Starting phenix.real_space_refine on Mon Mar 25 14:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g53_4351/03_2024/6g53_4351.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians P 1658 5.49 5 C 25618 2.51 5 N 5912 2.21 5 O 15864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49052 Number of models: 1 Model: "" Number of chains: 37 Chain: "2" Number of atoms: 19905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1659, 19905 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1659} Modifications used: {'5*END': 1, 'rna3p_pur': 882, 'rna3p_pyr': 777} Link IDs: {'rna3p': 1658} Chain breaks: 12 Unresolved non-hydrogen bonds: 18063 Unresolved non-hydrogen angles: 28608 Unresolved non-hydrogen dihedrals: 17772 Unresolved non-hydrogen chiralities: 1659 Planarities with less than four sites: {' G%rna3p_pur:plan2': 486, ' C%rna3p_pyr:plan': 399, ' A%rna3p_pur:plan2': 396, ' C%rna3p_pyr%5*END:plan2': 1, ' U%rna3p_pyr:plan': 377, ' C%rna3p_pyr%5*END:plan': 1, ' C%rna3p_pyr:plan2': 399, ' G%rna3p_pur:plan': 486, ' A%rna3p_pur:plan': 396} Unresolved non-hydrogen planarities: 18086 Chain: "R" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 604 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 207 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1068 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 12, 'TRANS': 203} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 870 Unresolved non-hydrogen dihedrals: 563 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 15, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 374 Chain: "B" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1054 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 5, 'TRANS': 207} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 347 Chain: "C" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1072 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 555 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 288 Chain: "E" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1287 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1050 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 12, 'GLU:plan': 9, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 401 Chain: "G" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1135 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 751 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 371 Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 920 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 9, 'TRANS': 176} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 303 Chain: "I" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1009 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 7, 'TRANS': 197} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 703 Unresolved non-hydrogen angles: 875 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 378 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 888 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 796 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 744 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 6, 'TRANS': 144} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 255 Chain: "N" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 737 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 140} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 233 Chain: "O" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 659 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "V" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 403 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 127 Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 634 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 218 Chain: "X" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 690 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 214 Chain: "Y" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 610 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 208 Chain: "b" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 405 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "e" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 270 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 82 Chain: "x" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 880 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 545 Unresolved non-hydrogen angles: 690 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 263 Chain: "y" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1606 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 286} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 845 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 534 Chain: "u" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 3042 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 545} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 573} Chain breaks: 3 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2061 Unresolved non-hydrogen angles: 2621 Unresolved non-hydrogen dihedrals: 1750 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'GLN:plan1': 33, 'ASP:plan': 34, 'TYR:plan': 14, 'ASN:plan1': 17, 'TRP:plan': 8, 'HIS:plan': 21, 'PHE:plan': 34, 'GLU:plan': 37, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1117 Chain: "t" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 304 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 113 Chain: "d" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 269 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1104 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 677 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 327 Chain: "F" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 935 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 5, 'TRANS': 183} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 581 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 10, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 309 Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 472 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 7, 'TRANS': 87} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Chain: "M" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 607 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 171 Chain: "P" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 