Starting phenix.real_space_refine on Mon Mar 25 19:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g51_4350/03_2024/6g51_4350.pdb" } resolution = 4.1 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 26578 2.51 5 N 6237 2.21 5 O 16189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50662 Number of models: 1 Model: "" Number of chains: 38 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: "v" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 1610 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 292} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1102 Unresolved non-hydrogen angles: 1396 Unresolved non-hydrogen dihedrals: 931 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 12, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 14, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 616 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: 29.64, per 1000 atoms: 0.59 Number of scatterers: 50662 At special positions: 0 Unit cell: (204.876, 253.656, 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 16189 8.00 N 6237 7.00 C 26578 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 Atom "ATOM 15763 O4' C 21503 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.79 Conformation dependent library (CDL) restraints added in 8.4 seconds 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11618 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 71 sheets defined 34.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.65 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: 3.847A 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: 3.922A pdb=" N LYS R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.912A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.895A 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 75 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: 3.912A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.573A 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: 3.654A 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: 3.909A 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: 4.739A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.006A 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: 4.060A 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: 3.904A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.749A 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: 3.731A 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: 3.923A pdb=" N ALA I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.156A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.624A 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: 6.154A 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: 3.610A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 45 removed outlier: 4.331A 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: 4.485A 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: 3.664A 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: 3.703A 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: 3.924A 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: 3.605A 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: 3.728A 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: 3.959A 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: 3.718A 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: 3.534A pdb=" N THR x 223 " --> pdb=" O LYS x 219 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 248 removed outlier: 3.512A 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: 3.502A pdb=" N SER x 248 " --> pdb=" O VAL x 244 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 4.098A 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: 3.598A 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: 3.518A 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: 3.834A 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: 3.531A 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: 3.692A pdb=" N ALA u 57 " --> pdb=" O GLN u 53 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.552A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 181 removed outlier: 3.500A 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: 3.545A 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: 3.851A 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 'v' and resid 14 through 28 removed outlier: 4.221A pdb=" N ARG v 18 " --> pdb=" O ARG v 14 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 42 removed outlier: 3.675A pdb=" N ILE v 38 " --> pdb=" O PRO v 34 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA v 39 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER v 40 " --> pdb=" O SER v 36 " (cutoff:3.500A) Processing helix chain 'v' and resid 49 through 57 Processing helix chain 'v' and resid 76 through 91 removed outlier: 3.737A pdb=" N LEU v 83 " --> pdb=" O GLY v 79 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA v 84 " --> pdb=" O TYR v 80 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU v 85 " --> pdb=" O ASP v 81 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER v 90 " --> pdb=" O LYS v 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 170 removed outlier: 3.552A pdb=" N SER v 154 " --> pdb=" O TRP v 150 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG v 155 " --> pdb=" O LEU v 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET v 159 " --> pdb=" O ARG v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 197 through 199 No H-bonds generated for 'chain 'v' and resid 197 through 199' Processing helix chain 'v' and resid 204 through 222 removed outlier: 3.594A pdb=" N VAL v 208 " --> pdb=" O ASP v 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE v 216 " --> pdb=" O ALA v 212 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL v 217 " --> pdb=" O MET v 213 " (cutoff:3.500A) Processing helix chain 'v' and resid 257 through 277 removed outlier: 3.541A pdb=" N TYR v 261 " --> pdb=" O ASN v 257 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP v 265 " --> pdb=" O TYR v 261 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET v 274 " --> pdb=" O LYS v 270 " (cutoff:3.500A) Processing helix chain 'v' and resid 497 through 522 removed outlier: 3.523A pdb=" N ARG v 519 " --> pdb=" O SER v 515 " (cutoff:3.500A) Processing helix chain 'v' and resid 527 through 544 removed outlier: 3.625A