Starting phenix.real_space_refine on Mon Mar 18 19:23:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqf_11362/03_2024/6zqf_11362_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1447 5.49 5 C 48778 2.51 5 N 17337 2.21 5 O 22019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 89582 Number of models: 1 Model: "" Number of chains: 43 Chain: "UA" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 3916 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 695} Link IDs: {'PTRANS': 21, 'TRANS': 770} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2552 Unresolved non-hydrogen angles: 3284 Unresolved non-hydrogen dihedrals: 2152 Unresolved non-hydrogen chiralities: 226 Planarities with less than four sites: {'GLN:plan1': 32, 'HIS:plan': 18, 'TYR:plan': 22, 'ASN:plan1': 43, 'TRP:plan': 13, 'ASP:plan': 46, 'PHE:plan': 59, 'GLU:plan': 38, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1467 Chain: "UB" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 1845 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 12, 'TRANS': 357} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1261 Unresolved non-hydrogen angles: 1593 Unresolved non-hydrogen dihedrals: 1047 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 10, 'TYR:plan': 13, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 20, 'GLU:plan': 24, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 650 Chain: "UC" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 233 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "UL" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 3841 Classifications: {'peptide': 777} Incomplete info: {'truncation_to_alanine': 688} Link IDs: {'PTRANS': 17, 'TRANS': 759} Chain breaks: 6 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 2471 Unresolved non-hydrogen angles: 3175 Unresolved non-hydrogen dihedrals: 2088 Unresolved non-hydrogen chiralities: 245 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 23, 'TYR:plan': 20, 'ASN:plan1': 28, 'TRP:plan': 18, 'ASP:plan': 59, 'PHE:plan': 36, 'GLU:plan': 38, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1265 Chain: "UM" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 3763 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 19, 'TRANS': 742} Chain breaks: 6 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2314 Unresolved non-hydrogen angles: 2977 Unresolved non-hydrogen dihedrals: 1908 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 52, 'TYR:plan': 20, 'ASN:plan1': 42, 'TRP:plan': 14, 'HIS:plan': 19, 'PHE:plan': 21, 'GLU:plan': 42, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 1168 Chain: "US" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 2486 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 462} Link IDs: {'PTRANS': 24, 'TRANS': 474} Chain breaks: 2 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 1700 Unresolved non-hydrogen angles: 2176 Unresolved non-hydrogen dihedrals: 1443 Unresolved non-hydrogen chiralities: 147 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 15, 'TYR:plan': 19, 'ASN:plan1': 33, 'TRP:plan': 6, 'ASP:plan': 24, 'PHE:plan': 33, 'GLU:plan': 35, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 903 Chain: "UU" Number of atoms: 4328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 4328 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 768} Link IDs: {'PTRANS': 25, 'TRANS': 852} Chain breaks: 3 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 2735 Unresolved non-hydrogen angles: 3501 Unresolved non-hydrogen dihedrals: 2279 Unresolved non-hydrogen chiralities: 259 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 23, 'TYR:plan': 23, 'ASN:plan1': 41, 'TRP:plan': 10, 'ASP:plan': 57, 'PHE:plan': 50, 'GLU:plan': 43, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1481 Chain: "UV" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 5417 Classifications: {'peptide': 1093} Incomplete info: {'truncation_to_alanine': 995} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1041} Chain breaks: 6 Unresolved chain link angles: 51 Unresolved non-hydrogen bonds: 3623 Unresolved non-hydrogen angles: 4630 Unresolved non-hydrogen dihedrals: 3057 Unresolved non-hydrogen chiralities: 331 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 54, 'TYR:plan': 45, 'ASN:plan1': 69, 'TRP:plan': 7, 'HIS:plan': 26, 'PHE:plan': 77, 'GLU:plan': 57, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 1878 Chain: "CI" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 781 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 6, 'TRANS': 150} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 703 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 306 Chain: "CJ" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1083 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 710 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 12, 'GLU:plan': 12, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 399 Chain: "CK" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1101 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 706 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 577 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 29, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 384 Chain: "CL" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 3433 Classifications: {'peptide': 695} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 610} Link IDs: {'PTRANS': 40, 'TRANS': 654} Chain breaks: 5 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2333 Unresolved non-hydrogen angles: 2960 Unresolved non-hydrogen dihedrals: 1982 Unresolved non-hydrogen chiralities: 193 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 16, 'TYR:plan': 22, 'ASN:plan1': 26, 'TRP:plan': 9, 'ASP:plan': 34, 'PHE:plan': 38, 'GLU:plan': 45, 'ARG:plan': 49} Unresolved non-hydrogen planarities: 1232 Chain: "CM" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1767 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 342} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1357 Unresolved non-hydrogen dihedrals: 883 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 13, 'GLU:plan': 24, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 498 Chain: "CN" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 916 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 13, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 351 Chain: "JD" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 3995 Classifications: {'peptide': 807} Incomplete info: {'truncation_to_alanine': 722} Link IDs: {'CIS': 5, 'PTRANS': 41, 'TRANS': 760} Chain breaks: 9 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 2623 Unresolved non-hydrogen angles: 3309 Unresolved non-hydrogen dihedrals: 2197 Unresolved non-hydrogen chiralities: 232 Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 33, 'TYR:plan': 28, 'ASN:plan1': 35, 'TRP:plan': 3, 'HIS:plan': 21, 'PHE:plan': 36, 'GLU:plan': 48, 'ARG:plan': 52} Unresolved non-hydrogen planarities: 1328 Chain: "JF" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1071 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 304 Chain: "JG" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1096 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 308 Chain: "JH" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1295 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 886 Unresolved non-hydrogen angles: 1141 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 472 Chain: "JL" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1401 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 265} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 905 Unresolved non-hydrogen angles: 1149 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 459 Chain: "JJ" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 893 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 9, 'TRANS': 171} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 720 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 266 Chain: "DF" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1055 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 505 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 341 Chain: "DQ" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 616 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 177 Chain: "DS" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 381 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "DT" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 700 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 5, 'TRANS': 137} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 431 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 246 Chain: "Dc" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 310 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "D2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 429 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "D3" Number of atoms: 29645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1392, 29645 Classifications: {'RNA': 1392} Modifications used: {'rna2p_pur': 133, 'rna2p_pyr': 129, 'rna3p_pur': 596, 'rna3p_pyr': 534} Link IDs: {'rna2p': 262, 'rna3p': 1129} Chain breaks: 7 Chain: "DA" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1061 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 853 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 337 Chain: "DE" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1276 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 12, 'TRANS': 247} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 834 Unresolved non-hydrogen angles: 1058 Unresolved non-hydrogen dihedrals: 694 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 426 Chain: "DG" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1113 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 25, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 12, 'PHE:plan': 9, 'GLU:plan': 17, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 397 Chain: "DH" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 913 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 10, 'TRANS': 173} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 747 Unresolved non-hydrogen dihedrals: 485 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 297 Chain: "DI" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 924 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 343 Chain: "DJ" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 915 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 8, 'TRANS': 176} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 605 Unresolved non-hydrogen angles: 755 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 326 Chain: "DL" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 766 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 507 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 433 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 251 Chain: "DN" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 742 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 239 Chain: "DO" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 620 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 164 Chain: "DZ" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 332 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 62} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 4, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 105 Chain: "DW" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 634 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 212 Chain: "DX" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 684 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 524 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 203 Chain: "DY" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 661 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 3, 'TRANS': 130} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 233 Chain: "Db" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 400 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "D4" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 743 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna2p': 4, 'rna3p': 30} Chain breaks: 2 Chain: "Db" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 39.07, per 1000 atoms: 0.44 Number of scatterers: 89582 At special positions: 0 Unit cell: (246.747, 292.284, 315.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 P 1447 15.00 O 22019 8.00 N 17337 7.00 C 48778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.09 Conformation dependent library (CDL) restraints added in 12.4 seconds 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22458 Finding SS restraints... Secondary structure from input PDB file: 388 helices and 131 sheets defined 38.2% alpha, 17.0% beta 323 base pairs and 698 stacking pairs defined. Time for finding SS restraints: 27.03 Creating SS restraints... Processing helix chain 'UA' and resid 176 through 181 removed outlier: 3.779A pdb=" N ASNUA 181 " --> pdb=" O GLUUA 178 " (cutoff:3.500A) Processing helix chain 'UA' and resid 722 through 733 removed outlier: 3.515A pdb=" N THRUA 726 " --> pdb=" O THRUA 722 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUUA 730 " --> pdb=" O THRUA 726 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGUA 731 " --> pdb=" O VALUA 727 " (cutoff:3.500A) Processing helix chain 'UA' and resid 734 through 746 removed outlier: 4.078A pdb=" N LEUUA 745 " --> pdb=" O METUA 741 " (cutoff:3.500A) Processing helix chain 'UA' and resid 747 through 756 Processing helix chain 'UA' and resid 759 through 761 No H-bonds generated for 'chain 'UA' and resid 759 through 761' Processing helix chain 'UA' and resid 762 through 770 Processing helix chain 'UA' and resid 774 through 786 Processing helix chain 'UA' and resid 791 through 806 removed outlier: 3.643A pdb=" N ASNUA 795 " --> pdb=" O HISUA 791 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILEUA 797 " --> pdb=" O GLUUA 793 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRPUA 798 " --> pdb=" O PHEUA 794 " (cutoff:3.500A) Processing helix chain 'UA' and resid 806 through 813 Processing helix chain 'UA' and resid 818 through 831 removed outlier: 3.961A pdb=" N VALUA 829 " --> pdb=" O GLNUA 825 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALUA 831 " --> pdb=" O PHEUA 827 " (cutoff:3.500A) Processing helix chain 'UA' and resid 831 through 852 removed outlier: 3.590A pdb=" N VALUA 835 " --> pdb=" O VALUA 831 " (cutoff:3.500A) Processing helix chain 'UB' and resid 384 through 395 removed outlier: 3.836A pdb=" N ASPUB 389 " --> pdb=" O ASPUB 385 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASPUB 395 " --> pdb=" O VALUB 391 " (cutoff:3.500A) Processing helix chain 'UB' and resid 399 through 414 removed outlier: 3.628A pdb=" N VALUB 403 " --> pdb=" O HISUB 399 " (cutoff:3.500A) Proline residue: UB 412 - end of helix Processing helix chain 'UB' and resid 420 through 440 removed outlier: 4.091A pdb=" N LYSUB 424 " --> pdb=" O GLUUB 420 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALAUB 427 " --> pdb=" O GLYUB 423 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILEUB 434 " --> pdb=" O LEUUB 430 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SERUB 437 " --> pdb=" O ILEUB 433 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASNUB 440 " --> pdb=" O LEUUB 436 " (cutoff:3.500A) Processing helix chain 'UB' and resid 448 through 464 removed outlier: 3.670A pdb=" N ALAUB 454 " --> pdb=" O ARGUB 450 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEUUB 455 " --> pdb=" O THRUB 451 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SERUB 461 " --> pdb=" O SERUB 457 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLUUB 464 " --> pdb=" O LYSUB 460 " (cutoff:3.500A) Processing helix chain 'UB' and resid 466 through 488 removed outlier: 