590 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 7, 'TRANS': 112} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 217 Chain: "Q" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 683 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 235 Chain: "S" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 704 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 285 Chain: "T" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 705 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 551 Unresolved non-hydrogen dihedrals: 372 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 239 Chain: "U" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 500 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 131 Chain: "Z" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 358 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Chain: "c" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 300 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 95 Chain: "f" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 356 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 119 Chain: "g" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1543 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 10, 'TRANS': 303} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 955 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 21, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 13, 'HIS:plan': 8, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 501 Time building chain proxies: 28.62, per 1000 atoms: 0.58 Number of scatterers: 49052 At special positions: 0 Unit cell: (210.296, 255.824, 202.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 1658 15.00 O 15864 8.00 N 5912 7.00 C 25618 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: 21.98 Conformation dependent library (CDL) restraints added in 8.1 seconds 11660 Ramachandran restraints generated. 5830 Oldfield, 0 Emsley, 5830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10998 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 67 sheets defined 33.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.22 Creating SS restraints... Processing helix chain 'R' and resid 6 through 19 Processing helix chain 'R' and resid 29 through 34 removed outlier: 3.911A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 34' Processing helix chain 'R' and resid 34 through 38 removed outlier: 3.846A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 34 through 38' Processing helix chain 'R' and resid 43 through 51 removed outlier: 3.923A pdb=" N LYS R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.859A pdb=" N THR R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 60' Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 77 through 83 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.658A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.911A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.572A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.565A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.655A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.518A pdb=" N ASP C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.908A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.465A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 removed outlier: 3.528A pdb=" N ALA C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 232 through 250 removed outlier: 3.557A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.059A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.535A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.662A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 37 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 75 Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 117 through 121 Processing helix chain 'H' and resid 122 through 134 removed outlier: 3.905A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.748A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.730A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.892A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.924A pdb=" N ALA I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 206 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.155A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.625A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.748A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 101 removed outlier: 3.555A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS J 101 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.609A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 45 removed outlier: 4.332A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY N 44 " --> pdb=" O LEU N 40 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.631A pdb=" N GLU O 68 " --> pdb=" O ASP O 65 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 65 through 69' Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.689A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.713A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.663A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.702A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 22 removed outlier: 3.923A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 34 through 39 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 removed outlier: 3.606A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 117 removed outlier: 3.669A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL Y 117 " --> pdb=" O ARG Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.579A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 10 through 16 removed outlier: 3.707A pdb=" N GLY e 14 " --> pdb=" O GLY e 10 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR e 16 " --> pdb=" O VAL e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 40 Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 102 Proline residue: x 98 - end of helix removed outlier: 3.740A pdb=" N HIS x 102 " --> pdb=" O PRO x 98 " (cutoff:3.500A) Processing helix chain 'x' and resid 128 through 143 Processing helix chain 'x' and resid 145 through 150 Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.719A pdb=" N ARG x 154 " --> pdb=" O LEU x 150 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 173 through 185 Processing