdb=" N SER C 498 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 71 through 74 removed outlier: 3.663A pdb=" N ALA E 82 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 123 through 127 removed outlier: 3.644A pdb=" N SER E 126 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 134 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 133 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP E 137 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG E 143 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 154 through 159 removed outlier: 6.825A pdb=" N GLY E 170 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS E 157 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS E 168 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 188 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.693A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 275 through 277 removed outlier: 3.590A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 291 through 293 removed outlier: 3.612A pdb=" N TYR E 310 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 323 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 351 through 355 Processing sheet with id= AC, first strand: chain 'O' and resid 36 through 39 Processing sheet with id= AD, first strand: chain 'O' and resid 270 through 272 Processing sheet with id= AE, first strand: chain 'R' and resid 175 through 180 Processing sheet with id= AF, first strand: chain 'S' and resid 55 through 57 removed outlier: 3.603A pdb=" N MET S 61 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE S 97 " --> pdb=" O THR S 115 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 15 through 18 Processing sheet with id= AH, first strand: chain 'S' and resid 24 through 27 removed outlier: 4.880A pdb=" N GLU S 26 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL S 132 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.634A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR T 227 " --> pdb=" O SER T 223 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.725A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL T 254 " --> pdb=" O TYR T 260 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR T 260 " --> pdb=" O VAL T 254 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG T 282 " --> pdb=" O CYS T 272 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.565A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS T 324 " --> pdb=" O ILE T 314 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 333 through 338 removed outlier: 7.149A pdb=" N GLY T 348 " --> pdb=" O ALA T 334 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL T 336 " --> pdb=" O ILE T 346 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE T 346 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE T 345 " --> pdb=" O TRP T 357 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP T 358 " --> pdb=" O THR T 364 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR T 364 " --> pdb=" O ASP T 358 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 377 through 380 removed outlier: 3.731A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN T 397 " --> pdb=" O GLN T 407 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 416 through 421 removed outlier: 7.088A pdb=" N GLY T 430 " --> pdb=" O ASN T 417 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU T 419 " --> pdb=" O VAL T 428 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL T 428 " --> pdb=" O LEU T 419 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL T 421 " --> pdb=" O VAL T 426 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL T 426 " --> pdb=" O VAL T 421 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP T 440 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN T 446 " --> pdb=" O ASP T 440 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'T' and resid 194 through 201 removed outlier: 6.771A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 137 through 139 Processing sheet with id= AQ, first strand: chain 'U' and resid 549 through 551 Processing sheet with id= AR, first strand: chain 'U' and resid 696 through 699 Processing sheet with id= AS, first strand: chain 'U' and resid 749 through 752 Processing sheet with id= AT, first strand: chain 'U' and resid 753 through 756 removed outlier: 5.184A pdb=" N PHE U 825 " --> pdb=" O GLY U 829 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLY U 829 " --> pdb=" O PHE U 825 