3.965A pdb=" N LEUUB 470 " --> pdb=" O TYRUB 466 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLUUB 472 " --> pdb=" O ARGUB 468 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLUUB 473 " --> pdb=" O GLUUB 469 " (cutoff:3.500A) Processing helix chain 'UB' and resid 496 through 508 removed outlier: 3.791A pdb=" N PHEUB 500 " --> pdb=" O GLYUB 496 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHEUB 501 " --> pdb=" O ASPUB 497 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SERUB 502 " --> pdb=" O LEUUB 498 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILEUB 504 " --> pdb=" O PHEUB 500 " (cutoff:3.500A) Processing helix chain 'UB' and resid 517 through 531 Processing helix chain 'UB' and resid 536 through 554 removed outlier: 4.659A pdb=" N LEUUB 546 " --> pdb=" O PHEUB 542 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VALUB 547 " --> pdb=" O GLYUB 543 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARGUB 548 " --> pdb=" O ALAUB 544 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLNUB 552 " --> pdb=" O ARGUB 548 " (cutoff:3.500A) Processing helix chain 'UB' and resid 561 through 573 removed outlier: 4.233A pdb=" N VALUB 565 " --> pdb=" O ILEUB 561 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYRUB 566 " --> pdb=" O PROUB 562 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEUUB 573 " --> pdb=" O GLNUB 569 " (cutoff:3.500A) Processing helix chain 'UB' and resid 574 through 577 removed outlier: 3.880A pdb=" N VALUB 577 " --> pdb=" O THRUB 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'UB' and resid 574 through 577' Processing helix chain 'UB' and resid 616 through 621 Processing helix chain 'UB' and resid 628 through 650 removed outlier: 4.079A pdb=" N CYSUB 632 " --> pdb=" O PROUB 628 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VALUB 633 " --> pdb=" O VALUB 629 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALUB 635 " --> pdb=" O GLNUB 631 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THRUB 646 " --> pdb=" O SERUB 642 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SERUB 648 " --> pdb=" O ASPUB 644 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THRUB 649 " --> pdb=" O ALAUB 645 " (cutoff:3.500A) Processing helix chain 'UB' and resid 656 through 661 Processing helix chain 'UB' and resid 661 through 673 removed outlier: 3.796A pdb=" N GLNUB 666 " --> pdb=" O LEUUB 662 " (cutoff:3.500A) Processing helix chain 'UB' and resid 679 through 695 removed outlier: 3.597A pdb=" N LYSUB 693 " --> pdb=" O GLUUB 689 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THRUB 695 " --> pdb=" O LEUUB 691 " (cutoff:3.500A) Processing helix chain 'UB' and resid 732 through 776 removed outlier: 3.653A pdb=" N LYSUB 749 " --> pdb=" O LYSUB 745 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THRUB 751 " --> pdb=" O GLUUB 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASPUB 758 " --> pdb=" O GLUUB 754 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLUUB 768 " --> pdb=" O ARGUB 764 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYSUB 770 " --> pdb=" O ARGUB 766 " (cutoff:3.500A) Processing helix chain 'UB' and resid 776 through 787 removed outlier: 3.575A pdb=" N ILEUB 784 " --> pdb=" O LYSUB 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THRUB 787 " --> pdb=" O HISUB 783 " (cutoff:3.500A) Processing helix chain 'UC' and resid 541 through 547 Processing helix chain 'UC' and resid 560 through 570 removed outlier: 3.639A pdb=" N ARGUC 566 " --> pdb=" O ARGUC 562 " (cutoff:3.500A) Processing helix chain 'UC' and resid 575 through 580 removed outlier: 3.521A pdb=" N ARGUC 580 " --> pdb=" O LEUUC 576 " (cutoff:3.500A) Processing helix chain 'UL' and resid 322 through 326 Processing helix chain 'UL' and resid 749 through 774 removed outlier: 3.504A pdb=" N ALAUL 755 " --> pdb=" O ARGUL 751 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEUUL 758 " --> pdb=" O GLUUL 754 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLYUL 759 " --> pdb=" O ALAUL 755 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILEUL 760 " --> pdb=" O LEUUL 756 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLUUL 762 " --> pdb=" O LEUUL 758 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASPUL 772 " --> pdb=" O ALAUL 768 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYSUL 774 " --> pdb=" O ASNUL 770 " (cutoff:3.500A) Processing helix chain 'UL' and resid 793 through 798 removed outlier: 3.582A pdb=" N VALUL 797 " --> pdb=" O VALUL 793 " (cutoff:3.500A) Processing helix chain 'UL' and resid 800 through 812 removed outlier: 3.924A pdb=" N LEUUL 810 " --> pdb=" O METUL 806 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARGUL 811 " --> pdb=" O ASPUL 807 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILEUL 812 " --> pdb=" O THRUL 808 " (cutoff:3.500A) Processing helix chain 'UL' and resid 813 through 818 removed outlier: 4.696A pdb=" N GLUUL 818 " --> pdb=" O METUL 814 " (cutoff:3.500A) Processing helix chain 'UL' and resid 825 through 840 removed outlier: 3.591A pdb=" N VALUL 829 " --> pdb=" O PROUL 825 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYSUL 834 " --> pdb=" O LEUUL 830 " (cutoff:3.500A) Processing helix chain 'UL' and resid 842 through 848 removed outlier: 3.505A pdb=" N SERUL 848 " --> pdb=" O THRUL 844 " (cutoff:3.500A) Processing helix chain 'UL' and resid 849 through 864 removed outlier: 3.536A pdb=" N PHEUL 858 " --> pdb=" O CYSUL 854 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHEUL 859 " --> pdb=" O LYSUL 855 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYSUL 862 " --> pdb=" O PHEUL 858 " (cutoff:3.500A) Processing helix chain 'UL' and resid 864 through 869 removed outlier: 3.597A pdb=" N LEUUL 868 " --> pdb=" O ASNUL 864 " (cutoff:3.500A) Processing helix chain 'UL' and resid 873 through 916 removed outlier: 3.553A pdb=" N ARGUL 882 " --> pdb=" O LEUUL 878 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLUUL 886 " --> pdb=" O ARGUL 882 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASPUL 897 " --> pdb=" O SERUL 893 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEUUL 898 " --> pdb=" O THRUL 894 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLYUL 899 " --> pdb=" O GLUUL 895 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLYUL 904 " --> pdb=" O PHEUL 900 " (cutoff:3.500A) Processing helix chain 'UM' and resid 650 through 676 removed outlier: 3.589A pdb=" N VALUM 663 " --> pdb=" O ALAUM 659 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLNUM 667 " --> pdb=" O VALUM 663 " (cutoff:3.500A) Processing helix chain 'UM' and resid 677 through 689 Processing helix chain 'UM' and resid 690 through 705 removed outlier: 3.509A pdb=" N VALUM 697 " --> pdb=" O ARGUM 693 " (cutoff:3.500A) Processing helix chain 'UM' and resid 721 through 730 removed outlier: 3.528A pdb=" N ILEUM 730 " --> pdb=" O GLNUM 726 " (cutoff:3.500A) Processing helix chain 'UM' and resid 732 through 747 removed outlier: 3.524A pdb=" N LEUUM 738 " --> pdb=" O GLUUM 734 " (cutoff:3.500A) Processing helix chain 'UM' and resid 752 through 766 removed outlier: 3.574A pdb=" N ALAUM 756 " --> pdb=" O THRUM 752 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THRUM 759 " --> pdb=" O ILEUM 755 " (cutoff:3.500A) Processing helix chain 'UM' and resid 769 through 775 removed outlier: 3.809A pdb=" N SERUM 773 " --> pdb=" O ILEUM 769 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLUUM 774 " --> pdb=" O ALAUM 770 " (cutoff:3.500A) Processing helix chain 'UM' and resid 777 through 802 removed outlier: 3.981A pdb=" N ILEUM 781 " --> pdb=" O GLYUM 777 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALAUM 784 " --> pdb=" O LYSUM 780 " (cutoff:3.500A) Proline residue: UM 787 - end of helix Processing helix chain 'UM' and resid 804 through 817 removed outlier: 3.972A pdb=" N METUM 813 " --> pdb=" O ALAUM 809 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUUM 816 " --> pdb=" O GLUUM 812 " (cutoff:3.500A) Processing helix chain 'US' and resid 2 through 13 removed outlier: 3.681A pdb=" N GLUUS 7 " --> pdb=" O LEUUS 3 " (cutoff:3.500A) Processing helix chain 'US' and resid 23 through 34 Processing helix chain 'US' and resid 40 through 45 Processing helix chain 'US' and resid 54 through 74 removed outlier: 3.795A pdb=" N LEUUS 59 " --> pdb=" O LEUUS 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLNUS 61 " --> pdb=" O METUS 57 " (cutoff:3.500A) Processing helix chain 'US' and resid 82 through 87 removed outlier: 3.618A pdb=" N GLNUS 86 " --> pdb=" O LEUUS 82 " (cutoff:3.500A) Processing helix chain 'US' and resid 87 through 106 removed outlier: 3.612A pdb=" N PHEUS 98 " --> pdb=" O VALUS 94 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILEUS 106 " --> pdb=" O LEUUS 102 " (cutoff:3.500A) Processing helix chain 'US' and resid 113 through 134 removed outlier: 3.638A pdb=" N LEUUS 117 " --> pdb=" O THRUS 113 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASPUS 121 " --> pdb=" O LEUUS 117 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEUUS 124 " --> pdb=" O LEUUS 120 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THRUS 132 " --> pdb=" O GLUUS 128 " (cutoff:3.500A) Processing helix chain 'US' and resid 145 through 157 Processing helix chain 'US' and resid 176 through 182 Processing helix chain 'US' and resid 188 through 205 removed outlier: 4.119A pdb=" N GLNUS 192 " --> pdb=" O PHEUS 188 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYRUS 193 " --> pdb=" O ALAUS 189 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYRUS 194 " --> pdb=" O ASPUS 190 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLNUS 196 " --> pdb=" O GLNUS 192 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SERUS 197 " --> pdb=" O TYRUS 193 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLUUS 198 " --> pdb=" O TYRUS 194 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHEUS 199 " --> pdb=" O PHEUS 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEUUS 203 " --> pdb=" O PHEUS 199 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASPUS 205 " --> pdb=" O GLNUS 201 " (cutoff:3.500A) Processing helix chain 'US' and resid 205 through 215 removed outlier: 3.877A pdb=" N LEUUS 211 " --> pdb=" O ALAUS 207 " (cutoff:3.500A) Processing helix chain 'US' and resid 216 through 224 removed outlier: 3.701A pdb=" N LEUUS 220 " --> pdb=" O VALUS 216 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALAUS 221 " --> pdb=" O GLYUS 217 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEUUS 222 " --> pdb=" O LYSUS 218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASNUS 224 " --> pdb=" O LEUUS 220 " (cutoff:3.500A) Processing helix chain 'US' and resid 249 through 265 removed outlier: 4.387A pdb=" N ASNUS 260 " --> pdb=" O ASNUS 256 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRPUS 261 " --> pdb=" O PHEUS 257 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEUUS 262 " --> pdb=" O GLUUS 258 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SERUS 263 " --> pdb=" O LYSUS 259 " (cutoff:3.500A) Processing helix chain 'US' and resid 270 through 284 removed outlier: 3.555A pdb=" N LYSUS 275 " --> pdb=" O LEUUS 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEUUS 278 " --> pdb=" O TYRUS 274 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEUS 280 " --> pdb=" O SERUS 276 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HISUS 282 " --> pdb=" O LEUUS 278 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYSUS 283 " --> pdb=" O LEUUS 279 " (cutoff:3.500A) Processing helix chain 'US' and resid 295 through 304 removed outlier: 3.659A pdb=" N LEUUS 299 " --> pdb=" O LEUUS 295 " (cutoff:3.500A) Processing helix chain 'US' and resid 310 through 313 Processing helix chain 'US' and resid 314 through 330 removed outlier: 4.057A pdb=" N LEUUS 318 " --> pdb=" O VALUS 314 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALAUS 319 " --> pdb=" O VALUS 315 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASNUS 321 " --> pdb=" O ILEUS 317 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLYUS 322 " --> pdb=" O LEUUS 318 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLUUS 325 " --> pdb=" O ASNUS 321 " (cutoff:3.500A) Processing helix chain 'US' and resid 336 through 345 removed outlier: 3.849A pdb=" N GLNUS 343 " --> pdb=" O METUS 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEUS 345 " --> pdb=" O LEUUS 341 " (cutoff:3.500A) Processing helix chain 'US' and resid 346 through 352 removed outlier: 4.075A pdb=" N METUS 350 " --> pdb=" O ASNUS 346 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HISUS 351 " --> pdb=" O PROUS 347 " (cutoff:3.500A) Processing helix chain 'US' and resid 354 through 367 removed outlier: 4.845A pdb=" N ARGUS 360 " --> pdb=" O ALAUS 356 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEUUS 361 " --> pdb=" O ARGUS 357 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VALUS 364 " --> pdb=" O ARGUS 360 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHEUS 365 " --> pdb=" O LEUUS 361 " (cutoff:3.500A) Processing helix chain 'US' and resid 372 through 387 removed outlier: 3.561A pdb=" N VALUS 376 " --> pdb=" O SERUS 372 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHEUS 379 " --> pdb=" O LEUUS 375 " (cutoff:3.500A) Processing helix chain 'US' and resid 391 through 393 No H-bonds generated for 'chain 'US' and resid 391 through 393' Processing helix chain 'US' and resid 394 through 409 removed outlier: 3.910A pdb=" N VALUS 398 " --> pdb=" O ALAUS 394 " (cutoff:3.500A) Proline residue: US 400 - end of helix Processing helix chain 'US' and resid 410 through 416 removed outlier: 3.820A pdb=" N ILEUS 414 " --> pdb=" O ASNUS 411 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N METUS 415 " --> pdb=" O CYSUS 412 " (cutoff:3.500A) Processing helix chain 'US' and resid 428 through 441 removed outlier: 3.657A pdb=" N THRUS 437 " --> pdb=" O ALAUS 433 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYSUS 439 " --> pdb=" O LEUUS 435 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLUUS 440 " --> pdb=" O LYSUS 436 " (cutoff:3.500A) Processing helix chain 'US' and resid 463 through 469 removed outlier: 4.162A pdb=" N ALAUS 467 " --> pdb=" O LEUUS 463 " (cutoff:3.500A) Processing helix chain 'US' and resid 474 through 482 Processing helix chain 'US' and resid 483 through 485 No H-bonds generated for 'chain 'US' and resid 483 through 485' Processing helix chain 'US' and resid 494 through 499 removed outlier: 3.740A pdb=" N PHEUS 498 " --> pdb=" O ASNUS 494 " (cutoff:3.500A) Processing helix chain 'US' and resid 502 through 511 removed outlier: 3.794A pdb=" N SERUS 511 " --> pdb=" O LEUUS 507 " (cutoff:3.500A) Processing helix chain 'UU' and resid 658 through 660 No H-bonds generated for 'chain 'UU' and resid 658 through 660' Processing helix chain 'UU' and resid 668 through 673 Processing helix chain 'UU' and resid 703 through 707 Processing helix chain 'UU' and resid 728 through 736 removed outlier: 4.589A pdb=" N ASNUU 732 " --> pdb=" O ARGUU 728 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HISUU 736 " --> pdb=" O ASNUU 732 " (cutoff:3.500A) Processing helix chain 'UU' and resid 736 through 745 removed outlier: 3.869A pdb=" N ILEUU 740 " --> pdb=" O HISUU 736 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARGUU 741 " --> pdb=" O LEUUU 737 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYSUU 745 " --> pdb=" O ARGUU 741 " (cutoff:3.500A) Processing helix chain 'UU' and resid 769 through 775 Processing helix chain 'UU' and resid 787 through 805 removed outlier: 3.620A pdb=" N LEUUU 796 " --> pdb=" O ALAUU 792 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASPUU 797 " --> pdb=" O GLNUU 793 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALAUU 798 " --> pdb=" O LYSUU 794 " (cutoff:3.500A) Processing helix chain 'UU' and