helix chain 'x' and resid 188 through 198 Processing helix chain 'x' and resid 214 through 230 removed outlier: 3.532A pdb=" N THR x 223 " --> pdb=" O LYS x 219 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 248 removed outlier: 3.513A pdb=" N GLY x 239 " --> pdb=" O SER x 235 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG x 247 " --> pdb=" O ALA x 243 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER x 248 " --> pdb=" O VAL x 244 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 4.097A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 30 through 36 removed outlier: 3.906A pdb=" N VAL y 34 " --> pdb=" O ILE y 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR y 35 " --> pdb=" O ARG y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 47 Processing helix chain 'y' and resid 59 through 71 removed outlier: 4.069A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 99 through 103 removed outlier: 3.835A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.532A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 399 removed outlier: 3.777A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 73 removed outlier: 3.693A pdb=" N ALA u 57 " --> pdb=" O GLN u 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG u 73 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 104 removed outlier: 4.040A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU u 102 " --> pdb=" O GLU u 98 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 151 removed outlier: 3.553A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 181 removed outlier: 3.501A pdb=" N ALA u 179 " --> pdb=" O SER u 175 " (cutoff:3.500A) Processing helix chain 'u' and resid 196 through 212 removed outlier: 3.712A pdb=" N ILE u 201 " --> pdb=" O LEU u 197 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG u 204 " --> pdb=" O GLN u 200 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.648A pdb=" N ASP u 248 " --> pdb=" O LEU u 244 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG u 249 " --> pdb=" O ALA u 245 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 244 through 250' Processing helix chain 'u' and resid 465 through 481 Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 523 through 527 removed outlier: 3.562A pdb=" N ARG u 526 " --> pdb=" O ASP u 523 " (cutoff:3.500A) Processing helix chain 'u' and resid 532 through 546 Processing helix chain 'u' and resid 567 through 576 Processing helix chain 'u' and resid 720 through 726 Processing helix chain 't' and resid 426 through 469 removed outlier: 3.518A pdb=" N ARG t 430 " --> pdb=" O ASP t 426 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL t 443 " --> pdb=" O LYS t 439 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG t 458 " --> pdb=" O LEU t 454 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU t 466 " --> pdb=" O GLU t 462 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS t 467 " --> pdb=" O LEU t 463 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS t 468 " --> pdb=" O LEU t 464 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.547A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 46 removed outlier: 3.539A pdb=" N GLN d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR d 46 " --> pdb=" O CYS d 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 41 through 46' Processing helix chain 'd' and resid 46 through 51 Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.927A pdb=" N PHE D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.784A pdb=" N ASN D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 28 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 18 through 29' Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.886A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.843A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 3.844A pdb=" N LYS D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 removed outlier: 3.908A pdb=" N CYS D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 123 " --> pdb=" O CYS D 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 removed outlier: 3.799A pdb=" N ASN D 165 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.837A pdb=" N LEU F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN F 74 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.846A pdb=" N VAL F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS F 95 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA F 96 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 removed outlier: 3.828A pdb=" N ASN F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE F 117 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.838A pdb=" N VAL F 147 " --> pdb=" O PRO F 143 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN F 149 " --> pdb=" O ARG F 145 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS F 155 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG F 159 " --> pdb=" O CYS F 155 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 183 removed outlier: 3.887A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 180 " --> pdb=" O GLU F 176 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 3.900A pdb=" N LYS F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.938A pdb=" N LEU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 192 through 202' Processing helix chain 'K' and resid 4 through 12 removed outlier: 3.886A pdb=" N ILE K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 19 removed outlier: 3.901A pdb=" N PHE K 16 " --> pdb=" O TYR K 12 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.551A pdb=" N VAL K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS K 47 " --> pdb=" O LEU K 43 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA K 48 " --> pdb=" O HIS K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 83 removed outlier: 4.115A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU K 79 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP K 81 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 26 removed outlier: 4.140A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 17 through 26' Processing helix chain 'M' and resid 35 through 41 removed outlier: 3.943A pdb=" N ALA M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 72 removed outlier: 3.887A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS M 69 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA M 70 " --> pdb=" O GLU M 66 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 removed outlier: 3.976A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 83 through 88' Processing helix chain 'M' and resid 119 through 130 removed outlier: 4.005A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU M 126 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS M 130 " --> pdb=" O GLU M 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 119 through 130' Processing helix chain 'P' and resid 22 through 28 removed outlier: 3.997A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 35 removed outlier: 3.605A pdb=" N LEU P 33 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 35' Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.957A pdb=" N ARG P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 64 removed outlier: 3.857A pdb=" N ARG P 59 " --> pdb=" O SER P 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 60 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 64' Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.577A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.560A pdb=" N MET P 111 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 112' Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.613A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 52 removed outlier: 3.761A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.927A pdb=" N LEU Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.845A pdb=" N ALA Q 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 82 removed outlier: 3.824A pdb=" N TYR Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 99 removed outlier: 3.864A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU Q 92 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA Q 94 " --> pdb=" O LYS Q 90 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.857A pdb=" N LYS Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU Q 112 " --> pdb=" O ILE Q 108 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.519A pdb=" N LEU Q 119 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.998A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.873A pdb=" N HIS S 42 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL S 44 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG S 46 " --> pdb=" O HIS S 42 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 71 removed outlier: 3.988A pdb=" N GLU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG S 66 " --> pdb=" O ASP S 62 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE S 68 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE S 70 " --> pdb=" O ARG S 66 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET S 71 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.970A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 112 removed outlier: 3.945A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS S 106 " --> pdb=" O GLY S 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU S 107 " --> pdb=" O LEU S 103 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU S 109 " --> pdb=" O ASN S 105 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU S 111 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU S 112 " --> pdb=" O ARG S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 128 removed outlier: 3.918A pdb=" N HIS S 125 " --> pdb=" O ARG S 121 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE S 126 " --> pdb=" O GLY S 122 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP S 127 " --> pdb=" O LEU S 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.653A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 17 removed outlier: 3.952A pdb=" N VAL T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 24 removed outlier: 3.653A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 19 through 24' Processing helix chain 'T' and resid 31 through 35 removed outlier: 3.805A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 31 through 35' Processing helix chain 'T' and resid 59 through 64 removed outlier: 3.819A pdb=" N HIS T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 59 through 64' Processing helix chain 'T' and resid 72 through 76 Processing helix chain 'T' and resid 100 through 106 removed outlier: 3.897A pdb=" N LEU T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 100 through 106' Processing helix chain 'T' and resid 107 through 111 Processing helix chain 'T' and resid 126 through 144 removed outlier: 3.944A pdb=" N ASP T 130 " --> pdb=" O GLN T 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU T 131 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP T 132 " --> pdb=" O GLN T 128 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG T 133 " --> pdb=" O ARG T 129 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA T 135 " --> pdb=" O LEU T 131 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY T 136 " --> pdb=" O ASP T 132 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL T 138 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA T 139 " --> pdb=" O ALA T 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA T 140 " --> pdb=" O GLY T 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA T 141 " --> pdb=" O GLN T 137 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN T 142 " --> pdb=" O VAL T 138 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS T 143 " --> pdb=" O ALA T 139 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 126 through 144' Processing helix chain 'U' and resid 41 through 46 removed outlier: 3.903A pdb=" N GLU U 45 " --> pdb=" O ARG U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 104 removed outlier: 3.974A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE U 101 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 94 through 104' Processing helix chain 'Z' and resid 51 through 59 removed outlier: 3.997A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU Z 58 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS Z 59 " --> pdb=" O TYR Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 65 Processing helix chain 'Z' and resid 69 through 77 removed outlier: 3.981A pdb=" N SER Z 74 " --> pdb=" O PRO Z 70 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU Z 75 " --> pdb=" O