pdb=" N GLU v 535 " --> pdb=" O LYS v 531 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN v 536 " --> pdb=" O GLN v 532 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET v 537 " --> pdb=" O ARG v 533 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN v 538 " --> pdb=" O ARG v 534 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN v 539 " --> pdb=" O GLU v 535 " (cutoff:3.500A) Processing helix chain 't' and resid 426 through 469 removed outlier: 3.519A 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: 3.688A pdb=" N LYS t 467 " --> pdb=" O LEU t 463 " (cutoff:3.500A) removed outlier: 3.698A 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: 3.811A 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: 3.925A 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: 3.785A pdb=" N ASN D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.960A pdb=" N THR D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 28 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.944A 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: 3.813A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.897A 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: 3.880A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.945A 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: 3.900A pdb=" N TYR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.877A 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: 3.949A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 removed outlier: 3.800A 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: 3.833A 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: 3.827A 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: 3.881A 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: 3.942A 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: 3.949A 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: 3.840A pdb=" N ASN F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.839A 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: 3.742A 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: 3.834A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.857A pdb=" N GLU F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 183 removed outlier: 3.888A 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: 3.995A pdb=" N GLU F 176 " --> pdb=" O CYS F 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.889A 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: 3.887A 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: 3.901A pdb=" N LYS F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.940A pdb=" N LEU F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.917A 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: 3.887A 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: 3.944A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 19 removed outlier: 3.900A 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: 3.550A pdb=" N VAL K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.874A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 3.990A 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: 3.914A pdb=" N TYR K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 3.922A 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: 3.975A pdb=" N LEU M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.959A 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: 4.019A 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: 3.886A 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: 3.935A 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: 3.949A 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: 3.897A pdb=" N ALA M 70 " --> pdb=" O GLU M 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 removed outlier: 3.975A 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: 3.891A 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: 3.968A 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: 3.604A pdb=" N LEU P 33 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.959A pdb=" N ARG P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.937A 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: 3.940A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 3.932A 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: 3.559A 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: 3.614A 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: 3.760A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.926A 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: 3.846A pdb=" N ALA Q 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 82 removed outlier: 3.825A 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: 3.809A 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: 3.856A 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: 4.007A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.962A 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: 3.892A pdb=" N ARG S 46 " --> pdb=" O HIS S 42 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS S 47 " --> pdb=" O VAL S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 71 removed outlier: 3.987A 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: 3.903A pdb=" N THR S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.944A 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: 3.862A pdb=" N LYS S 106 " --> pdb=" O GLY S 102 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU S 107 " --> pdb=" O LEU S 103 " (cutoff:3.500A) removed outlier: 4.044A 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: 3.920A pdb=" N LEU S 111 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.978A 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: 3.654A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 17 removed outlier: 3.954A pdb=" N VAL T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA T 17 " --> pdb=" O GLU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 24 removed outlier: 3.654A 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 59 through 64 removed outlier: 3.819A pdb=" N HIS T 63 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.780A 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: 4.006A pdb=" N ILE T 134 " --> pdb=" O ASP T 130 " (cutoff:3.500A) removed outlier: 3.870A 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: 3.839A 