resid 815 through 828 Processing helix chain 'UU' and resid 830 through 839 removed outlier: 3.598A pdb=" N ALAUU 835 " --> pdb=" O SERUU 831 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THRUU 836 " --> pdb=" O SERUU 832 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASNUU 839 " --> pdb=" O ALAUU 835 " (cutoff:3.500A) Processing helix chain 'UU' and resid 841 through 850 removed outlier: 3.799A pdb=" N ASPUU 846 " --> pdb=" O PROUU 842 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEUUU 847 " --> pdb=" O ALAUU 843 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGUU 850 " --> pdb=" O ASPUU 846 " (cutoff:3.500A) Processing helix chain 'UU' and resid 858 through 873 removed outlier: 4.078A pdb=" N VALUU 862 " --> pdb=" O PHEUU 858 " (cutoff:3.500A) Processing helix chain 'UU' and resid 877 through 892 removed outlier: 3.900A pdb=" N GLUUU 882 " --> pdb=" O PHEUU 878 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUUU 888 " --> pdb=" O PHEUU 884 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHEUU 889 " --> pdb=" O METUU 885 " (cutoff:3.500A) Processing helix chain 'UU' and resid 892 through 899 Processing helix chain 'UU' and resid 904 through 917 removed outlier: 3.571A pdb=" N ALAUU 908 " --> pdb=" O ASPUU 904 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALUU 915 " --> pdb=" O ASNUU 911 " (cutoff:3.500A) Processing helix chain 'UU' and resid 918 through 921 Processing helix chain 'UU' and resid 922 through 939 removed outlier: 3.846A pdb=" N LYSUU 927 " --> pdb=" O ASPUU 923 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHEUU 928 " --> pdb=" O ASPUU 924 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALAUU 933 " --> pdb=" O CYSUU 929 " (cutoff:3.500A) Processing helix chain 'UV' and resid 82 through 115 removed outlier: 6.112A pdb=" N PHEUV 98 " --> pdb=" O THRUV 94 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYSUV 99 " --> pdb=" O ALAUV 95 " (cutoff:3.500A) Processing helix chain 'UV' and resid 117 through 138 Processing helix chain 'UV' and resid 145 through 156 Processing helix chain 'UV' and resid 168 through 172 removed outlier: 3.870A pdb=" N THRUV 172 " --> pdb=" O PROUV 169 " (cutoff:3.500A) Processing helix chain 'UV' and resid 222 through 247 Processing helix chain 'UV' and resid 285 through 289 Processing helix chain 'UV' and resid 329 through 341 Processing helix chain 'UV' and resid 341 through 356 removed outlier: 4.189A pdb=" N TYRUV 345 " --> pdb=" O THRUV 341 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEUUV 346 " --> pdb=" O HISUV 342 " (cutoff:3.500A) Processing helix chain 'UV' and resid 358 through 374 Processing helix chain 'UV' and resid 389 through 402 Processing helix chain 'UV' and resid 417 through 432 Processing helix chain 'UV' and resid 481 through 501 Processing helix chain 'UV' and resid 506 through 512 Processing helix chain 'UV' and resid 518 through 523 Processing helix chain 'UV' and resid 538 through 543 Processing helix chain 'UV' and resid 548 through 555 Processing helix chain 'UV' and resid 557 through 575 Processing helix chain 'UV' and resid 621 through 624 Processing helix chain 'UV' and resid 639 through 650 Processing helix chain 'UV' and resid 676 through 690 Processing helix chain 'UV' and resid 698 through 708 Processing helix chain 'UV' and resid 724 through 744 Processing helix chain 'UV' and resid 795 through 818 Processing helix chain 'UV' and resid 856 through 870 removed outlier: 4.295A pdb=" N GLUUV 860 " --> pdb=" O THRUV 856 " (cutoff:3.500A) Processing helix chain 'UV' and resid 874 through 890 removed outlier: 3.700A pdb=" N LEUUV 878 " --> pdb=" O LEUUV 874 " (cutoff:3.500A) Processing helix chain 'UV' and resid 890 through 906 Processing helix chain 'UV' and resid 908 through 923 Processing helix chain 'UV' and resid 924 through 928 removed outlier: 3.651A pdb=" N GLYUV 927 " --> pdb=" O LEUUV 924 " (cutoff:3.500A) Processing helix chain 'UV' and resid 930 through 944 Proline residue: UV 941 - end of helix Processing helix chain 'UV' and resid 953 through 968 Processing helix chain 'UV' and resid 1013 through 1030 Processing helix chain 'UV' and resid 1057 through 1079 removed outlier: 3.860A pdb=" N GLYUV1079 " --> pdb=" O LEUUV1075 " (cutoff:3.500A) Processing helix chain 'UV' and resid 1081 through 1090 Processing helix chain 'UV' and resid 1108 through 1113 Processing helix chain 'UV' and resid 1135 through 1143 Processing helix chain 'UV' and resid 1145 through 1158 Processing helix chain 'UV' and resid 1168 through 1173 Processing helix chain 'UV' and resid 1215 through 1227 Processing helix chain 'CI' and resid 28 through 37 removed outlier: 3.861A pdb=" N THRCI 35 " --> pdb=" O GLNCI 31 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYRCI 36 " --> pdb=" O VALCI 32 " (cutoff:3.500A) Processing helix chain 'CI' and resid 42 through 61 removed outlier: 4.111A pdb=" N ILECI 50 " --> pdb=" O LYSCI 46 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARGCI 55 " --> pdb=" O CYSCI 51 " (cutoff:3.500A) Processing helix chain 'CI' and resid 68 through 85 removed outlier: 3.557A pdb=" N LYSCI 73 " --> pdb=" O PROCI 69 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLUCI 75 " --> pdb=" O ARGCI 71 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLNCI 76 " --> pdb=" O ARGCI 72 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYSCI 81 " --> pdb=" O LEUCI 77 " (cutoff:3.500A) Processing helix chain 'CI' and resid 95 through 100 Processing helix chain 'CI' and resid 102 through 107 Processing helix chain 'CI' and resid 110 through 118 Processing helix chain 'CI' and resid 123 through 133 removed outlier: 3.510A pdb=" N ALACI 127 " --> pdb=" O THRCI 123 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VALCI 128 " --> pdb=" O ILECI 124 " (cutoff:3.500A) Processing helix chain 'CI' and resid 153 through 156 removed outlier: 3.605A pdb=" N ASPCI 156 " --> pdb=" O ASNCI 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'CI' and resid 153 through 156' Processing helix chain 'CI' and resid 166 through 174 removed outlier: 3.793A pdb=" N LEUCI 170 " --> pdb=" O ILECI 166 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEUCI 171 " --> pdb=" O LYSCI 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARGCI 174 " --> pdb=" O LEUCI 170 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 4.074A pdb=" N LYSCJ 105 " --> pdb=" O SERCJ 101 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 123 through 133 removed outlier: 3.644A pdb=" N ALACJ 130 " --> pdb=" O ASNCJ 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYSCJ 131 " --> pdb=" O LEUCJ 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYSCJ 133 " --> pdb=" O ASPCJ 129 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 172 through 176 removed outlier: 3.595A pdb=" N ASPCJ 175 " --> pdb=" O METCJ 172 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 196 through 208 removed outlier: 4.201A pdb=" N HISCJ 208 " --> pdb=" O CYSCJ 204 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 227 through 230 removed outlier: 3.756A pdb=" N PHECJ 230 " --> pdb=" O ARGCJ 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 227 through 230' Processing helix chain 'CK' and resid 298 through 319 removed outlier: 3.510A pdb=" N GLNCK 303 " --> pdb=" O SERCK 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLUCK 312 " --> pdb=" O ARGCK 308 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLNCK 313 " --> pdb=" O LYSCK 309 " (cutoff:3.500A) Processing helix chain 'CK' and resid 339 through 344 removed outlier: 3.531A pdb=" N GLUCK 344 " --> pdb=" O LEUCK 340 " (cutoff:3.500A) Processing helix chain 'CK' and resid 358 through 375 removed outlier: 3.558A pdb=" N THRCK 362 " --> pdb=" O THRCK 358 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASPCK 367 " --> pdb=" O GLUCK 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N METCK 368 " --> pdb=" O SERCK 364 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARGCK 371 " --> pdb=" O ASPCK 367 " (cutoff:3.500A) Processing helix chain 'CK' and resid 408 through 418 Processing helix chain 'CK' and resid 427 through 453 removed outlier: 3.827A pdb=" N LYSCK 432 " --> pdb=" O GLUCK 428 " (cutoff:3.500A) Processing helix chain 'CK' and resid 485 through 490 removed outlier: 3.936A pdb=" N SERCK 489 " --> pdb=" O SERCK 485 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEUCK 490 " --> pdb=" O ASNCK 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'CK' and resid 485 through 490' Processing helix chain 'CK' and resid 492 through 496 removed outlier: 3.545A pdb=" N TYRCK 496 " --> pdb=" O GLNCK 493 " (cutoff:3.500A) Processing helix chain 'CK' and resid 521 through 538 Processing helix chain 'CL' and resid 18 through 23 removed outlier: 4.145A pdb=" N HISCL 22 " --> pdb=" O LYSCL 18 " (cutoff:3.500A) Processing helix chain 'CL' and resid 35 through 54 removed outlier: 3.731A pdb=" N METCL 39 " --> pdb=" O ALACL 35 " (cutoff:3.500A) Processing helix chain 'CL' and resid 82 through 91 removed outlier: 3.580A pdb=" N LEUCL 89 " --> pdb=" O LEUCL 85 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARGCL 91 " --> pdb=" O ARGCL 87 " (cutoff:3.500A) Processing helix chain 'CL' and resid 124 through 133 removed outlier: 3.867A pdb=" N ASPCL 130 " --> pdb=" O ASNCL 126 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALACL 132 " --> pdb=" O METCL 128 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYSCL 133 " --> pdb=" O ILECL 129 " (cutoff:3.500A) Processing helix chain 'CL' and resid 149 through 163 removed outlier: 3.516A pdb=" N HISCL 161 " --> pdb=" O ASNCL 157 " (cutoff:3.500A) Processing helix chain 'CL' and resid 173 through 177 removed outlier: 3.673A pdb=" N PHECL 177 " --> pdb=" O LEUCL 174 " (cutoff:3.500A) Processing helix chain 'CL' and resid 179 through 198 Processing helix chain 'CL' and resid 216 through 229 removed outlier: 3.621A pdb=" N VALCL 229 " --> pdb=" O ARGCL 225 " (cutoff:3.500A) Processing helix chain 'CL' and resid 236 through 240 Processing helix chain 'CL' and resid 254 through 262 Processing helix chain 'CL' and resid 310 through 322 Processing helix chain 'CL' and resid 549 through 554 Processing helix chain 'CL' and resid 559 through 569 Processing helix chain 'CL' and resid 617 through 625 removed outlier: 3.664A pdb=" N LYSCL 623 " --> pdb=" O GLUCL 619 " (cutoff:3.500A) Processing helix chain 'CL' and resid 630 through 635 removed outlier: 4.298A pdb=" N GLUCL 633 " --> pdb=" O ALACL 630 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHECL 635 " --> pdb=" O LYSCL 632 " (cutoff:3.500A) Processing helix chain 'CL' and resid 717 through 734 Processing helix chain 'CL' and resid 749 through 773 removed outlier: 3.867A pdb=" N ILECL 758 " --> pdb=" O GLNCL 754 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLNCL 761 " --> pdb=" O LYSCL 757 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASNCL 765 " --> pdb=" O GLNCL 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLUCL 768 " --> pdb=" O ILECL 764 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUCL 771 " --> pdb=" O ILECL 767 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N METCL 772 " --> pdb=" O GLUCL 768 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THRCL 773 " --> pdb=" O TYRCL 769 " (cutoff:3.500A) Processing helix chain 'CL' and resid 775 through 782 removed outlier: 3.712A pdb=" N ARGCL 779 " --> pdb=" O GLUCL 775 " (cutoff:3.500A) Processing helix chain 'CL' and resid 797 through 803 removed outlier: 4.003A pdb=" N VALCL 801 " --> pdb=" O PROCL 797 " (cutoff:3.500A) Processing helix chain 'CL' and resid 954 through 960 removed outlier: 3.734A pdb=" N ALACL 959 " --> pdb=" O ALACL 955 " (cutoff:3.500A) Processing helix chain 'CL' and resid 1034 through 1043 Processing helix chain 'CM' and resid 16 through 28 removed outlier: 3.543A pdb=" N VALCM 22 " --> pdb=" O ARGCM 18 " (cutoff:3.500A) Processing helix chain 'CM' and resid 46 through 59 Processing helix chain 'CM' and resid 95 through 107 removed outlier: 3.789A pdb=" N PHECM 99 " --> pdb=" O PROCM 95 " (cutoff:3.500A) Proline residue: CM 102 - end of helix removed outlier: 3.844A pdb=" N TYRCM 105 " --> pdb=" O GLUCM 101 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUCM 106 " --> pdb=" O PROCM 102 " (cutoff:3.500A) Processing helix chain 'CM' and resid 108 through 110 No H-bonds generated for 'chain 'CM' and resid 108 through 110' Processing helix chain 'CM' and resid 129 through 145 removed outlier: 4.167A pdb=" N METCM 138 " --> pdb=" O LYSCM 134 " (cutoff:3.500A) Proline residue: CM 139 - end of helix Processing helix chain 'CM' and resid 201 through 217 removed outlier: 4.031A pdb=" N VALCM 205 " --> pdb=" O SERCM 201 " (cutoff:3.500A) Processing helix chain 'CM' and resid 232 through 236 Processing helix chain 'CM' and resid 267 through 285 removed outlier: 3.879A pdb=" N ALACM 276 " --> pdb=" O GLYCM 272 " (cutoff:3.500A) Processing helix chain 'CM' and resid 293 through 303 removed outlier: 3.562A pdb=" N VALCM 299 " --> pdb=" O PROCM 295 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYRCM 300 " --> pdb=" O LEUCM 296 " (cutoff:3.500A) Processing helix chain 'CM' and resid 319 through 330 removed outlier: 3.581A pdb=" N ILECM 323 " --> pdb=" O ASPCM 319 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYSCM 330 " --> pdb=" O LEUCM 326 " (cutoff:3.500A) Processing helix chain 'CN' and resid 63 through 79 Processing helix chain 'CN' and resid 99 through 105 Processing helix chain 'CN' and resid 130 through 150 Processing helix chain 'CN' and resid 151 through 155 removed outlier: 3.895A pdb=" N LEUCN 155 " --> pdb=" O PROCN 152 " (cutoff:3.500A) Processing helix chain 'CN' and resid 164 through 173 Processing helix chain 'CN' and resid 176 through 203 Processing helix chain 'JD' and resid 13 through 28 Processing helix chain 'JD' and resid 28 through 33 Processing helix chain 'JD' and resid 88 through 121 removed outlier: 3.551A pdb=" N GLNJD 118 " --> pdb=" O ILEJD 114 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASPJD 119 " --> pdb=" O GLYJD 115 " (cutoff:3.500A) Processing helix chain 'JD' and resid 362 through 380 removed outlier: 3.615A pdb=" N ASNJD 366 " --> pdb=" O TYRJD 362 " (cutoff:3.500A) Processing helix chain 'JD' and resid 383 through 390 removed outlier: 3.723A pdb=" N ALAJD 387 " --> pdb=" O GLUJD 383 " (cutoff:3.500A) Processing helix chain 'JD' and resid 391 through 396 removed outlier: 4.290A pdb=" N GLYJD 395 " --> pdb=" O LEUJD 391 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLUJD 396 " --> pdb=" O PROJD 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'JD' and resid 391 through 396' Processing helix chain 'JD' and resid 396 through 407 Processing helix chain 'JD' and resid 419 through 434 Proline residue: JD 425 - end of helix removed outlier: 3.500A pdb=" N LEUJD 428 " --> pdb=" O VALJD 424 " (cutoff:3.500A) Processing helix chain 'JD' and resid 451 through 466 Processing helix chain 'JD' and resid 494 through 501 Processing helix chain 'JD' and resid 517 through 521 Processing helix chain 'JD' and resid 522 through 540 removed outlier: 3.577A pdb=" N SERJD 533 " --> pdb=" O ILEJD 529 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARGJD 534 " --> pdb=" O GLYJD 530 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARGJD 537 " --> pdb=" O SERJD 533 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEUJD 538 " --> pdb=" O ARGJD 534 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARGJD 539 " --> pdb=" O CYSJD 535 " (cutoff:3.500A) Processing helix chain 'JD' and resid 563 through 567 Processing helix chain 'JD' and resid 602 through 616 removed outlier: 3.630A pdb=" N GLNJD 615 " --> pdb=" O CYSJD 611 " (cutoff:3.500A) Processing helix chain 'JD' and resid 628 through 639 Processing helix chain 'JD' and resid 722 through 727 removed