ALA Z 71 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG Z 76 " --> pdb=" O VAL Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 89 removed outlier: 4.031A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Z 88 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 82 through 89' Processing helix chain 'Z' and resid 89 through 95 removed outlier: 3.669A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 removed outlier: 4.000A pdb=" N TYR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR f 106 " --> pdb=" O VAL f 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 101 through 106' Processing sheet with id=AA1, first strand: chain 'R' and resid 39 through 40 removed outlier: 3.672A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.338A pdb=" N ILE R 96 " --> pdb=" O GLN R 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.835A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.421A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 34 removed outlier: 4.096A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.842A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.437A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.842A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.437A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 140 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 210 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE B 142 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 116 removed outlier: 5.159A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG C 121 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.802A pdb=" N VAL C 205 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA C 226 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.325A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 4.614A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.864A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 217 through 221 removed outlier: 7.328A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.420A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB8, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB9, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.684A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 184 through 188 removed outlier: 4.656A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.851A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.368A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.368A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AC6, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.740A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.491A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.667A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE O 95 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE O 129 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU O 97 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP O 131 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA O 99 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 32 through 39 removed outlier: 5.072A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.106A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.595A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.777A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AD4, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.968A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.463A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'x' and resid 162 through 164 Processing sheet with id=AD7, first strand: chain 'y' and resid 8 through 9 removed outlier: 7.891A pdb=" N VAL y 8 " --> pdb=" O LEU y 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AD9, first strand: chain 'y' and resid 111 through 112 removed outlier: 3.913A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 110 through 112 removed outlier: 3.680A pdb=" N CYS u 126 " --> pdb=" O HIS u 131 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'u' and resid 251 through 254 removed outlier: 4.125A pdb=" N ALA u 251 " --> pdb=" O SER u 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU u 289 " --> pdb=" O PHE u 297 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.559A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS u 346 " --> pdb=" O ILE u 302 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'u' and resid 623 through 625 removed outlier: 7.080A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'u' and resid 637 through 639 removed outlier: 6.325A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL u 693 " --> pdb=" O VAL u 773 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN u 768 " --> pdb=" O GLU u 730 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU u 730 " --> pdb=" O ASN u 768 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS u 750 " --> pdb=" O PRO u 744 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS u 705 " --> pdb=" O VAL u 712 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.917A pdb=" N GLU D 38 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 49 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 40 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 47 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.883A pdb=" N CYS D 134 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 154 " --> pdb=" O CYS D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 139 through 140 removed outlier: 3.876A pdb=" N SER D 139 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY D 183 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 182 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 175 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 184 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 173 " --> pdb=" O ILE D 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AF2, first strand: chain 'F' and resid 123 through 124 removed outlier: 3.923A pdb=" N ASP F 124 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL F 139 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 76 through 79 removed outlier: 3.724A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU M 52 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL M 79 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL M 111 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 