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= AV, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.827A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.214A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.685A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= AZ, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.029A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= BB, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.581A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.569A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.673A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.722A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP e 59 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.924A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.474A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'q' and resid 15 through 17 Processing sheet with id= BJ, first strand: chain 'r' and resid 15 through 17 Processing sheet with id= BK, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id= BL, first strand: chain 'Q' and resid 511 through 513 removed outlier: 6.827A pdb=" N ARG Q 626 " --> pdb=" O GLN Q 598 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET Q 600 " --> pdb=" O THR Q 624 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR Q 624 " --> pdb=" O MET Q 600 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL Q 535 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN Q 542 " --> pdb=" O ILE Q 514 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE Q 514 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'Q' and resid 732 through 735 removed outlier: 3.611A pdb=" N PHE Q 747 " --> pdb=" O ASN Q 715 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN Q 715 " --> pdb=" O PHE Q 747 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE Q 749 " --> pdb=" O ASP Q 713 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP Q 713 " --> pdb=" O ILE Q 749 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Q' and resid 1131 through 1133 Processing sheet with id= BO, first strand: chain 'Q' and resid 1177 through 1181 removed outlier: 6.779A pdb=" N LEU Q1301 " --> pdb=" O GLN Q1178 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE Q1180 " --> pdb=" O LEU Q1301 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE Q1303 " --> pdb=" O ILE Q1180 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 1330 through 1332 Processing sheet with id= BQ, first strand: chain 'y' and resid 8 through 11 Processing sheet with id= BR, first strand: chain 'y' and resid 32 through 36 removed outlier: 6.858A pdb=" N GLU y 53 " --> pdb=" O THR y 33 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE y 35 " --> pdb=" O PHE y 51 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE y 51 " --> pdb=" O ILE y 35 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BT, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.828A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.216A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BX, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BZ, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.583A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.671A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.724A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.792A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.922A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.475A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'o' and resid 14 through 16 removed outlier: 7.109A pdb=" N ALA o 46 " --> pdb=" O LEU o 24 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR o 68 " --> pdb=" O ILE o 47 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU o 92 " --> pdb=" O LEU o 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR o 117 " --> pdb=" O LEU o 93 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'p' and resid 80 through 83 removed outlier: 3.519A pdb=" N ASP p 39 " --> pdb=" O ILE p 55 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'V' and resid 309 through 312 removed outlier: 9.053A pdb=" N LEU V 310 " --> pdb=" O SER V 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL V 157 " --> pdb=" O LEU V 310 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE V 312 " --> pdb=" O VAL V 157 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL V 159 " --> pdb=" O ILE V 312 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL V 288 " --> pdb=" O PHE V 156 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU V 158 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL V 290 " --> pdb=" O LEU V 158 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY V 160 " --> pdb=" O