outlier: 4.765A pdb=" N ASPJD 727 " --> pdb=" O GLNJD 723 " (cutoff:3.500A) Processing helix chain 'JD' and resid 738 through 742 removed outlier: 4.105A pdb=" N LYSJD 741 " --> pdb=" O LEUJD 738 " (cutoff:3.500A) Processing helix chain 'JD' and resid 743 through 748 removed outlier: 4.552A pdb=" N PHEJD 747 " --> pdb=" O GLNJD 743 " (cutoff:3.500A) Processing helix chain 'JD' and resid 762 through 765 Processing helix chain 'JD' and resid 802 through 811 Processing helix chain 'JD' and resid 826 through 832 removed outlier: 3.522A pdb=" N GLUJD 831 " --> pdb=" O SERJD 827 " (cutoff:3.500A) Processing helix chain 'JD' and resid 847 through 855 removed outlier: 3.746A pdb=" N LYSJD 855 " --> pdb=" O VALJD 851 " (cutoff:3.500A) Processing helix chain 'JD' and resid 861 through 865 Processing helix chain 'JD' and resid 872 through 886 Processing helix chain 'JD' and resid 896 through 904 Processing helix chain 'JD' and resid 908 through 921 removed outlier: 3.640A pdb=" N GLUJD 920 " --> pdb=" O LEUJD 916 " (cutoff:3.500A) Processing helix chain 'JD' and resid 923 through 936 removed outlier: 3.608A pdb=" N ILEJD 930 " --> pdb=" O TYRJD 926 " (cutoff:3.500A) Processing helix chain 'JD' and resid 987 through 996 removed outlier: 3.837A pdb=" N LYSJD 996 " --> pdb=" O SERJD 992 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1001 through 1014 Processing helix chain 'JD' and resid 1019 through 1028 removed outlier: 3.643A pdb=" N ILEJD1023 " --> pdb=" O GLUJD1019 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1031 through 1052 removed outlier: 3.572A pdb=" N LYSJD1043 " --> pdb=" O VALJD1039 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLNJD1044 " --> pdb=" O LYSJD1040 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1076 through 1089 removed outlier: 3.670A pdb=" N GLNJD1082 " --> pdb=" O LYSJD1078 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1101 through 1105 removed outlier: 3.595A pdb=" N LYSJD1105 " --> pdb=" O ASPJD1102 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1125 through 1129 Processing helix chain 'JD' and resid 1174 through 1182 removed outlier: 4.032A pdb=" N ASNJD1180 " --> pdb=" O THRJD1176 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILEJD1181 " --> pdb=" O PROJD1177 " (cutoff:3.500A) Processing helix chain 'JD' and resid 1183 through 1185 No H-bonds generated for 'chain 'JD' and resid 1183 through 1185' Processing helix chain 'JF' and resid 74 through 81 Processing helix chain 'JF' and resid 89 through 102 removed outlier: 3.536A pdb=" N HISJF 93 " --> pdb=" O PROJF 89 " (cutoff:3.500A) Processing helix chain 'JF' and resid 102 through 107 Processing helix chain 'JF' and resid 133 through 148 removed outlier: 4.076A pdb=" N GLYJF 139 " --> pdb=" O LYSJF 135 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEUJF 140 " --> pdb=" O ARGJF 136 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N METJF 141 " --> pdb=" O PHEJF 137 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VALJF 142 " --> pdb=" O SERJF 138 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HISJF 146 " --> pdb=" O VALJF 142 " (cutoff:3.500A) Processing helix chain 'JF' and resid 166 through 170 removed outlier: 3.767A pdb=" N ASPJF 169 " --> pdb=" O PROJF 166 " (cutoff:3.500A) Processing helix chain 'JF' and resid 188 through 195 removed outlier: 3.500A pdb=" N LYSJF 195 " --> pdb=" O ASPJF 191 " (cutoff:3.500A) Processing helix chain 'JF' and resid 233 through 249 removed outlier: 3.657A pdb=" N GLYJF 244 " --> pdb=" O LYSJF 240 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASPJF 247 " --> pdb=" O HISJF 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALAJF 248 " --> pdb=" O GLYJF 244 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRPJF 249 " --> pdb=" O ALAJF 245 " (cutoff:3.500A) Processing helix chain 'JG' and resid 74 through 81 removed outlier: 3.882A pdb=" N LYSJG 78 " --> pdb=" O GLNJG 74 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYSJG 79 " --> pdb=" O GLYJG 75 " (cutoff:3.500A) Processing helix chain 'JG' and resid 89 through 101 removed outlier: 3.606A pdb=" N THRJG 98 " --> pdb=" O GLNJG 94 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASPJG 101 " --> pdb=" O LEUJG 97 " (cutoff:3.500A) Processing helix chain 'JG' and resid 102 through 107 Processing helix chain 'JG' and resid 133 through 148 removed outlier: 3.540A pdb=" N PHEJG 137 " --> pdb=" O THRJG 133 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HISJG 146 " --> pdb=" O VALJG 142 " (cutoff:3.500A) Processing helix chain 'JG' and resid 166 through 171 removed outlier: 4.312A pdb=" N HISJG 170 " --> pdb=" O PROJG 166 " (cutoff:3.500A) Processing helix chain 'JG' and resid 188 through 195 removed outlier: 3.669A pdb=" N LYSJG 195 " --> pdb=" O ASPJG 191 " (cutoff:3.500A) Processing helix chain 'JG' and resid 233 through 249 removed outlier: 3.625A pdb=" N CYSJG 238 " --> pdb=" O ALAJG 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHEJG 241 " --> pdb=" O ALAJG 237 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLYJG 244 " --> pdb=" O LYSJG 240 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASPJG 247 " --> pdb=" O HISJG 243 " (cutoff:3.500A) Processing helix chain 'JH' and resid 207 through 222 Processing helix chain 'JH' and resid 230 through 235 Processing helix chain 'JH' and resid 236 through 239 Processing helix chain 'JH' and resid 241 through 249 removed outlier: 3.592A pdb=" N TYRJH 247 " --> pdb=" O GLNJH 243 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VALJH 248 " --> pdb=" O ASPJH 244 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THRJH 249 " --> pdb=" O VALJH 245 " (cutoff:3.500A) Processing helix chain 'JH' and resid 250 through 254 Processing helix chain 'JH' and resid 255 through 270 Processing helix chain 'JH' and resid 271 through 282 Processing helix chain 'JH' and resid 282 through 294 Processing helix chain 'JH' and resid 300 through 311 Processing helix chain 'JH' and resid 313 through 321 Processing helix chain 'JH' and resid 321 through 327 Processing helix chain 'JH' and resid 331 through 345 Processing helix chain 'JH' and resid 348 through 361 Processing helix chain 'JH' and resid 365 through 378 Processing helix chain 'JH' and resid 383 through 396 Processing helix chain 'JH' and resid 406 through 410 Processing helix chain 'JH' and resid 414 through 429 removed outlier: 3.721A pdb=" N HISJH 418 " --> pdb=" O PROJH 414 " (cutoff:3.500A) Processing helix chain 'JH' and resid 430 through 432 No H-bonds generated for 'chain 'JH' and resid 430 through 432' Processing helix chain 'JH' and resid 433 through 448 Processing helix chain 'JH' and resid 451 through 462 removed outlier: 4.176A pdb=" N GLUJH 455 " --> pdb=" O ASPJH 451 " (cutoff:3.500A) Processing helix chain 'JL' and resid 44 through 52 Processing helix chain 'JL' and resid 70 through 78 removed outlier: 3.676A pdb=" N GLUJL 76 " --> pdb=" O VALJL 72 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLNJL 77 " --> pdb=" O ARGJL 73 " (cutoff:3.500A) Processing helix chain 'JL' and resid 87 through 99 Processing helix chain 'JL' and resid 103 through 105 No H-bonds generated for 'chain 'JL' and resid 103 through 105' Processing helix chain 'JL' and resid 113 through 117 Processing helix chain 'JL' and resid 130 through 144 removed outlier: 3.542A pdb=" N SERJL 134 " --> pdb=" O PROJL 130 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SERJL 135 " --> pdb=" O TYRJL 131 " (cutoff:3.500A) Proline residue: JL 136 - end of helix removed outlier: 4.033A pdb=" N PHEJL 139 " --> pdb=" O SERJL 135 " (cutoff:3.500A) Processing helix chain 'JL' and resid 157 through 165 Processing helix chain 'JL' and resid 173 through 182 removed outlier: 3.875A pdb=" N TRPJL 182 " --> pdb=" O ASNJL 178 " (cutoff:3.500A) Processing helix chain 'JL' and resid 219 through 232 removed outlier: 3.622A pdb=" N VALJL 230 " --> pdb=" O LEUJL 226 " (cutoff:3.500A) Processing helix chain 'JL' and resid 237 through 242 Processing helix chain 'JL' and resid 244 through 263 Processing helix chain 'JL' and resid 272 through 288 removed outlier: 3.833A pdb=" N VALJL 276 " --> pdb=" O SERJL 272 " (cutoff:3.500A) Processing helix chain 'JL' and resid 294 through 298 Processing helix chain 'JL' and resid 299 through 313 removed outlier: 3.749A pdb=" N VALJL 313 " --> pdb=" O ALAJL 309 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 102 through 124 removed outlier: 4.007A pdb=" N THRJJ 107 " --> pdb=" O PROJJ 103 " (cutoff:3.500A) Proline residue: JJ 108 - end of helix removed outlier: 4.676A pdb=" N THRJJ 114 " --> pdb=" O ARGJJ 110 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LYSJJ 115 " --> pdb=" O ASNJJ 111 " (cutoff:3.500A) Proline residue: JJ 118 - end of helix Processing helix chain 'JJ' and resid 148 through 164 removed outlier: 4.202A pdb=" N LEUJJ 152 " --> pdb=" O ASPJJ 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLNJJ 153 " --> pdb=" O PROJJ 149 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 167 through 177 removed outlier: 3.636A pdb=" N LEUJJ 175 " --> pdb=" O SERJJ 171 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 187 through 191 Processing helix chain 'JJ' and resid 195 through 207 Processing helix chain 'JJ' and resid 210 through 219 removed outlier: 3.757A pdb=" N ILEJJ 216 " --> pdb=" O THRJJ 212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLUJJ 217 " --> pdb=" O LYSJJ 213 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 237 through 252 removed outlier: 3.696A pdb=" N METJJ 242 " --> pdb=" O THRJJ 238 " (cutoff:3.500A) Processing helix chain 'JJ' and resid 255 through 273 removed outlier: 3.513A pdb=" N VALJJ 259 " --> pdb=" O PROJJ 255 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARGJJ 273 " --> pdb=" O ARGJJ 269 " (cutoff:3.500A) Processing helix chain 'DF' and resid 30 through 35 removed outlier: 3.587A pdb=" N GLNDF 35 " --> pdb=" O GLUDF 31 " (cutoff:3.500A) Processing helix chain 'DF' and resid 36 through 38 No H-bonds generated for 'chain 'DF' and resid 36 through 38' Processing helix chain 'DF' and resid 43 through 45 No H-bonds generated for 'chain 'DF' and resid 43 through 45' Processing helix chain 'DF' and resid 82 through 87 removed outlier: 3.777A pdb=" N CYSDF 87 " --> pdb=" O LYSDF 84 " (cutoff:3.500A) Processing helix chain 'DF' and resid 88 through 96 removed outlier: 3.794A pdb=" N SERDF 96 " --> pdb=" O ARGDF 92 " (cutoff:3.500A) Processing helix chain 'DF' and resid 106 through 125 removed outlier: 3.690A pdb=" N ALADF 110 " --> pdb=" O LYSDF 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASPDF 119 " --> pdb=" O LYSDF 115 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILEDF 120 " --> pdb=" O HISDF 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASNDF 122 " --> pdb=" O LEUDF 118 " (cutoff:3.500A) Processing helix chain 'DF' and resid 128 through 141 removed outlier: 3.665A pdb=" N VALDF 132 " --> pdb=" O ASNDF 128 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASNDF 139 " --> pdb=" O ASPDF 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLYDF 141 " --> pdb=" O ILEDF 137 " (cutoff:3.500A) Processing helix chain 'DF' and resid 163 through 183 removed outlier: 3.553A pdb=" N ALADF 171 " --> pdb=" O ARGDF 167 " (cutoff:3.500A) Processing helix chain 'DF' and resid 189 through 204 removed outlier: 3.534A pdb=" N ALADF 195 " --> pdb=" O ALADF 191 " (cutoff:3.500A) Processing helix chain 'DF' and resid 208 through 224 removed outlier: 3.715A pdb=" N LYSDF 212 " --> pdb=" O SERDF 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARGDF 219 " --> pdb=" O ASPDF 215 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALADF 221 " --> pdb=" O LEUDF 217 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYSDF 222 " --> pdb=" O GLUDF 218 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASNDF 224 " --> pdb=" O VALDF 220 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 35 through 39 removed outlier: 3.914A pdb=" N VALDQ 39 " --> pdb=" O ILEDQ 36 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 44 through 49 removed outlier: 3.709A pdb=" N VALDQ 48 " --> pdb=" O LEUDQ 44 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 49 through 54 Processing helix chain 'DQ' and resid 56 through 61 removed outlier: 3.618A pdb=" N PHEDQ 60 " --> pdb=" O LEUDQ 57 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 74 through 91 removed outlier: 3.831A pdb=" N VALDQ 78 " --> pdb=" O HISDQ 74 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALADQ 80 " --> pdb=" O SERDQ 76 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLNDQ 83 " --> pdb=" O TYRDQ 79 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALADQ 86 " --> pdb=" O ARGDQ 82 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 98 through 113 removed outlier: 3.614A pdb=" N LYSDQ 102 " --> pdb=" O ASPDQ 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THRDQ 110 " --> pdb=" O LYSDQ 106 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SERDQ 111 " --> pdb=" O LYSDQ 107 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 114 through 117 Processing helix chain 'DS' and resid 27 through 32 Processing helix chain 'DS' and resid 33 through 35 No H-bonds generated for 'chain 'DS' and resid 33 through 35' Processing helix chain 'DS' and resid 39 through 50 removed outlier: 3.900A pdb=" N CYSDS 47 " --> pdb=" O SERDS 43 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSDS 48 " --> pdb=" O ASNDS 44 " (cutoff:3.500A) Processing helix chain 'DS' and resid 62 through 75 removed outlier: 3.712A pdb=" N ARGDS 68 " --> pdb=" O GLUDS 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILEDS 69 " --> pdb=" O GLUDS 65 " (cutoff:3.500A) Processing helix chain 'DS' and resid 82 through 86 removed outlier: 3.836A pdb=" N LEUDS 86 " --> pdb=" O ALADS 83 " (cutoff:3.500A) Processing helix chain 'DT' and resid 5 through 9 Processing helix chain 'DT' and resid 10 through 20 Processing helix chain 'DT' and resid 20 through 26 removed outlier: 3.591A pdb=" N ARGDT 24 " --> pdb=" O SERDT 20 " (cutoff:3.500A) Processing helix chain 'DT' and resid 52 through 68 removed outlier: 3.594A pdb=" N ARGDT 63 " --> pdb=" O ALADT 59 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N METDT 67 " --> pdb=" O ARGDT 63 " (cutoff:3.500A) Processing helix chain 'DT' and resid 72 through 81 removed outlier: 3.581A pdb=" N LYSDT 78 " --> pdb=" O GLYDT 74 " (cutoff:3.500A) Processing helix chain 'DT' and resid 97 through 109 removed outlier: 3.704A pdb=" N ASNDT 101 " --> pdb=" O SERDT 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALADT 107 " --> pdb=" O LYSDT 103 " (cutoff:3.500A) Processing helix chain 'DT' and resid 125 through 141 Processing helix chain 'DA' and resid 56 through 62 removed outlier: 4.120A pdb=" N ALADA 60 " --> pdb=" O SERDA 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEUDA 61 " --> pdb=" O ALADA 57 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYSDA 62 " --> pdb=" O SERDA 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 56 through 62' Processing helix chain 'DA' and resid 70 through 75 Processing helix chain 'DA' and resid 106 through 114 Processing helix chain 'DA' and resid 158 through 179 Processing helix chain 'DA' and resid 181 through 189 Processing helix chain 'DA' and resid 191 through 202 removed outlier: 3.833A pdb=" N LYSDA 195 " --> pdb=" O GLUDA 191 " (cutoff:3.500A) Processing helix chain 'DA' and resid 224 through 232 removed outlier: 3.590A pdb=" N LEUDA 228 " --> pdb=" O ASPDA 224 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEUDA 231 " --> pdb=" O ALADA 227 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HISDA 232 " --> pdb=" O LEUDA 228 " (cutoff:3.500A) Processing helix chain 'DE' and resid 15 through 19 removed outlier: 3.596A pdb=" N TRPDE 18 " --> pdb=" O PRODE 15 " (cutoff:3.500A) Processing helix chain 