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: 3.852A pdb=" N ALA T 140 " --> pdb=" O GLY T 136 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.918A 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: 3.901A 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: 4.017A 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: 3.954A 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: 3.982A pdb=" N SER Z 74 " --> pdb=" O PRO Z 70 " (cutoff:3.500A) removed outlier: 3.876A 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: 4.032A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.001A pdb=" N TYR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) removed outlier: 4.078A 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: 3.673A 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: 6.836A 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: 6.420A 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: 6.265A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.746A 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: 6.677A 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: 4.095A 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: 6.840A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.441A 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: 6.873A 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: 13.438A 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: 4.220A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.840A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.441A 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: 6.873A 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: 13.438A 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: 4.220A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.143A 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: 5.160A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.854A 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: 6.803A pdb=" N VAL C 205 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.829A 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: 3.865A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.044A 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: 4.966A 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: 4.630A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.259A 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: 6.419A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.046A 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: 3.683A 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: 6.048A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.575A 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: 4.522A 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: 3.852A 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: 7.369A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.227A 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: 6.977A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.915A 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: 8.373A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.020A 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: 7.571A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 9.893A 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: 8.392A 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: 6.892A 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: 6.666A 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: 6.291A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.213A 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: 4.451A 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: 8.023A 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: 6.594A 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: 6.870A 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: 7.050A 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: 5.656A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.261A 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: 7.398A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.405A 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: 6.969A 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: 7.890A 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: 3.679A pdb=" N CYS u 126 " --> pdb=" O HIS u 131 " (cutoff:3.500A) removed outlier: 9.804A 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: 4.126A pdb=" N ALA u 251 " --> pdb=" O SER u 583 " (cutoff:3.500A) removed outlier: 3.552A 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: 6.478A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.056A 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: 7.079A 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: 6.904A 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: 7.364A 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: 4.925A 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: 3.576A pdb=" N LYS u 705 " --> pdb=" O VAL u 712 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'v' and resid 62 through 66 Processing sheet with id=AE7, first strand: chain 'v' and resid 96 through 103 removed outlier: 3.903A pdb=" N ILE v 111 " --> pdb=" O GLY v 98 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN v 100 " --> pdb=" O ILE v 109 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE v 109 " --> pdb=" O GLN v 100 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY v 102 " --> pdb=" O SER v 107 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER v 107 " --> pdb=" O GLY v 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP v 180 " --> pdb=" O VAL v 187 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'v' and resid 194 through 195 Processing sheet with id=AE9, first strand: chain 'v' and resid 224 through 225 Processing sheet with id=AF1, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AF2, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.916A 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: 3.923A 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=AF3, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.882A pdb=" N CYS D 134 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP D 154 " --> pdb=" O CYS D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, 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: 3.851A 