VAL V 290 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER V 292 " --> pdb=" O GLY V 160 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY V 187 " --> pdb=" O GLY V 255 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE V 257 " --> pdb=" O GLY V 187 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA V 189 " --> pdb=" O ILE V 257 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU V 259 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR V 191 " --> pdb=" O LEU V 259 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'V' and resid 319 through 322 removed outlier: 6.908A pdb=" N GLY V 479 " --> pdb=" O GLU V 320 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE V 322 " --> pdb=" O GLY V 479 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS V 481 " --> pdb=" O PHE V 322 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP V 351 " --> pdb=" O VAL V 434 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL V 436 " --> pdb=" O ASP V 351 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU V 353 " --> pdb=" O VAL V 436 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP V 438 " --> pdb=" O LEU V 353 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE V 355 " --> pdb=" O ASP V 438 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'V' and resid 441 through 448 removed outlier: 3.573A pdb=" N ASN V 448 " --> pdb=" O VAL V 453 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL V 453 " --> pdb=" O ASN V 448 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'V' and resid 710 through 712 Processing sheet with id= CM, first strand: chain 'V' and resid 738 through 741 3379 hydrogen bonds defined for protein. 9387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 47.26 Time building geometry restraints manager: 30.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 13466 1.32 - 1.44: 22636 1.44 - 1.57: 44564 1.57 - 1.70: 830 1.70 - 1.83: 351 Bond restraints: 81847 Sorted by residual: bond pdb=" CB CYS K 106 " pdb=" SG CYS K 106 " ideal model delta sigma weight residual 1.808 1.425 0.383 3.30e-02 9.18e+02 1.35e+02 bond pdb=" CB CYS N 101 " pdb=" SG CYS N 101 " ideal model delta sigma weight residual 1.808 1.545 0.263 3.30e-02 9.18e+02 6.34e+01 bond pdb=" CA VAL K 186 " pdb=" CB VAL K 186 " ideal model delta sigma weight residual 1.542 1.436 0.106 1.45e-02 4.76e+03 5.34e+01 bond pdb=" O5' A G 4 " pdb=" C5' A G 4 " ideal model delta sigma weight residual 1.420 1.530 -0.110 1.50e-02 4.44e+03 5.34e+01 bond pdb=" O3' G F 34 " pdb=" P A F 35 " ideal model delta sigma weight residual 1.607 1.716 -0.109 1.50e-02 4.44e+03 5.28e+01 ... (remaining 81842 not shown) Histogram of bond angle deviations from ideal: 91.08 - 100.99: 223 100.99 - 110.90: 31208 110.90 - 120.81: 52753 120.81 - 130.72: 28773 130.72 - 140.64: 434 Bond angle restraints: 113391 Sorted by residual: angle pdb=" C4' A F 35 " pdb=" C3' A F 35 " pdb=" O3' A F 35 " ideal model delta sigma weight residual 113.00 133.43 -20.43 1.50e+00 4.44e-01 1.85e+02 angle pdb=" C2' A G 3 " pdb=" C1' A G 3 " pdb=" N9 A G 3 " ideal model delta sigma weight residual 114.00 131.71 -17.71 1.50e+00 4.44e-01 1.39e+02 angle pdb=" C4' U G 148 " pdb=" C3' U G 148 " pdb=" O3' U G 148 " ideal model delta sigma weight residual 113.00 95.63 17.37 1.50e+00 4.44e-01 1.34e+02 angle pdb=" N PHE I 388 " pdb=" CA PHE I 388 " pdb=" C PHE I 388 " ideal model delta sigma weight residual 111.14 122.79 -11.65 1.08e+00 8.57e-01 1.16e+02 angle pdb=" N GLU y 16 " pdb=" CA GLU y 16 " pdb=" C GLU y 16 " ideal model delta sigma weight residual 111.28 122.97 -11.69 1.09e+00 8.42e-01 1.15e+02 ... (remaining 113386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 47895 35.55 - 71.11: 1591 71.11 - 106.66: 165 106.66 - 142.22: 24 142.22 - 177.77: 11 Dihedral angle restraints: 49686 sinusoidal: 18496 harmonic: 31190 Sorted by residual: dihedral pdb=" CA GLU T 342 " pdb=" C GLU T 342 " pdb=" N PRO T 343 " pdb=" CA PRO T 343 " ideal model delta harmonic sigma weight residual -180.00 -106.74 -73.26 0 5.00e+00 4.00e-02 2.15e+02 dihedral pdb=" C5' G G 25 " pdb=" C4' G G 25 " pdb=" C3' G G 25 " pdb=" O3' G G 25 " ideal model delta sinusoidal sigma weight residual 82.00 168.01 -86.01 1 8.00e+00 1.56e-02 1.40e+02 dihedral pdb=" C5' C G 8 " pdb=" C4' C G 8 " pdb=" C3' C G 8 " pdb=" O3' C G 8 " ideal model delta sinusoidal sigma weight residual 147.00 70.05 76.95 1 8.00e+00 1.56e-02 1.16e+02 ... (remaining 49683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 13644 1.007 - 2.015: 0 2.015 - 3.022: 0 3.022 - 4.030: 0 4.030 - 