'DE' and resid 37 through 39 No H-bonds generated for 'chain 'DE' and resid 37 through 39' Processing helix chain 'DE' and resid 44 through 50 Processing helix chain 'DE' and resid 58 through 67 removed outlier: 3.845A pdb=" N GLNDE 67 " --> pdb=" O ALADE 63 " (cutoff:3.500A) Processing helix chain 'DE' and resid 94 through 96 No H-bonds generated for 'chain 'DE' and resid 94 through 96' Processing helix chain 'DE' and resid 115 through 120 Processing helix chain 'DE' and resid 133 through 135 No H-bonds generated for 'chain 'DE' and resid 133 through 135' Processing helix chain 'DE' and resid 247 through 256 Processing helix chain 'DG' and resid 20 through 25 Processing helix chain 'DG' and resid 26 through 28 No H-bonds generated for 'chain 'DG' and resid 26 through 28' Processing helix chain 'DG' and resid 59 through 61 No H-bonds generated for 'chain 'DG' and resid 59 through 61' Processing helix chain 'DG' and resid 121 through 126 removed outlier: 3.531A pdb=" N ASPDG 126 " --> pdb=" O GLUDG 122 " (cutoff:3.500A) Processing helix chain 'DG' and resid 137 through 146 Processing helix chain 'DG' and resid 180 through 226 Processing helix chain 'DH' and resid 14 through 29 Processing helix chain 'DH' and resid 30 through 35 removed outlier: 3.735A pdb=" N LEUDH 34 " --> pdb=" O SERDH 30 " (cutoff:3.500A) Processing helix chain 'DH' and resid 66 through 71 Processing helix chain 'DH' and resid 76 through 84 Processing helix chain 'DH' and resid 117 through 130 removed outlier: 3.550A pdb=" N LEUDH 126 " --> pdb=" O HISDH 122 " (cutoff:3.500A) Processing helix chain 'DH' and resid 158 through 162 Processing helix chain 'DH' and resid 165 through 178 Processing helix chain 'DI' and resid 25 through 27 No H-bonds generated for 'chain 'DI' and resid 25 through 27' Processing helix chain 'DI' and resid 68 through 71 Processing helix chain 'DI' and resid 88 through 93 Processing helix chain 'DI' and resid 106 through 117 Processing helix chain 'DI' and resid 137 through 146 Processing helix chain 'DI' and resid 153 through 163 removed outlier: 3.894A pdb=" N GLNDI 159 " --> pdb=" O SERDI 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHEDI 160 " --> pdb=" O VALDI 156 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SERDI 161 " --> pdb=" O GLUDI 157 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALADI 162 " --> pdb=" O SERDI 158 " (cutoff:3.500A) Processing helix chain 'DI' and resid 172 through 177 Processing helix chain 'DI' and resid 185 through 198 Processing helix chain 'DJ' and resid 20 through 35 removed outlier: 3.557A pdb=" N LEUDJ 30 " --> pdb=" O ALADJ 26 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 38 through 62 removed outlier: 4.011A pdb=" N ILEDJ 42 " --> pdb=" O ASNDJ 38 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILEDJ 45 " --> pdb=" O GLUDJ 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGDJ 62 " --> pdb=" O ASPDJ 58 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 66 through 83 removed outlier: 3.664A pdb=" N VALDJ 83 " --> pdb=" O ARGDJ 79 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 100 through 106 removed outlier: 3.827A pdb=" N PHEDJ 104 " --> pdb=" O LYSDJ 100 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 108 through 117 Processing helix chain 'DJ' and resid 121 through 131 Processing helix chain 'DJ' and resid 149 through 156 removed outlier: 5.452A pdb=" N LYSDJ 154 " --> pdb=" O ASPDJ 151 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 170 through 181 removed outlier: 3.769A pdb=" N ASNDJ 176 " --> pdb=" O VALDJ 172 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALADJ 181 " --> pdb=" O ALADJ 177 " (cutoff:3.500A) Processing helix chain 'DL' and resid 45 through 50 removed outlier: 3.762A pdb=" N ILEDL 49 " --> pdb=" O PRODL 45 " (cutoff:3.500A) Processing helix chain 'DL' and resid 149 through 153 removed outlier: 3.537A pdb=" N GLNDL 152 " --> pdb=" O ALADL 149 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHEDL 153 " --> pdb=" O ASNDL 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'DL' and resid 149 through 153' Processing helix chain 'DN' and resid 29 through 43 Processing helix chain 'DN' and resid 46 through 57 removed outlier: 3.514A pdb=" N ALADN 57 " --> pdb=" O LEUDN 53 " (cutoff:3.500A) Processing helix chain 'DN' and resid 62 through 67 removed outlier: 3.624A pdb=" N ILEDN 66 " --> pdb=" O GLNDN 62 " (cutoff:3.500A) Processing helix chain 'DN' and resid 70 through 78 Processing helix chain 'DN' and resid 85 through 105 Processing helix chain 'DN' and resid 108 through 132 removed outlier: 3.548A pdb=" N ARGDN 124 " --> pdb=" O SERDN 120 " (cutoff:3.500A) Processing helix chain 'DN' and resid 142 through 151 removed outlier: 4.325A pdb=" N SERDN 147 " --> pdb=" O SERDN 143 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALADN 148 " --> pdb=" O ALADN 144 " (cutoff:3.500A) Processing helix chain 'DO' and resid 56 through 75 removed outlier: 4.143A pdb=" N GLYDO 75 " --> pdb=" O CYSDO 71 " (cutoff:3.500A) Processing helix chain 'DO' and resid 95 through 107 removed outlier: 4.561A pdb=" N GLNDO 99 " --> pdb=" O GLYDO 95 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALADO 100 " --> pdb=" O PRODO 96 " (cutoff:3.500A) Processing helix chain 'DZ' and resid 45 through 52 Processing helix chain 'DZ' and resid 60 through 65 Processing helix chain 'DZ' and resid 76 through 85 removed outlier: 3.867A pdb=" N LEUDZ 80 " --> pdb=" O ALADZ 76 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUDZ 84 " --> pdb=" O LEUDZ 80 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYSDZ 85 " --> pdb=" O ARGDZ 81 " (cutoff:3.500A) Processing helix chain 'DW' and resid 5 through 20 removed outlier: 3.563A pdb=" N ASPDW 9 " --> pdb=" O SERDW 5 " (cutoff:3.500A) Processing helix chain 'DW' and resid 31 through 44 Processing helix chain 'DW' and resid 84 through 94 removed outlier: 4.515A pdb=" N LYSDW 88 " --> pdb=" O GLYDW 84 " (cutoff:3.500A) Processing helix chain 'DW' and resid 113 through 120 Processing helix chain 'DX' and resid 11 through 24 removed outlier: 3.934A pdb=" N TRPDX 24 " --> pdb=" O ARGDX 20 " (cutoff:3.500A) Processing helix chain 'DX' and resid 26 through 35 Processing helix chain 'DX' and resid 89 through 95 Processing helix chain 'DX' and resid 132 through 137 Processing helix chain 'DY' and resid 16 through 18 No H-bonds generated for 'chain 'DY' and resid 16 through 18' Processing helix chain 'DY' and resid 36 through 46 removed outlier: 3.526A pdb=" N LEUDY 40 " --> pdb=" O SERDY 36 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLUDY 46 " --> pdb=" O GLUDY 42 " (cutoff:3.500A) Processing helix chain 'DY' and resid 51 through 53 No H-bonds generated for 'chain 'DY' and resid 51 through 53' Processing helix chain 'DY' and resid 78 through 86 removed outlier: 3.749A pdb=" N LYSDY 84 " --> pdb=" O ALADY 80 " (cutoff:3.500A) Processing helix chain 'DY' and resid 87 through 95 Processing helix chain 'DY' and resid 104 through 116 Processing helix chain 'DY' and resid 122 through 133 removed outlier: 3.716A pdb=" N ARGDY 132 " --> pdb=" O LYSDY 128 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASNDY 133 " --> pdb=" O VALDY 129 " (cutoff:3.500A) Processing helix chain 'Db' and resid 11 through 17 Processing sheet with id=AA1, first strand: chain 'UA' and resid 6 through 11 removed outlier: 5.541A pdb=" N PHEUA 7 " --> pdb=" O SERUA 705 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SERUA 705 " --> pdb=" O PHEUA 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYRUA 704 " --> pdb=" O PHEUA 693 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SERUA 683 " --> pdb=" O ALAUA 696 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'UA' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'UA' and resid 58 through 63 removed outlier: 3.954A pdb=" N HISUA 91 " --> pdb=" O LEUUA 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'UA' and resid 99 through 104 removed outlier: 4.192A pdb=" N ALAUA 101 " --> pdb=" O ALAUA 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALAUA 114 " --> pdb=" O ALAUA 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'UA' and resid 149 through 154 removed outlier: 6.927A pdb=" N THRUA 164 " --> pdb=" O THRUA 150 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEUUA 152 " --> pdb=" O LEUUA 162 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEUUA 162 " --> pdb=" O LEUUA 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'UA' and resid 197 through 199 removed outlier: 3.579A pdb=" N PHEUA 216 " --> pdb=" O THRUA 208 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYSUA 252 " --> pdb=" O VALUA 217 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLUUA 219 " --> pdb=" O ILEUA 250 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILEUA 250 " --> pdb=" O GLUUA 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'UA' and resid 263 through 269 removed outlier: 6.519A pdb=" N GLYUA 278 " --> pdb=" O LYSUA 264 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VALUA 266 " --> pdb=" O ALAUA 276 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALAUA 276 " --> pdb=" O VALUA 266 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHEUA 268 " --> pdb=" O LEUUA 274 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEUUA 274 " --> pdb=" O PHEUA 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALUA 277 " --> pdb=" O ARGUA 285 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARGUA 285 " --> pdb=" O VALUA 277 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHEUA 279 " --> pdb=" O GLUUA 283 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLUUA 283 " --> pdb=" O PHEUA 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLNUA 296 " --> pdb=" O LEUUA 286 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASPUA 288 " --> pdb=" O LEUUA 294 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEUUA 294 " --> pdb=" O ASPUA 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'UA' and resid 307 through 310 removed outlier: 3.607A pdb=" N THRUA 307 " --> pdb=" O GLYUA 320 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEUUA 339 " --> pdb=" O VALUA 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'UA' and resid 351 through 353 removed outlier: 3.812A pdb=" N LYSUA 370 " --> pdb=" O THRUA 362 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALAUA 381 " --> pdb=" O VALUA 371 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASPUA 373 " --> pdb=" O CYSUA 379 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N CYSUA 379 " --> pdb=" O ASPUA 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'UA' and resid 390 through 395 removed outlier: 3.674A pdb=" N SERUA 404 " --> pdb=" O ARGUA 412 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARGUA 412 " --> pdb=" O SERUA 404 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SERUA 406 " --> pdb=" O THRUA 410 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THRUA 410 " --> pdb=" O SERUA 406 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARGUA 423 " --> pdb=" O ALAUA 413 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASPUA 415 " --> pdb=" O ASNUA 421 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASNUA 421 " --> pdb=" O ASPUA 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'UA' and resid 435 through 438 removed outlier: 3.567A pdb=" N ASPUA 467 " --> pdb=" O VALUA 457 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SERUA 459 " --> pdb=" O LEUUA 465 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEUUA 465 " --> pdb=" O SERUA 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'UA' and resid 476 through 482 removed outlier: 4.432A pdb=" N CYSUA 478 " --> pdb=" O ALAUA 491 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SERUA 480 " --> pdb=" O ALAUA 489 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VALUA 487 " --> pdb=" O SERUA 482 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'UA' and resid 496 through 499 Processing sheet with id=AB5, first strand: chain 'UA' and resid 518 through 523 removed outlier: 3.630A pdb=" N GLYUA 551 " --> pdb=" O ILEUA 541 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASNUA 543 " --> pdb=" O GLNUA 549 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLNUA 549 " --> pdb=" O ASNUA 543 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'UA' and resid 583 through 585 Processing sheet with id=AB7, first strand: chain 'UL' and resid 7 through 14 removed outlier: 6.863A pdb=" N ILEUL 683 " --> pdb=" O ALAUL 11 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALAUL 13 " --> pdb=" O ILEUL 681 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILEUL 681 " --> pdb=" O ALAUL 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'UL' and resid 24 through 25 Processing sheet with id=AB9, first strand: chain 'UL' and resid 84 through 88 removed outlier: 3.868A pdb=" N VALUL 105 " --> pdb=" O LEUUL 115 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEUUL 115 " --> pdb=" O VALUL 105 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASPUL 107 " --> pdb=" O VALUL 113 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VALUL 113 " --> pdb=" O ASPUL 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'UL' and resid 124 through 126 removed outlier: 3.594A pdb=" N VALUL 147 " --> pdb=" O TYRUL 157 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYRUL 157 " --> pdb=" O VALUL 147 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASPUL 149 " --> pdb=" O GLYUL 155 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLYUL 155 " --> pdb=" O ASPUL 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'UL' and resid 168 through 171 removed outlier: 3.974A pdb=" N GLUUL 198 " --> pdb=" O LEUUL 188 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASPUL 190 " --> pdb=" O CYSUL 196 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYSUL 196 " --> pdb=" O ASPUL 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'UL' and resid 210 through 212 removed outlier: 3.697A pdb=" N ALAUL 211 " --> pdb=" O ILEUL 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THRUL 219 " --> pdb=" O LYSUL 227 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYSUL 227 " --> pdb=" O THRUL 219 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'UL' and resid 256 through 260 removed outlier: 6.779A pdb=" N GLNUL 275 " --> pdb=" O LEUUL 257 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILEUL 259 " --> pdb=" O TYRUL 273 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYRUL 273 " --> pdb=" O ILEUL 259 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THRUL 280 " --> pdb=" O ASNUL 276 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILEUL 281 " --> pdb=" O THRUL 331 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THRUL 331 " --> pdb=" O ILEUL 281 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THRUL 283 " --> pdb=" O PHEUL 329 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'UL' and resid 338 through 346 removed outlier: 3.587A pdb=" N LYSUL 350 " --> pdb=" O VALUL 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'UL' and resid 394 through 398 removed outlier: 3.991A pdb=" N SERUL 396 " --> pdb=" O THRUL 408 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALAUL 407 " --> pdb=" O LYSUL 415 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALAUL 409 " --> pdb=" O SERUL 413 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SERUL 413 " --> pdb=" O ALAUL 409 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'UL' and resid 433 through 438 removed outlier: 3.657A pdb=" N THRUL 435 " --> pdb=" O GLYUL 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'UL' and resid 476 through 481 removed outlier: 6.519A pdb=" N GLYUL 491 " --> pdb=" O TRPUL 477 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEUUL 479 " --> pdb=" O VALUL 489 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VALUL 