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: 3.944A 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=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AF6, first strand: chain 'F' and resid 123 through 124 removed outlier: 3.921A 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=AF6 Processing sheet with id=AF7, first strand: chain 'M' and resid 76 through 79 removed outlier: 3.723A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) removed outlier: 3.877A 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: 3.947A pdb=" N VAL M 51 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL M 109 " --> pdb=" O VAL M 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AF9, 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=AF9 Processing sheet with id=AG1, first strand: chain 'Q' and resid 33 through 34 Processing sheet with id=AG2, first strand: chain 'S' and resid 12 through 14 removed outlier: 3.916A 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=AG2 Processing sheet with id=AG3, first strand: chain 'T' and resid 81 through 83 removed outlier: 3.950A 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: 3.924A 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=AG3 Processing sheet with id=AG4, first strand: chain 'T' and resid 113 through 115 removed outlier: 3.931A pdb=" N GLU T 114 " --> pdb=" O LYS T 122 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS T 122 " --> pdb=" O GLU T 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, 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=AG6, 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: 3.863A pdb=" N ARG U 87 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU U 24 " --> pdb=" O ARG U 87 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.914A pdb=" N ARG U 21 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 3.877A 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: 3.880A 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: 3.910A pdb=" N GLU U 111 " --> pdb=" O THR U 25 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.370A 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: 4.220A 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=AG7 Processing sheet with id=AG8, 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=AG8 Processing sheet with id=AG9, 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: 3.907A pdb=" N VAL c 30 " --> pdb=" O ARG c 44 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG c 44 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 139 through 140 Processing sheet with id=AH2, first strand: chain 'g' and resid 4 through 11 removed outlier: 6.369A 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: 6.455A 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: 3.996A pdb=" N ALA g 300 " --> pdb=" O ARG g 308 " (cutoff:3.500A) Processing sheet with id=AH3, 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: 3.890A pdb=" N ILE g 41 " --> pdb=" O SER g 33 " (cutoff:3.500A) removed outlier: 6.081A 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: 6.095A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AH5, 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: 3.859A pdb=" N VAL g 121 " --> pdb=" O ALA g 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, 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: 3.705A pdb=" N ILE g 164 " --> pdb=" O SER g 157 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE g 165 " --> pdb=" O TRP g 177 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP g 177 " --> pdb=" O ILE g 165 " (cutoff:3.500A) removed outlier: 3.922A 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=AH7, 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: 7.302A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS g 225 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AH8, 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: 6.157A 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) 1469 hydrogen bonds defined for protein. 4119 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: 23.13 Time building geometry restraints manager: 23.51 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: 6239 1.29 - 1.38: 6191 1.38 - 1.47: 13428 1.47 - 1.56: 23005 1.56 - 1.65: 3399 Bond restraints: 52262 Sorted by residual: bond pdb=" O3' C 21389 " pdb=" P U 21390 " ideal model delta sigma weight residual 1.607 1.464 0.143 1.50e-02 4.44e+03 9.12e+01 bond pdb=" C MET D 189 " pdb=" N LEU D 190 " ideal model delta sigma weight residual 1.330 1.199 0.131 1.47e-02 4.63e+03 7.94e+01 bond pdb=" C VAL T 87 " pdb=" N MET T 88 " ideal model delta sigma weight residual 1.331 1.225 0.106 1.48e-02 4.57e+03 5.09e+01 bond pdb=" CA PRO x 233 " pdb=" C PRO x 233 " ideal model delta sigma weight residual 1.514 1.540 -0.025 5.50e-03 3.31e+04 2.12e+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 1.89e+01 ... (remaining 52257 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.85: 6976 105.85 - 113.05: 33126 113.05 - 120.25: 17423 120.25 - 127.46: 18232 127.46 - 134.66: 31 Bond angle restraints: 75788 Sorted by residual: angle pdb=" O4' C 21389 " pdb=" C1' C 21389 " pdb=" C2' C 21389 " ideal model delta sigma weight residual 107.60 99.14 8.46 1.00e+00 1.00e+00 7.16e+01 angle pdb=" C GLY u 80 " pdb=" N PRO u 81 " pdb=" CA PRO u 81 " ideal model delta sigma weight residual 120.38 128.99 -8.61 1.03e+00 9.43e-01 6.99e+01 angle pdb=" O3' G 2 958 " pdb=" C3' G 2 958 " pdb=" C2' G 2 958 " ideal model delta sigma weight residual 113.70 125.87 -12.17 1.50e+00 4.44e-01 6.59e+01 angle pdb=" C ASP A 206 " pdb=" N PRO A 207 " pdb=" CA PRO A 207 " ideal model delta sigma weight residual 119.84 129.86 -10.02 1.25e+00 6.40e-01 6.43e+01 angle pdb=" O3' G 21210 " pdb=" C3' G 21210 " pdb=" C2' G 21210 " ideal model delta sigma weight residual 113.70 125.53 -11.83 1.50e+00 4.44e-01 6.22e+01 ... (remaining 75783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 34865 35.51 - 71.03: 3399 71.03 - 106.54: 234 106.54 - 142.06: 21 142.06 - 177.57: 21 Dihedral angle restraints: 38540 sinusoidal: 20730 harmonic: 17810 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 -125.15 -54.85 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 -42.01 78.01 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 -40.95 76.95 1 8.00e+00 1.56e-02 1.16e+02 ... (remaining 