51 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL M 109 " --> pdb=" O VAL M 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AF5, first strand: chain 'Q' and resid 26 through 27 removed outlier: 3.972A pdb=" N LYS Q 26 " --> pdb=" O ASP Q 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP Q 67 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Q' and resid 33 through 34 Processing sheet with id=AF7, first strand: chain 'S' and resid 12 through 14 removed outlier: 3.917A pdb=" N LEU S 13 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE S 20 " --> pdb=" O LEU S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'T' and resid 81 through 83 removed outlier: 3.951A pdb=" N GLY T 81 " --> pdb=" O SER T 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER T 93 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN T 83 " --> pdb=" O HIS T 91 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS T 91 " --> pdb=" O GLN T 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'T' and resid 113 through 115 removed outlier: 3.932A pdb=" N GLU T 114 " --> pdb=" O LYS T 122 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS T 122 " --> pdb=" O GLU T 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'U' and resid 54 through 55 removed outlier: 3.900A pdb=" N PHE U 80 " --> pdb=" O ILE U 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE U 63 " --> pdb=" O PHE U 80 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET U 82 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU U 61 " --> pdb=" O MET U 82 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE U 84 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS U 59 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 54 through 55 removed outlier: 3.996A pdb=" N HIS U 85 " --> pdb=" O SER U 26 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER U 26 " --> pdb=" O HIS U 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG U 87 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU U 24 " --> pdb=" O ARG U 87 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE U 89 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE U 22 " --> pdb=" O ILE U 89 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG U 21 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR U 115 " --> pdb=" O ARG U 21 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR U 23 " --> pdb=" O GLU U 113 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU U 113 " --> pdb=" O THR U 23 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR U 25 " --> pdb=" O GLU U 111 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU U 111 " --> pdb=" O THR U 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.369A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER Z 101 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE Z 108 " --> pdb=" O SER Z 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'c' and resid 10 through 11 removed outlier: 3.967A pdb=" N LYS c 10 " --> pdb=" O LEU c 58 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU c 58 " --> pdb=" O LYS c 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'c' and resid 17 through 19 removed outlier: 6.626A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL c 30 " --> pdb=" O ARG c 44 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG c 44 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 139 through 140 Processing sheet with id=AG7, first strand: chain 'g' and resid 4 through 11 removed outlier: 6.370A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA g 300 " --> pdb=" O ARG g 308 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 32 through 33 removed outlier: 3.881A pdb=" N SER g 33 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE g 41 " --> pdb=" O SER g 33 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AH1, first strand: chain 'g' and resid 112 through 113 removed outlier: 3.883A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL g 121 " --> pdb=" O ALA g 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'g' and resid 153 through 157 removed outlier: 4.452A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE g 164 " --> pdb=" O SER g 157 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE g 165 " --> pdb=" O TRP g 177 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP g 177 " --> pdb=" O ILE g 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER g 167 " --> pdb=" O LYS g 175 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 199 through 200 removed outlier: 3.970A pdb=" N CYS g 207 " --> pdb=" O TRP g 219 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP g 219 " --> pdb=" O CYS g 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS g 225 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 247 through 249 removed outlier: 3.964A pdb=" N LEU g 248 " --> pdb=" O TRP g 259 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP g 259 " --> pdb=" O LEU g 248 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.83 Time building geometry restraints manager: 23.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.29: 5914 1.29 - 1.38: 5869 1.38 - 1.47: 13356 1.47 - 1.56: 22144 1.56 - 1.65: 3373 Bond restraints: 50656 Sorted by residual: bond pdb=" C MET D 189 " pdb=" N LEU D 190 " ideal model delta sigma weight residual 1.330 1.200 0.130 1.47e-02 4.63e+03 7.87e+01 bond pdb=" C VAL T 87 " pdb=" N MET T 88 " ideal model delta sigma weight residual 1.331 1.224 0.107 1.48e-02 4.57e+03 5.19e+01 bond pdb=" CA PRO x 233 " pdb=" C PRO x 233 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" C LYS G 188 " pdb=" O LYS G 188 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" C ARG N 124 " pdb=" O ARG N 124 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.79e+01 ... (remaining 50651 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.27: 7327 106.27 - 113.38: 32716 113.38 - 120.50: 17618 120.50 - 127.61: 15865 127.61 - 134.72: 29 Bond angle restraints: 73555 Sorted by residual: angle pdb=" C GLY u 80 " pdb=" N PRO u 81 " pdb=" CA PRO u 81 " ideal model delta sigma weight residual 120.38 128.97 -8.59 1.03e+00 9.43e-01 6.95e+01 angle pdb=" O3' G 2 958 " pdb=" C3' G 2 958 " pdb=" C2' G 2 958 " ideal model delta sigma weight residual 113.70 125.89 -12.19 1.50e+00 4.44e-01 6.61e+01 