489 " --> pdb=" O LEUUL 479 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEUUL 481 " --> pdb=" O ARGUL 487 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARGUL 487 " --> pdb=" O LEUUL 481 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THRUL 496 " --> pdb=" O SERUL 492 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'UL' and resid 476 through 481 removed outlier: 6.519A pdb=" N GLYUL 491 " --> pdb=" O TRPUL 477 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEUUL 479 " --> pdb=" O VALUL 489 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VALUL 489 " --> pdb=" O LEUUL 479 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEUUL 481 " --> pdb=" O ARGUL 487 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARGUL 487 " --> pdb=" O LEUUL 481 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THRUL 496 " --> pdb=" O SERUL 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'UL' and resid 537 through 539 Processing sheet with id=AD2, first strand: chain 'UL' and resid 576 through 581 removed outlier: 3.726A pdb=" N THRUL 590 " --> pdb=" O LYSUL 598 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYSUL 598 " --> pdb=" O THRUL 590 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SERUL 592 " --> pdb=" O ASNUL 596 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASNUL 596 " --> pdb=" O SERUL 592 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYSUL 609 " --> pdb=" O ILEUL 599 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLYUL 601 " --> pdb=" O CYSUL 607 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N CYSUL 607 " --> pdb=" O GLYUL 601 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'UL' and resid 618 through 620 removed outlier: 3.546A pdb=" N GLNUL 651 " --> pdb=" O TYRUL 641 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASPUL 643 " --> pdb=" O CYSUL 649 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N CYSUL 649 " --> pdb=" O ASPUL 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'UM' and resid 10 through 12 removed outlier: 3.651A pdb=" N GLNUM 642 " --> pdb=" O SERUM 634 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'UM' and resid 24 through 25 removed outlier: 3.521A pdb=" N THRUM 24 " --> pdb=" O ALAUM 33 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILEUM 40 " --> pdb=" O LYSUM 55 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYSUM 55 " --> pdb=" O ILEUM 40 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILEUM 42 " --> pdb=" O LEUUM 53 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYSUM 51 " --> pdb=" O ASPUM 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THRUM 46 " --> pdb=" O SERUM 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'UM' and resid 64 through 69 removed outlier: 4.076A pdb=" N ALAUM 66 " --> pdb=" O VALUM 79 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYRUM 78 " --> pdb=" O LYSUM 86 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYSUM 86 " --> pdb=" O TYRUM 78 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARGUM 97 " --> pdb=" O ILEUM 87 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HISUM 89 " --> pdb=" O VALUM 95 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VALUM 95 " --> pdb=" O HISUM 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'UM' and resid 108 through 110 removed outlier: 4.103A pdb=" N HISUM 138 " --> pdb=" O VALUM 128 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASPUM 130 " --> pdb=" O ILEUM 136 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILEUM 136 " --> pdb=" O ASPUM 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'UM' and resid 147 through 153 removed outlier: 6.347A pdb=" N VALUM 172 " --> pdb=" O THRUM 185 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THRUM 185 " --> pdb=" O VALUM 172 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VALUM 174 " --> pdb=" O LEUUM 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUUM 183 " --> pdb=" O VALUM 174 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSUM 181 " --> pdb=" O ASPUM 176 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'UM' and resid 196 through 198 Processing sheet with id=AE1, first strand: chain 'UM' and resid 219 through 221 Processing sheet with id=AE2, first strand: chain 'UM' and resid 245 through 249 removed outlier: 3.547A pdb=" N LEUUM 249 " --> pdb=" O ILEUM 257 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILEUM 257 " --> pdb=" O LEUUM 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYSUM 279 " --> pdb=" O LEUUM 269 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'UM' and resid 292 through 295 removed outlier: 4.084A pdb=" N GLYUM 292 " --> pdb=" O VALUM 305 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SERUM 331 " --> pdb=" O LEUUM 313 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASNUM 315 " --> pdb=" O VALUM 329 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VALUM 329 " --> pdb=" O ASNUM 315 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'UM' and resid 340 through 345 removed outlier: 6.573A pdb=" N ALAUM 356 " --> pdb=" O ALAUM 341 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N METUM 343 " --> pdb=" O ALAUM 354 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALAUM 354 " --> pdb=" O METUM 343 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGUM 363 " --> pdb=" O LEUUM 355 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'UM' and resid 391 through 396 removed outlier: 3.763A pdb=" N ILEUM 413 " --> pdb=" O THRUM 405 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALAUM 412 " --> pdb=" O TYRUM 430 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALAUM 428 " --> pdb=" O VALUM 414 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'UM' and resid 439 through 441 removed outlier: 3.835A pdb=" N ALAUM 439 " --> pdb=" O ALAUM 457 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALAUM 457 " --> pdb=" O ALAUM 439 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'UM' and resid 494 through 499 removed outlier: 6.736A pdb=" N ALAUM 509 " --> pdb=" O ASNUM 495 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEUUM 497 " --> pdb=" O ALAUM 507 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALAUM 507 " --> pdb=" O LEUUM 497 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VALUM 499 " --> pdb=" O ILEUM 505 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILEUM 505 " --> pdb=" O VALUM 499 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHEUM 506 " --> pdb=" O TRPUM 518 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRPUM 518 " --> pdb=" O PHEUM 506 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYSUM 515 " --> pdb=" O LEUUM 529 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASNUM 519 " --> pdb=" O LEUUM 525 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEUUM 525 " --> pdb=" O ASNUM 519 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'UM' and resid 536 through 541 removed outlier: 3.611A pdb=" N ASPUM 538 " --> pdb=" O SERUM 551 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'UM' and resid 581 through 582 removed outlier: 7.147A pdb=" N ASPUM 603 " --> pdb=" O CYSUM 609 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYSUM 609 " --> pdb=" O ASPUM 603 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'UU' and resid 24 through 30 removed outlier: 5.685A pdb=" N THRUU 655 " --> pdb=" O PROUU 26 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARGUU 28 " --> pdb=" O ILEUU 653 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEUUU 640 " --> pdb=" O PHEUU 634 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHEUU 634 " --> pdb=" O LEUUU 640 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALAUU 642 " --> pdb=" O VALUU 632 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VALUU 632 " --> pdb=" O ALAUU 642 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THRUU 644 " --> pdb=" O THRUU 630 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'UU' and resid 40 through 44 removed outlier: 3.564A pdb=" N ALAUU 40 " --> pdb=" O VALUU 51 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHEUU 58 " --> pdb=" O VALUU 71 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VALUU 71 " --> pdb=" O PHEUU 58 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILEUU 60 " --> pdb=" O LEUUU 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'UU' and resid 82 through 86 removed outlier: 3.835A pdb=" N HISUU 108 " --> pdb=" O ILEUU 100 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYSUU 102 " --> pdb=" O GLUUU 106 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLUUU 106 " --> pdb=" O LYSUU 102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'UU' and resid 118 through 124 removed outlier: 4.092A pdb=" N SERUU 136 " --> pdb=" O THRUU 132 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THRUU 155 " --> pdb=" O ILEUU 139 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYSUU 141 " --> pdb=" O PHEUU 153 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHEUU 153 " --> pdb=" O LYSUU 141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'UU' and resid 167 through 171 removed outlier: 6.858A pdb=" N VALUU 188 " --> pdb=" O THRUU 201 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THRUU 201 " --> pdb=" O VALUU 188 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEUUU 190 " --> pdb=" O VALUU 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'UU' and resid 209 through 214 removed outlier: 6.595A pdb=" N GLYUU 224 " --> pdb=" O THRUU 210 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALAUU 212 " --> pdb=" O ALAUU 222 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALAUU 222 " --> pdb=" O ALAUU 212 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILEUU 220 " --> pdb=" O PROUU 214 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLUUU 229 " --> pdb=" O THRUU 225 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARGUU 242 " --> pdb=" O METUU 232 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASNUU 234 " --> pdb=" O ARGUU 240 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARGUU 240 " --> pdb=" O ASNUU 234 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'UU' and resid 251 through 256 removed outlier: 6.468A pdb=" N GLYUU 267 " --> pdb=" O SERUU 252 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEUUU 254 " --> pdb=" O SERUU 265 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SERUU 265 " --> pdb=" O LEUUU 254 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HISUU 285 " --> pdb=" O PHEUU 275 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASPUU 277 " --> pdb=" O ARGUU 283 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARGUU 283 " --> pdb=" O ASPUU 277 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'UU' and resid 300 through 303 removed outlier: 6.836A pdb=" N LEUUU 319 " --> pdb=" O SERUU 345 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SERUU 345 " --> pdb=" O LEUUU 319 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLUUU 321 " --> pdb=" O LEUUU 343 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'UU' and resid 353 through 358 removed outlier: 6.922A pdb=" N ALAUU 369 " --> pdb=" O SERUU 354 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILEUU 356 " --> pdb=" O LEUUU 367 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEUUU 367 " --> pdb=" O ILEUU 356 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'UU' and resid 414 through 419 removed outlier: 4.662A pdb=" N HISUU 434 " --> pdb=" O PHEUU 439 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHEUU 439 " --> pdb=" O HISUU 434 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALAUU 440 " --> pdb=" O TRPUU 453 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRPUU 453 " --> pdb=" O ALAUU 440 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THRUU 442 " --> pdb=" O GLYUU 451 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARGUU 449 " --> pdb=" O ASPUU 444 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'UU' and resid 463 through 468 removed outlier: 3.579A pdb=" N SERUU 465 " --> pdb=" O GLYUU 478 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALAUU 467 " --> pdb=" O PHEUU 476 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SERUU 483 " --> pdb=" O SERUU 479 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYSUU 496 " --> pdb=" O ILEUU 486 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASNUU 488 " --> pdb=" O LEUUU 494 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEUUU 494 " --> pdb=" O ASNUU 488 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSUU 499 " --> pdb=" O GLUDF 15 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUDF 15 " --> pdb=" O LYSUU 499 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'UU' and resid 505 through 510 removed outlier: 5.917A pdb=" N CYSUU 520 " --> pdb=" O THRUU 506 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILEUU 508 " --> pdb=" O VALUU 518 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VALUU 518 " --> pdb=" O ILEUU 508 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEUUU 510 " --> pdb=" O LYSUU 516 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYSUU 516 " --> pdb=" O LEUUU 510 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILEUU 525 " --> pdb=" O GLYUU 521 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASPUU 530 " --> pdb=" O LEUUU 536 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEUUU 536 " --> pdb=" O ASPUU 530 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'UU' and resid 546 through 552 removed outlier: 6.756A pdb=" N ALAUU 561 " --> pdb=" O THRUU 547 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N METUU 549 " --> pdb=" O ALAUU 559 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALAUU 559 " --> pdb=" O METUU 549 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYRUU 551 " --> pdb=" O LEUUU 557 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEUUU 557 " --> pdb=" O TYRUU 551 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASPUU 571 " --> pdb=" O VALUU 577 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VALUU 577 " --> pdb=" O ASPUU 571 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'UU' and resid 588 through 593 removed outlier: 3.530A pdb=" N ALAUU 590 " --> pdb=" O ALAUU 603 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THRUU 608 " --> pdb=" O SERUU 604 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASPUU 621 " --> pdb=" O THRUU 611 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASPUU 613 " --> pdb=" O CYSUU 619 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYSUU 619 " --> pdb=" O ASPUU 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'UV' and resid 141 through 144 removed outlier: 5.691A pdb=" N PHEUV 176 " --> pdb=" O GLUUV 143 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'UV' and resid 182 through 186 Processing sheet with id=AG8, first strand: chain 'UV' and resid 456 through 458 removed outlier: 6.824A pdb=" N LEUUV 440 " --> pdb=" O PHEUV 468 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'UV' and resid 578 through 586 removed outlier: 6.564A pdb=" N ILEUV 618 " --> pdb=" O LYSUV 579 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILEUV 581 " --> pdb=" O LYSUV 616 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYSUV 616 " --> pdb=" O ILEUV 581 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILEUV 583 " --> pdb=" O ARGUV 614 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARGUV 614 " --> pdb=" O ILEUV 583 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N METUV 585 " --> pdb=" O PHEUV 612 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHEUV 612 " --> pdb=" O METUV 585 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'UV' and resid 629 through 633 removed outlier: 4.939A pdb=" N HISUV 665 " --> pdb=" O GLYUV 631 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALAUV 633 " --> pdb=" O