38537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 10047 0.136 - 0.273: 2228 0.273 - 0.409: 152 0.409 - 0.545: 14 0.545 - 0.682: 3 Chirality restraints: 12444 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 1.16e+01 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 8.16e+00 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 8.02e+00 ... (remaining 12441 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR g 303 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C THR g 303 " -0.041 2.00e-02 2.50e+03 pdb=" O THR g 303 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP g 304 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 146 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ARG F 146 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG F 146 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL F 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 162 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+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 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 0.26 - 1.19: 15 1.19 - 2.12: 63 2.12 - 3.05: 25380 3.05 - 3.97: 109390 3.97 - 4.90: 161379 Warning: very small nonbonded interaction distances. Nonbonded interactions: 296227 Sorted by model distance: nonbonded pdb=" N GLN v 100 " pdb=" O PRO P 131 " model vdw 0.264 2.520 nonbonded pdb=" O3' C 21384 " pdb=" O MET D 157 " model vdw 0.593 3.040 nonbonded pdb=" C ILE u 706 " pdb=" O LYS f 78 " model vdw 0.650 3.270 nonbonded pdb=" N PHE u 707 " pdb=" O LYS f 78 " model vdw 0.813 2.520 nonbonded pdb=" CB PHE u 707 " pdb=" CA LYS f 78 " model vdw 0.833 3.870 ... (remaining 296222 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: 4.420 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: 12.710 Check model and map are aligned: 0.750 Set scattering table: 0.440 Process input model: 140.150 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 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 0.143 52262 Z= 0.528 Angle : 1.441 12.675 75788 Z= 1.002 Chirality : 0.103 0.682 12444 Planarity : 0.004 0.024 6192 Dihedral : 23.125 177.574 26922 Min Nonbonded Distance : 0.264 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.98 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.38 % 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: -2.90 (0.09), residues: 6147 helix: -1.73 (0.11), residues: 1674 sheet: -1.92 (0.15), residues: 995 loop : -2.03 (0.09), residues: 3478 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) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4641 time to fit residues: 117.8876 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 653 optimal weight: 40.0000 chunk 586 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 395 optimal weight: 5.9990 chunk 313 optimal weight: 40.0000 chunk 606 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 chunk 702 optimal weight: 40.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 52262 Z= 0.259 Angle : 0.757 10.864 75788 Z= 0.424 Chirality : 0.041 0.338 12444 Planarity : 0.004 0.041 6192 Dihedral : 20.554 178.356 26922 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.77 (0.10), residues: 6147 helix: -0.51 (0.12), residues: 1841 sheet: -1.48 (0.14), residues: 1113 loop : -1.41 (0.11), residues: 3193 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 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4668 time to fit residues: 118.4887 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 390 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 584 optimal weight: 6.9990 chunk 478 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 704 optimal weight: 20.0000 chunk 760 optimal weight: 50.0000 chunk 627 optimal weight: 2.9990 chunk 698 optimal weight: 40.0000 chunk 240 optimal weight: 9.9990 chunk 564 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52262 Z= 0.215 Angle : 0.682 13.512 75788 Z= 0.387 Chirality : 0.040 0.291 12444 Planarity : 0.003 0.030 6192 Dihedral : 21.250 178.392 26922 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.28 (0.11), residues: 6147 helix: 0.07 (0.12), residues: 1994 sheet: -1.24 (0.15), residues: 1079 loop : -1.26 (0.11), residues: 3074 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 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4428 time to fit residues: 111.8326 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 695 optimal weight: 0.0570 chunk 529 optimal weight: 20.0000 chunk 365 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 chunk 472 optimal weight: 0.9980 chunk 706 optimal weight: 8.9990 chunk 748 optimal weight: 50.0000 chunk 369 optimal weight: 5.9990 chunk 669 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.043 52262 Z= 0.100 Angle : 0.376 10.221 75788 Z= 0.217 Chirality : 0.032 0.176 12444 Planarity : 0.001 0.023 6192 Dihedral : 20.831 179.183 26922 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 6147 helix: 1.02 (0.12), residues: 2011 sheet: -1.03 (0.15), residues: 1088 loop : -0.94 (0.12), residues: 3048 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 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 5.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4409 time to fit residues: 111.8340 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 623 optimal weight: 0.0050 chunk 424 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 557 optimal weight: 6.9990 chunk 308 optimal weight: 0.0270 chunk 638 optimal weight: 9.9990 chunk 517 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 671 optimal weight: 30.0000 chunk 188 optimal weight: 40.0000 overall best weight: 7.