angle pdb=" C ASP A 206 " pdb=" N PRO A 207 " pdb=" CA PRO A 207 " ideal model delta sigma weight residual 119.84 129.85 -10.01 1.25e+00 6.40e-01 6.41e+01 angle pdb=" C MET D 189 " pdb=" N LEU D 190 " pdb=" CA LEU D 190 " ideal model delta sigma weight residual 120.68 132.24 -11.56 1.52e+00 4.33e-01 5.78e+01 angle pdb=" O3' A 2 980 " pdb=" C3' A 2 980 " pdb=" C2' A 2 980 " ideal model delta sigma weight residual 113.70 124.61 -10.91 1.50e+00 4.44e-01 5.29e+01 ... (remaining 73550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 33926 35.52 - 71.04: 3397 71.04 - 106.55: 235 106.55 - 142.07: 20 142.07 - 177.59: 21 Dihedral angle restraints: 37599 sinusoidal: 20730 harmonic: 16869 Sorted by residual: dihedral pdb=" CA ASN F 165 " pdb=" C ASN F 165 " pdb=" N ILE F 166 " pdb=" CA ILE F 166 " ideal model delta harmonic sigma weight residual -180.00 -125.11 -54.89 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" C4' U 2 591 " pdb=" C3' U 2 591 " pdb=" C2' U 2 591 " pdb=" C1' U 2 591 " ideal model delta sinusoidal sigma weight residual 36.00 -42.02 78.02 1 8.00e+00 1.56e-02 1.19e+02 dihedral pdb=" C4' A 21580 " pdb=" C3' A 21580 " pdb=" C2' A 21580 " pdb=" C1' A 21580 " ideal model delta sinusoidal sigma weight residual 36.00 -40.99 76.99 1 8.00e+00 1.56e-02 1.16e+02 ... (remaining 37596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 9768 0.137 - 0.274: 2204 0.274 - 0.411: 146 0.411 - 0.547: 13 0.547 - 0.684: 3 Chirality restraints: 12134 Sorted by residual: chirality pdb=" CA GLN X 61 " pdb=" N GLN X 61 " pdb=" C GLN X 61 " pdb=" CB GLN X 61 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.48 -1.91 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" C3' G 2 958 " pdb=" C4' G 2 958 " pdb=" O3' G 2 958 " pdb=" C2' G 2 958 " both_signs ideal model delta sigma weight residual False -2.48 -1.91 -0.57 2.00e-01 2.50e+01 8.12e+00 ... (remaining 12131 not shown) Planarity restraints: 5871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 162 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ASP D 162 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP D 162 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO D 163 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR g 303 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C THR g 303 " -0.040 2.00e-02 2.50e+03 pdb=" O THR g 303 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP g 304 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR f 87 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C THR f 87 " 0.040 2.00e-02 2.50e+03 pdb=" O THR f 87 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO f 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 5868 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 8 1.99 - 2.72: 2065 2.72 - 3.44: 58783 3.44 - 4.17: 90873 4.17 - 4.90: 133518 Nonbonded interactions: 285247 Sorted by model distance: nonbonded pdb=" OP1 A 21386 " pdb=" O2' A 21483 " model vdw 1.260 2.440 nonbonded pdb=" O2' C 21373 " pdb=" O2' A 21465 " model vdw 1.308 2.440 nonbonded pdb=" O2' C 21374 " pdb=" C1' C 21464 " model vdw 1.473 3.470 nonbonded pdb=" CB ASP y 365 " pdb=" CB ILE c 43 " model vdw 1.495 3.870 nonbonded pdb=" CB ALA y 368 " pdb=" O ALA c 65 " model vdw 1.581 3.460 ... (remaining 285242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.510 Check model and map are aligned: 0.670 Set scattering table: 0.380 Process input model: 136.350 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 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 : 0.007 0.130 50656 Z= 0.523 Angle : 1.440 12.681 73555 Z= 1.000 Chirality : 0.103 0.684 12134 Planarity : 0.004 0.023 5871 Dihedral : 23.240 177.591 26601 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.08 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.02 % Twisted Proline : 0.40 % Twisted General : 0.12 % 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: -2.88 (0.10), residues: 5830 helix: -1.66 (0.11), residues: 1517 sheet: -1.91 (0.15), residues: 965 loop : -2.06 (0.09), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 55 PHE 0.000 0.000 PHE R 28 TYR 0.000 0.000 TYR R 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11660 Ramachandran restraints generated. 5830 Oldfield, 0 Emsley, 5830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11660 Ramachandran restraints generated. 5830 Oldfield, 0 Emsley, 5830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 4.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4191 time to fit residues: 96.5500 Evaluate side-chains 115 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** 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 306, in __init__ self.caller(self.refine_xyz) 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 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.996 > 50: distance: 20 - 117: 24.020 distance: 23 - 124: 23.659 distance: 43 - 114: 20.316 distance: 50 - 107: 17.567 distance: 53 - 104: 20.557 distance: 58 - 97: 22.575 distance: 61 - 94: 22.423 distance: 78 - 80: 10.406 distance: 80 - 81: 7.603 distance: 81 - 82: 12.229 distance: 82 - 83: 12.576 distance: 82 - 84: 9.353 distance: 84 - 85: 11.857 distance: 85 - 88: 10.075 distance: 86 - 87: 12.772 distance: 86 - 89: 4.875 distance: 89 - 90: 15.790 distance: 90 - 91: 9.711 distance: 90 - 93: 8.891 distance: 91 - 92: 7.391 distance: 91 - 94: 4.746 distance: 94 - 95: 15.511 distance: 95 - 96: 4.142 distance: 95 - 98: 22.071 distance: 96 - 97: 4.332 distance: 96 - 99: 18.162 distance: 100 - 101: 5.916 distance: 100 - 103: 5.536 distance: 101 - 102: 10.815 distance: 101 - 104: 6.766 distance: 104 - 105: 12.659 distance: 105 - 106: 6.564 distance: 105 - 108: 7.740 distance: 106 - 107: 11.552 distance: 106 - 109: 6.476 distance: 109 - 110: 17.698 distance: 110 - 111: 15.213 distance: 110 - 113: 19.318 distance: 111 - 112: 21.726 distance: 111 - 114: 20.268 distance: 114 - 115: 14.384 distance: 115 - 116: 4.292 distance: 115 - 118: 21.746 distance: 116 - 117: 5.523 distance: 116 - 119: 6.158 distance: 119 - 120: 5.063 distance: 120 - 121: 13.685 distance: 120 - 123: 13.412 distance: 121 - 124: 12.000 distance: 124 - 125: 17.111 distance: 125 - 126: 11.607 distance: 125 - 128: 11.360 distance: 126 - 127: 4.693 distance: 126 - 129: 5.900 distance: 137 - 149: 3.109