ILEUV 663 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILEUV 663 " --> pdb=" O ALAUV 633 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THRUV 664 " --> pdb=" O ARGUV 656 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGUV 656 " --> pdb=" O THRUV 664 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'UV' and resid 750 through 755 removed outlier: 6.357A pdb=" N GLNUV 780 " --> pdb=" O LYSUV 851 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ARGUV 853 " --> pdb=" O GLNUV 780 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VALUV 782 " --> pdb=" O ARGUV 853 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEUUV 855 " --> pdb=" O VALUV 782 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEUUV 784 " --> pdb=" O LEUUV 855 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VALUV 854 " --> pdb=" O VALUV 838 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VALUV 838 " --> pdb=" O VALUV 854 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'UV' and resid 975 through 976 removed outlier: 6.750A pdb=" N LEUUV 975 " --> pdb=" O ALAUV1042 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'UV' and resid 1161 through 1164 removed outlier: 6.389A pdb=" N ARGUV1103 " --> pdb=" O VALUV1231 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VALUV1231 " --> pdb=" O ARGUV1103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'UV' and resid 1193 through 1195 Processing sheet with id=AH6, first strand: chain 'CI' and resid 141 through 142 removed outlier: 3.732A pdb=" N ASNCI 141 " --> pdb=" O VALCI 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'CJ' and resid 114 through 117 removed outlier: 6.208A pdb=" N ILECJ 89 " --> pdb=" O VALCJ 140 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEUCJ 142 " --> pdb=" O ILECJ 89 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THRCJ 91 " --> pdb=" O LEUCJ 142 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N GLUCJ 144 " --> pdb=" O THRCJ 91 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEUCJ 139 " --> pdb=" O ILECJ 154 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILECJ 154 " --> pdb=" O LEUCJ 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VALCJ 141 " --> pdb=" O LEUCJ 152 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEUCJ 152 " --> pdb=" O VALCJ 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HISCJ 143 " --> pdb=" O THRCJ 150 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THRCJ 162 " --> pdb=" O LEUCJ 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEUCJ 261 " --> pdb=" O THRCJ 162 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLNCJ 164 " --> pdb=" O PHECJ 259 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'CJ' and resid 188 through 192 removed outlier: 6.532A pdb=" N HISCJ 188 " --> pdb=" O ILECJ 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHECJ 224 " --> pdb=" O HISCJ 188 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILECJ 190 " --> pdb=" O PHECJ 224 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VALCJ 233 " --> pdb=" O PROCJ 252 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLNCJ 235 " --> pdb=" O VALCJ 250 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'CK' and resid 506 through 508 Processing sheet with id=AI1, first strand: chain 'CL' and resid 166 through 167 removed outlier: 6.112A pdb=" N ILECL 71 " --> pdb=" O LEUCL 137 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEUCL 139 " --> pdb=" O ILECL 71 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALACL 73 " --> pdb=" O LEUCL 139 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'CL' and resid 170 through 171 Processing sheet with id=AI3, first strand: chain 'CL' and resid 294 through 297 removed outlier: 3.564A pdb=" N GLYCL 294 " --> pdb=" O ILECL 290 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N METCL 244 " --> pdb=" O METCL 812 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYRCL 243 " --> pdb=" O HISCL 276 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEUCL 245 " --> pdb=" O TYRCL 274 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYRCL 274 " --> pdb=" O LEUCL 245 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYRCL 272 " --> pdb=" O ASPCL 247 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHECL 249 " --> pdb=" O ALACL 270 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALACL 270 " --> pdb=" O PHECL 249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLNCL 300 " --> pdb=" O VALCL 792 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'CL' and resid 870 through 871 removed outlier: 4.026A pdb=" N ASNCL 882 " --> pdb=" O THRCL 861 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYSCL 826 " --> pdb=" O GLUCL 920 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THRCL 916 " --> pdb=" O ARGCL 830 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'CL' and resid 845 through 849 Processing sheet with id=AI6, first strand: chain 'CL' and resid 928 through 941 removed outlier: 6.985A pdb=" N PHECL 947 " --> pdb=" O TYRCL 939 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYRCL 987 " --> pdb=" O ILECL 948 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARGCL 988 " --> pdb=" O LYSCL 977 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLNCL 965 " --> pdb=" O ARGCL1004 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARGCL1004 " --> pdb=" O GLNCL 965 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILECL 928 " --> pdb=" O VALCL1009 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'CM' and resid 9 through 12 removed outlier: 6.321A pdb=" N THRCM 9 " --> pdb=" O LYSCM 32 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLUCM 34 " --> pdb=" O THRCM 9 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHECM 11 " --> pdb=" O GLUCM 34 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'CM' and resid 60 through 61 removed outlier: 3.574A pdb=" N ILECM 80 " --> pdb=" O ASNCM 61 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'CM' and resid 85 through 89 removed outlier: 6.627A pdb=" N HISCM 167 " --> pdb=" O THRCM 153 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N THRCM 153 " --> pdb=" O HISCM 167 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VALCM 169 " --> pdb=" O LEUCM 151 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEUCM 151 " --> pdb=" O VALCM 169 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'CM' and resid 181 through 182 removed outlier: 7.588A pdb=" N GLUCM 182 " --> pdb=" O ARGCM 312 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASNCM 314 " --> pdb=" O GLUCM 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILECM 354 " --> pdb=" O GLYCM 309 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'CM' and resid 222 through 230 removed outlier: 6.392A pdb=" N ILECM 191 " --> pdb=" O ASNCM 224 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THRCM 226 " --> pdb=" O ILECM 191 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLYCM 193 " --> pdb=" O THRCM 226 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASPCM 228 " --> pdb=" O GLYCM 193 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALACM 195 " --> pdb=" O ASPCM 228 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRPCM 230 " --> pdb=" O ALACM 195 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SERCM 197 " --> pdb=" O TRPCM 230 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'CN' and resid 38 through 41 Processing sheet with id=AJ4, first strand: chain 'JD' and resid 480 through 481 removed outlier: 3.545A pdb=" N ASPJD 480 " --> pdb=" O ILEJD 477 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLYJD 474 " --> pdb=" O PHEJD 491 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THRJD 493 " --> pdb=" O GLYJD 474 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLNJD 476 " --> pdb=" O THRJD 493 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N METJD 444 " --> pdb=" O SERJD 512 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILEJD 514 " --> pdb=" O METJD 444 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLYJD 446 " --> pdb=" O ILEJD 514 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILEJD 513 " --> pdb=" O ILEJD 556 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N METJD 558 " --> pdb=" O ILEJD 513 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILEJD 515 " --> pdb=" O METJD 558 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEUJD 581 " --> pdb=" O VALJD 409 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILEJD 411 " --> pdb=" O LEUJD 581 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VALJD 583 " --> pdb=" O ILEJD 411 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYSJD 413 " --> pdb=" O VALJD 583 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'JD' and resid 542 through 543 removed outlier: 3.522A pdb=" N ASNJD 546 " --> pdb=" O HISJD 543 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'JD' and resid 590 through 593 removed outlier: 6.513A pdb=" N SERJD 591 " --> pdb=" O CYSJD 821 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARGJD 823 " --> pdb=" O SERJD 591 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HISJD 593 " --> pdb=" O ARGJD 823 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARGJD 774 " --> pdb=" O HISJD 820 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYRJD 822 " --> pdb=" O ARGJD 774 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VALJD 776 " --> pdb=" O TYRJD 822 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALAJD 621 " --> pdb=" O TYRJD 775 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VALJD 777 " --> pdb=" O ALAJD 621 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEUJD 623 " --> pdb=" O VALJD 777 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYRJD 730 " --> pdb=" O CYSJD 757 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VALJD 759 " --> pdb=" O TYRJD 730 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEUJD 732 " --> pdb=" O VALJD 759 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'JD' and resid 781 through 787 Processing sheet with id=AJ8, first strand: chain 'JD' and resid 1157 through 1160 removed outlier: 3.938A pdb=" N GLYJD1160 " --> pdb=" O LYSJD1164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSJD1164 " --> pdb=" O GLYJD1160 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHEJD1132 " --> pdb=" O THRJD1165 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N METJD1167 " --> pdb=" O PHEJD1132 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYRJD1134 " --> pdb=" O METJD1167 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILEJD1118 " --> pdb=" O VALJD1133 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VALJD1092 " --> pdb=" O LEUJD1121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYRJD1151 " --> pdb=" O ILEJD1173 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'JD' and resid 1188 through 1189 Processing sheet with id=AK1, first strand: chain 'JD' and resid 1208 through 1213 removed outlier: 3.671A pdb=" N ARGJD1209 " --> pdb=" O GLNJD1238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLNJD1238 " --> pdb=" O ARGJD1209 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALJD1236 " --> pdb=" O CYSJD1211 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALAJD1235 " --> pdb=" O PHEJD1250 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHEJD1250 " --> pdb=" O ALAJD1235 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N HISJD1237 " --> pdb=" O ILEJD1248 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'JF' and resid 149 through 151 removed outlier: 6.567A pdb=" N ILEJF 150 " --> pdb=" O LEUJF 159 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEUJF 121 " --> pdb=" O ILEJF 163 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VALJF 112 " --> pdb=" O VALJF 124 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N METJF 41 " --> pdb=" O GLNJF 111 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYRJF 113 " --> pdb=" O METJF 41 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VALJF 43 " --> pdb=" O TYRJF 113 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLNJF 115 " --> pdb=" O VALJF 43 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEUJF 45 " --> pdb=" O GLNJF 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUJF 180 " --> pdb=" O PHEJF 205 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLYJF 207 " --> pdb=" O LEUJF 180 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLUJF 223 " --> pdb=" O CYSJF 175 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYSJF 177 " --> pdb=" O GLUJF 223 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VALJF 225 " --> pdb=" O LYSJF 177 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THRJF 179 " --> pdb=" O VALJF 225 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'JF' and resid 52 through 54 Processing sheet with id=AK4, first strand: chain 'JG' and resid 149 through 151 removed outlier: 6.308A pdb=" N ILEJG 150 " --> pdb=" O LEUJG 159 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VALJG 112 " --> pdb=" O VALJG 124 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N METJG 41 " --> pdb=" O GLNJG 111 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYRJG 113 " --> pdb=" O METJG 41 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VALJG 43 " --> pdb=" O TYRJG 113 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLNJG 115 " --> pdb=" O VALJG 43 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEUJG 45 " --> pdb=" O GLNJG 115 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILEJG 42 " --> pdb=" O VALJG 204 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VALJG 206 " --> pdb=" O ILEJG 42 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VALJG 44 " --> pdb=" O VALJG 206 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'JG' and resid 52 through 54 Processing sheet with id=AK6, first strand: chain 'JL' and resid 107 through 111 removed outlier: 6.323A pdb=" N VALJL 60 " --> pdb=" O VALJL 82 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VALJL 84 " --> pdb=" O VALJL 60 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLUJL 62 " --> pdb=" O VALJL 84 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYSJL 125 " --> pdb=" O ILEJL 152 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N METJL 154 " --> pdb=" O CYSJL 125 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SERJL 127 " --> pdb=" O METJL 154 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N GLNJL 156 " --> pdb=" O SERJL 127 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N METJL 189 " --> pdb=" O VALJL 206 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARGJL 208 " --> pdb=" O HISJL 187 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N HISJL 187 " --> pdb=" O ARGJL 208 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLUJL 210 " --> pdb=" O VALJL 185 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VALJL 185 " --> pdb=" O GLUJL 210 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'JJ' and resid 96 through 100 Processing sheet with id=AK8, first strand: chain 'JJ' and resid 180 through 186 Processing sheet with id=AK9, first strand: chain 'DF' and resid 41 through 42 Processing sheet with id=AL1, first strand: chain 'DF' and resid 146 through 148 Processing sheet with id=AL2, first strand: chain 'DQ' and resid 6 through 10 removed outlier: 3.716A pdb=" N THRDQ 70 " --> pdb=" O THRDQ 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARGDQ 68 " --> pdb=" O VALDQ 19 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'DS' and resid 15 through 17 Processing sheet with id=AL4, first strand: chain 'DT' and resid 83 through 84 removed outlier: 3.708A pdb=" N LYSDT 92 " --> pdb=" O LYSDT 84 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'DT' and resid 114 through 115 Processing sheet with id=AL6, first strand: chain 'Dc' and resid 39 through 44 removed outlier: 3.566A pdb=" N