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 52262 Z= 0.255 Angle : 0.650 13.543 75788 Z= 0.369 Chirality : 0.038 0.195 12444 Planarity : 0.003 0.022 6192 Dihedral : 21.832 179.880 26922 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.71 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.11), residues: 6147 helix: 0.29 (0.12), residues: 1987 sheet: -1.13 (0.15), residues: 1065 loop : -1.20 (0.11), residues: 3095 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 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4406 time to fit residues: 112.3155 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 251 optimal weight: 4.9990 chunk 673 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 439 optimal weight: 30.0000 chunk 184 optimal weight: 10.0000 chunk 748 optimal weight: 0.1980 chunk 621 optimal weight: 30.0000 chunk 346 optimal weight: 20.0000 chunk 62 optimal weight: 40.0000 chunk 247 optimal weight: 0.0470 chunk 393 optimal weight: 20.0000 overall best weight: 7.0488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.9467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52262 Z= 0.179 Angle : 0.468 11.020 75788 Z= 0.269 Chirality : 0.034 0.184 12444 Planarity : 0.002 0.024 6192 Dihedral : 22.142 179.573 26922 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.77 (0.11), residues: 6147 helix: 0.81 (0.12), residues: 2014 sheet: -1.07 (0.16), residues: 1060 loop : -1.17 (0.12), residues: 3073 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 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4708 time to fit residues: 118.7704 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 722 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 426 optimal weight: 40.0000 chunk 546 optimal weight: 40.0000 chunk 423 optimal weight: 50.0000 chunk 630 optimal weight: 9.9990 chunk 418 optimal weight: 40.0000 chunk 746 optimal weight: 50.0000 chunk 466 optimal weight: 9.9990 chunk 454 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 overall best weight: 15.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 1.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 52262 Z= 0.399 Angle : 0.928 16.340 75788 Z= 0.526 Chirality : 0.045 0.237 12444 Planarity : 0.005 0.026 6192 Dihedral : 23.689 178.318 26922 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.96 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.37 (0.10), residues: 6147 helix: -0.99 (0.11), residues: 1950 sheet: -1.55 (0.16), residues: 981 loop : -1.94 (0.11), residues: 3216 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 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4533 time to fit residues: 114.4477 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 461 optimal weight: 7.9990 chunk 297 optimal weight: 30.0000 chunk 445 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 474 optimal weight: 20.0000 chunk 508 optimal weight: 6.9990 chunk 368 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 586 optimal weight: 0.6980 overall best weight: 6.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 1.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 52262 Z= 0.188 Angle : 0.515 9.615 75788 Z= 0.296 Chirality : 0.034 0.184 12444 Planarity : 0.002 0.024 6192 Dihedral : 23.109 177.637 26922 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.56 (0.11), residues: 6147 helix: 0.18 (0.12), residues: 1996 sheet: -1.45 (0.16), residues: 1006 loop : -1.70 (0.11), residues: 3145 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 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4470 time to fit residues: 114.0341 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 678 optimal weight: 40.0000 chunk 714 optimal weight: 40.0000 chunk 652 optimal weight: 30.0000 chunk 695 optimal weight: 0.0370 chunk 418 optimal weight: 20.0000 chunk 302 optimal weight: 0.3980 chunk 545 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 628 optimal weight: 0.0770 chunk 657 optimal weight: 0.7980 chunk 692 optimal weight: 0.1980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 1.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.045 52262 Z= 0.077 Angle : 0.343 8.796 75788 Z= 0.199 Chirality : 0.031 0.179 12444 Planarity : 0.002 0.021 6192 Dihedral : 22.126 178.540 26922 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.45 (0.11), residues: 6147 helix: 1.51 (0.12), residues: 2050 sheet: -1.21 (0.15), residues: 1084 loop : -1.23 (0.12), residues: 3013 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 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.515 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4545 time to fit residues: 115.5058 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 456 optimal weight: 7.9990 chunk 735 optimal weight: 0.3980 chunk 448 optimal weight: 20.0000 chunk 348 optimal weight: 0.9990 chunk 511 optimal weight: 1.9990 chunk 771 optimal weight: 0.0370 chunk 709 optimal weight: 0.7980 chunk 614 optimal weight: 40.0000 chunk 63 optimal weight: 20.0000 chunk 474 optimal weight: 0.6980 chunk 376 optimal weight: 40.0000 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 1.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.031 52262 Z= 0.066 Angle : 0.306 7.935 75788 Z= 0.179 Chirality : 0.031 0.181 12444 Planarity : 0.001 0.024 6192 Dihedral : 21.327 179.943 26922 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.11 (0.12), residues: 6147 helix: 2.07 (0.12), residues: 2073 sheet: -0.97 (0.15), residues: 1137 loop : -0.96 (0.12), residues: 2937 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 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12294 Ramachandran restraints generated. 6147 Oldfield, 0 Emsley, 6147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4438 time to fit residues: 111.7452 Evaluate side-chains 127 residues out of total 5412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 487 optimal weight: 20.0000 chunk 654 optimal weight: 40.0000 chunk 188 optimal weight: 40.0000 chunk 566 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 615 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 631 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 113 optimal weight: 50.0000 overall best weight: 15.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067526 restraints weight = 384131.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.068131 restraints weight = 227159.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.068305 restraints weight = 175662.440| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 1.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 52262 Z= 0.386 Angle : 0.898 15.748 75788 Z= 0.507 Chirality : 0.045 0.230 12444 Planarity : 0.004 0.021 6192 Dihedral : 23.530 179.702 26922 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.50 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.82 (0.11), residues: 6147 helix: -0.31 (0.11), residues: 1965 sheet: -1.32 (0.17), residues: 927 loop : -1.75 (0.11), residues: 3255 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5567.39 seconds wall clock time: 103 minutes 25.75 seconds (6205.75 seconds total)