5.037: 2 Chirality restraints: 13646 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.52 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C1' U G 142 " pdb=" O4' U G 142 " pdb=" C2' U G 142 " pdb=" N1 U G 142 " both_signs ideal model delta sigma weight residual False 2.45 1.45 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 13643 not shown) Planarity restraints: 13643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 5 " 0.206 2.00e-02 2.50e+03 1.20e-01 4.31e+02 pdb=" N9 G G 5 " 0.161 2.00e-02 2.50e+03 pdb=" C8 G G 5 " -0.183 2.00e-02 2.50e+03 pdb=" N7 G G 5 " -0.081 2.00e-02 2.50e+03 pdb=" C5 G G 5 " -0.048 2.00e-02 2.50e+03 pdb=" C6 G G 5 " 0.056 2.00e-02 2.50e+03 pdb=" O6 G G 5 " 0.139 2.00e-02 2.50e+03 pdb=" N1 G G 5 " 0.057 2.00e-02 2.50e+03 pdb=" C2 G G 5 " -0.030 2.00e-02 2.50e+03 pdb=" N2 G G 5 " -0.013 2.00e-02 2.50e+03 pdb=" N3 G G 5 " -0.129 2.00e-02 2.50e+03 pdb=" C4 G G 5 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G F 38 " -0.084 2.00e-02 2.50e+03 1.15e-01 3.97e+02 pdb=" N9 G F 38 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G F 38 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G F 38 " -0.104 2.00e-02 2.50e+03 pdb=" C5 G F 38 " -0.023 2.00e-02 2.50e+03 pdb=" C6 G F 38 " -0.021 2.00e-02 2.50e+03 pdb=" O6 G F 38 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G F 38 " 0.077 2.00e-02 2.50e+03 pdb=" C2 G F 38 " 0.162 2.00e-02 2.50e+03 pdb=" N2 G F 38 " -0.275 2.00e-02 2.50e+03 pdb=" N3 G F 38 " 0.160 2.00e-02 2.50e+03 pdb=" C4 G F 38 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 145 " -0.146 2.00e-02 2.50e+03 1.28e-01 3.71e+02 pdb=" N1 U G 145 " -0.053 2.00e-02 2.50e+03 pdb=" C2 U G 145 " -0.106 2.00e-02 2.50e+03 pdb=" O2 U G 145 " 0.228 2.00e-02 2.50e+03 pdb=" N3 U G 145 " -0.113 2.00e-02 2.50e+03 pdb=" C4 U G 145 " -0.048 2.00e-02 2.50e+03 pdb=" O4 U G 145 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U G 145 " 0.026 2.00e-02 2.50e+03 pdb=" C6 U G 145 " 0.213 2.00e-02 2.50e+03 ... (remaining 13640 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 121 2.26 - 2.92: 33500 2.92 - 3.58: 114724 3.58 - 4.24: 179023 4.24 - 4.90: 289076 Nonbonded interactions: 616444 Sorted by model distance: nonbonded pdb=" P G G 1 " pdb=" O2' A G 144 " model vdw 1.603 3.400 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C1501 " model vdw 1.671 2.170 nonbonded pdb=" O LEU A1518 " pdb=" OG1 THR A1519 " model vdw 1.847 2.440 nonbonded pdb=" O2' U G 27 " pdb=" O5' A G 28 " model vdw 1.860 2.440 nonbonded pdb=" OP1 C G 147 " pdb=" CD LYS U 659 " model vdw 1.934 3.440 ... (remaining 616439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 4 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 85)) selection = chain 'h' } ncs_group { reference = chain 'b' selection = chain 'i' } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 5 through 48 or resid 54 through 76)) selection = chain 'n' } ncs_group { reference = (chain 'q' and resid 3 through 133) selection = chain 'r' } ncs_group { reference = (chain 's' and resid 68 through 133) selection = (chain 't' and resid 68 through 133) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 16.720 Check model and map are aligned: 0.880 Set scattering table: 0.580 Process input model: 214.900 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 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 : 0.009 0.383 81847 Z= 0.592 Angle : 1.348 20.426 113391 Z= 0.882 Chirality : 0.098 5.037 13646 Planarity : 0.008 0.168 13643 Dihedral : 16.993 177.774 29340 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.61 % Favored : 92.48 % Rotamer: Outliers : 3.66 % Allowed : 5.73 % Favored : 90.61 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.99 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.07), residues: 10520 helix: -1.69 (0.06), residues: 4523 sheet: -0.79 (0.14), residues: 1314 loop : -2.13 (0.08), residues: 4683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP J 336 HIS 0.022 0.002 HIS A 755 PHE 0.050 0.003 PHE J 419 TYR 0.059 0.003 TYR J 349 ARG 0.015 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21040 Ramachandran restraints generated. 10520 Oldfield, 0 Emsley, 10520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21040 Ramachandran restraints generated. 10520 Oldfield, 0 Emsley, 10520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1553 residues out of total 9540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1366 time to evaluate : 6.623 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 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