ILEDc 40 " --> pdb=" O VALDc 30 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLNDc 27 " --> pdb=" O VALDc 15 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VALDc 15 " --> pdb=" O GLNDc 27 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARGDc 29 " --> pdb=" O ILEDc 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THRDc 8 " --> pdb=" O LEUDc 56 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'DA' and resid 29 through 33 removed outlier: 3.943A pdb=" N GLYDA 44 " --> pdb=" O ILEDA 32 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'DA' and resid 65 through 69 removed outlier: 3.653A pdb=" N GLYDA 102 " --> pdb=" O LYSDA 85 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARGDA 87 " --> pdb=" O PHEDA 100 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N PHEDA 100 " --> pdb=" O ARGDA 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASPDA 89 " --> pdb=" O THRDA 98 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THRDA 98 " --> pdb=" O ASPDA 89 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VALDA 91 " --> pdb=" O LEUDA 96 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEUDA 96 " --> pdb=" O VALDA 91 " (cutoff:3.500A) removed outlier: 14.160A pdb=" N ASNDA 99 " --> pdb=" O LYSDA 219 " (cutoff:3.500A) removed outlier: 13.475A pdb=" N LYSDA 219 " --> pdb=" O ASNDA 99 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N HISDA 101 " --> pdb=" O LEUDA 217 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEUDA 217 " --> pdb=" O HISDA 101 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEUDA 217 " --> pdb=" O ARGDA 136 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARGDA 136 " --> pdb=" O LEUDA 217 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'DA' and resid 120 through 122 removed outlier: 6.445A pdb=" N ILEDA 140 " --> pdb=" O ILEDA 210 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'DE' and resid 41 through 43 Processing sheet with id=AM2, first strand: chain 'DE' and resid 70 through 72 Processing sheet with id=AM3, first strand: chain 'DE' and resid 102 through 103 removed outlier: 4.676A pdb=" N VALDE 102 " --> pdb=" O ALADE 110 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'DE' and resid 146 through 148 removed outlier: 6.707A pdb=" N TYRDE 138 " --> pdb=" O VALDE 129 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VALDE 129 " --> pdb=" O TYRDE 138 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VALDE 140 " --> pdb=" O LYSDE 127 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASPDE 171 " --> pdb=" O LYSDE 161 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'DE' and resid 181 through 183 Processing sheet with id=AM6, first strand: chain 'DE' and resid 197 through 199 Processing sheet with id=AM7, first strand: chain 'DG' and resid 12 through 17 removed outlier: 6.617A pdb=" N LYSDG 2 " --> pdb=" O LEUDG 109 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEUDG 111 " --> pdb=" O LYSDG 2 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASNDG 4 " --> pdb=" O LEUDG 111 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILEDG 113 " --> pdb=" O ASNDG 4 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SERDG 6 " --> pdb=" O ILEDG 113 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LYSDG 115 " --> pdb=" O SERDG 6 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEUDG 106 " --> pdb=" O ASPDG 57 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASPDG 57 " --> pdb=" O LEUDG 106 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VALDG 108 " --> pdb=" O GLYDG 55 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLYDG 55 " --> pdb=" O VALDG 108 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALADG 110 " --> pdb=" O SERDG 53 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VALDG 49 " --> pdb=" O VALDG 114 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'DG' and resid 72 through 77 removed outlier: 3.513A pdb=" N LYSDG 93 " --> pdb=" O LEUDG 77 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'DG' and resid 160 through 163 Processing sheet with id=AN1, first strand: chain 'DH' and resid 45 through 50 removed outlier: 3.880A pdb=" N SERDH 45 " --> pdb=" O PHEDH 61 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'DH' and resid 181 through 184 removed outlier: 6.109A pdb=" N ILEDH 149 " --> pdb=" O VALDH 140 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VALDH 140 " --> pdb=" O ILEDH 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYSDH 151 " --> pdb=" O LYSDH 138 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYSDH 138 " --> pdb=" O LYSDH 151 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEUDH 153 " --> pdb=" O VALDH 136 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHEDW 50 " --> pdb=" O TYRDH 142 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'DI' and resid 3 through 4 removed outlier: 3.914A pdb=" N ILEDI 3 " --> pdb=" O GLYDI 30 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'DI' and resid 43 through 47 Processing sheet with id=AN5, first strand: chain 'DI' and resid 72 through 77 removed outlier: 3.740A pdb=" N ILEDI 72 " --> pdb=" O TRPDI 67 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N GLYDI 181 " --> pdb=" O THRDI 62 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASNDI 64 " --> pdb=" O GLYDI 181 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILEDI 183 " --> pdb=" O ASNDI 64 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SERDI 66 " --> pdb=" O ILEDI 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYRDI 83 " --> pdb=" O ILEDI 101 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLNDI 103 " --> pdb=" O VALDI 81 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VALDI 81 " --> pdb=" O GLNDI 103 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'DL' and resid 70 through 77 removed outlier: 18.412A pdb=" N ILEDL 70 " --> pdb=" O LEUDL 91 " (cutoff:3.500A) removed outlier: 15.765A pdb=" N LEUDL 91 " --> pdb=" O ILEDL 70 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THRDL 72 " --> pdb=" O ALADL 89 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALADL 89 " --> pdb=" O THRDL 72 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VALDL 85 " --> pdb=" O VALDL 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGDL 99 " --> pdb=" O ILEDL 94 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHEDL 137 " --> pdb=" O PRODL 108 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VALDL 139 " --> pdb=" O GLYDL 126 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLYDL 126 " --> pdb=" O VALDL 139 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'DO' and resid 38 through 39 removed outlier: 3.910A pdb=" N VALDO 30 " --> pdb=" O ILEDO 39 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLYDO 15 " --> pdb=" O HISDO 80 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'DO' and resid 19 through 22 removed outlier: 4.118A pdb=" N ASPDO 25 " --> pdb=" O SERDO 22 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'DO' and resid 82 through 83 Processing sheet with id=AO1, first strand: chain 'DW' and resid 71 through 74 removed outlier: 7.128A pdb=" N ILEDW 103 " --> pdb=" O LEUDW 126 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHEDW 128 " --> pdb=" O TYRDW 101 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYRDW 101 " --> pdb=" O PHEDW 128 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'DX' and resid 130 through 131 removed outlier: 5.961A pdb=" N VALDX 124 " --> pdb=" O ALADX 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALADX 105 " --> pdb=" O VALDX 124 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYSDX 126 " --> pdb=" O LEUDX 103 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VALDX 53 " --> pdb=" O GLNDX 75 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLNDX 75 " --> pdb=" O VALDX 53 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLUDX 55 " --> pdb=" O ARGDX 73 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHEDX 122 " --> pdb=" O THRDX 84 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'DY' and resid 7 through 15 removed outlier: 4.903A pdb=" N VALDY 12 " --> pdb=" O GLNDY 22 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLNDY 22 " --> pdb=" O VALDY 12 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SERDY 14 " --> pdb=" O ARGDY 20 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ARGDY 20 " --> pdb=" O SERDY 14 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYSDY 68 " --> pdb=" O THRDY 62 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THRDY 62 " --> pdb=" O LYSDY 68 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VALDY 70 " --> pdb=" O PHEDY 60 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'Db' and resid 44 through 47 removed outlier: 3.524A pdb=" N LYSDb 36 " --> pdb=" O SERDb 78 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SERDb 78 " --> pdb=" O LYSDb 36 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'Db' and resid 64 through 65 3705 hydrogen bonds defined for protein. 10518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 771 hydrogen bonds 1256 hydrogen bond angles 0 basepair planarities 323 basepair parallelities 698 stacking parallelities Total time for adding SS restraints: 77.01 Time building geometry restraints manager: 38.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.28: 13342 1.28 - 1.38: 20665 1.38 - 1.48: 22351 1.48 - 1.57: 33903 1.57 - 1.67: 2869 Bond restraints: 93130 Sorted by residual: bond pdb=" C ILEJL 188 " pdb=" N METJL 189 " ideal model delta sigma weight residual 1.331 1.537 -0.205 1.37e-02 5.33e+03 2.25e+02 bond pdb=" C VALCL 56 " pdb=" N PROCL 57 " ideal model delta sigma weight residual 1.332 1.497 -0.165 1.30e-02 5.92e+03 1.61e+02 bond pdb=" C LYSJD 996 " pdb=" N LEUJD 997 " ideal model delta sigma weight residual 1.331 1.219 0.111 1.37e-02 5.33e+03 6.57e+01 bond pdb=" N ALAJD 540 " pdb=" CA ALAJD 540 " ideal model delta sigma weight residual 1.461 1.363 0.098 1.51e-02 4.39e+03 4.21e+01 bond pdb=" C1' AD4 19 " pdb=" N9 AD4 19 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.71e+01 ... (remaining 93125 not shown) Histogram of bond angle deviations from ideal: 77.04 - 92.46: 10 92.46 - 107.87: 14106 107.87 - 123.29: 109298 123.29 - 138.71: 11850 138.71 - 154.13: 2 Bond angle restraints: 135266 Sorted by residual: angle pdb=" C4' UD3 15 " pdb=" C3' UD3 15 " pdb=" O3' UD3 15 " ideal model delta sigma weight residual 113.00 154.13 -41.13 1.50e+00 4.44e-01 7.52e+02 angle pdb=" C3' CD3 897 " pdb=" O3' CD3 897 " pdb=" P AD3 898 " ideal model delta sigma weight residual 120.20 87.27 32.93 1.50e+00 4.44e-01 4.82e+02 angle pdb=" O3' UD3 15 " pdb=" C3' UD3 15 " pdb=" C2' UD3 15 " ideal model delta sigma weight residual 113.70 86.41 27.29 1.50e+00 4.44e-01 3.31e+02 angle pdb=" C VALCL 56 " pdb=" N PROCL 57 " pdb=" CA PROCL 57 " ideal model delta sigma weight residual 119.76 138.38 -18.62 1.03e+00 9.43e-01 3.27e+02 angle pdb=" O3' CD3 897 " pdb=" P AD3 898 " pdb=" O5' AD3 898 " ideal model delta sigma weight residual 104.00 77.04 26.96 1.50e+00 4.44e-01 3.23e+02 ... (remaining 135261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 52607 35.95 - 71.89: 3419 71.89 - 107.84: 388 107.84 - 143.78: 44 143.78 - 179.73: 43 Dihedral angle restraints: 56501 sinusoidal: 22250 harmonic: 34251 Sorted by residual: dihedral pdb=" CA METCL 772 " pdb=" C METCL 772 " pdb=" N THRCL 773 " pdb=" CA THRCL 773 " ideal model delta harmonic sigma weight residual -180.00 -112.71 -67.29 0 5.00e+00 4.00e-02 1.81e+02 dihedral pdb=" CA ILEDZ 41 " pdb=" C ILEDZ 41 " pdb=" N LEUDZ 42 " pdb=" CA LEUDZ 42 " ideal model delta harmonic sigma weight residual -180.00 -123.76 -56.24 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" C5' AD31781 " pdb=" C4' AD31781 " pdb=" C3' AD31781 " pdb=" O3' AD31781 " ideal model delta sinusoidal sigma weight residual 147.00 78.32 68.68 1 8.00e+00 1.56e-02 9.55e+01 ... (remaining 56498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 18259 0.248 - 0.496: 191 0.496 - 0.744: 12 0.744 - 0.992: 1 0.992 - 1.240: 1 Chirality restraints: 18464 Sorted by residual: chirality pdb=" C3' UD3 15 " pdb=" C4' UD3 15 " pdb=" O3' UD3 15 " pdb=" C2' UD3 15 " both_signs ideal model delta sigma weight residual False -2.48 -1.24 -1.24 2.00e-01 2.50e+01 3.84e+01 chirality pdb=" C2' UD3 1 " pdb=" C3' UD3 1 " pdb=" O2' UD3 1 " pdb=" C1' UD3 1 " both_signs ideal model delta sigma weight residual False -2.52 -1.74 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" C2' CD3 25 " pdb=" C3' CD3 25 " pdb=" O2' CD3 25 " pdb=" C1' CD3 25 " both_signs ideal model delta sigma weight residual False -2.52 -1.81 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 18461 not shown) Planarity restraints: 13240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GD31111 " -0.207 2.00e-02 2.50e+03 7.85e-02 1.85e+02 pdb=" N9 GD31111 " 0.093 2.00e-02 2.50e+03 pdb=" C8 GD31111 " 0.070 2.00e-02 2.50e+03 pdb=" N7 GD31111 " 0.025 2.00e-02 2.50e+03 pdb=" C5 GD31111 " 0.021 2.00e-02 2.50e+03 pdb=" C6 GD31111 " -0.035 2.00e-02 2.50e+03 pdb=" O6 GD31111 " -0.083 2.00e-02 2.50e+03 pdb=" N1 GD31111 " -0.030 2.00e-02 2.50e+03 pdb=" C2 GD31111 " 0.014 2.00e-02 2.50e+03 pdb=" N2 GD31111 " 0.015 2.00e-02 2.50e+03 pdb=" N3 GD31111 " 0.059 2.00e-02 2.50e+03 pdb=" C4 GD31111 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AD31124 " -0.179 2.00e-02 2.50e+03 7.10e-02 1.39e+02 pdb=" N9 AD31124 " 0.080 2.00e-02 2.50e+03 pdb=" C8 AD31124 " 0.054 2.00e-02 2.50e+03 pdb=" N7 AD31124 " 0.015 2.00e-02 2.50e+03 pdb=" C5 AD31124 " 0.013 2.00e-02 2.50e+03 pdb=" C6 AD31124 " -0.028 2.00e-02 2.50e+03 pdb=" N6 AD31124 " -0.070 2.00e-02 2.50e+03 pdb=" N1 AD31124 " -0.024 2.00e-02 2.50e+03 pdb=" C2 AD31124 " 0.021 2.00e-02 2.50e+03 pdb=" N3 AD31124 " 0.063 2.00e-02 2.50e+03 pdb=" C4 AD31124 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UD3 15 " -0.151 2.00e-02 2.50e+03 6.83e-02 1.05e+02 pdb=" N1 UD3 15 " 0.076 2.00e-02 2.50e+03 pdb=" C2 UD3 15 " 0.036 2.00e-02 2.50e+03 pdb=" O2 UD3 15 " 0.042 2.00e-02 2.50e+03 pdb=" N3 UD3 15 " -0.013 2.00e-02 2.50e+03 pdb=" C4 UD3 15 " -0.021 2.00e-02 2.50e+03 pdb=" O4 UD3 15 " -0.066 2.00e-02 2.50e+03 pdb=" C5 UD3 15 " 0.027 2.00e-02 2.50e+03 pdb=" C6 UD3 15 " 0.069 2.00e-02 2.50e+03 ... (remaining 13237 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 58 1.69 - 2.49: 692 2.49 - 3.29: 97962 3.29 - 4.10: 223300 4.10 - 4.90: 333102 Warning: very small nonbonded interaction distances. Nonbonded interactions: 655114 Sorted by model distance: nonbonded pdb=" N VALDT 73 " pdb=" OP1 GD31499 " model vdw 0.887 2.520 nonbonded pdb=" N VALDT 73 " pdb=" P GD31499 " model vdw 0.901 3.480 nonbonded pdb=" C ALAUA 134 " pdb=" O4 UD2 297 " model vdw 0.995 3.270 nonbonded pdb=" CB ALAUA 692 " pdb=" O TYRUA 704 " model vdw 1.064 3.460 nonbonded pdb=" O ILECL 838 " pdb=" O2' UD3 578 " model vdw 1.072 2.440 ... (remaining 655109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'JF' selection = (chain 'JG' and (resid 29 through 55 or resid 63 through 251)) } 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: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 25.210 Check model and map are aligned: 0.950 Set scattering table: 0.600 Process input model: 259.450 Find NCS groups from input model: 3.800 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 298.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.205 93130 Z= 0.619 Angle : 1.419 41.125 135266 Z= 0.932 Chirality : 0.078 1.240 18464 Planarity : 0.006 0.079 13240 Dihedral : 22.516 179.730 34043 Min Nonbonded Distance : 0.887 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 1.50 % Allowed : 6.19 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.07), residues: 11702 helix: -1.86 (0.07), residues: 3937 sheet: -1.21 (0.11), residues: 2140 loop : -2.14 (0.07), residues: 5625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.755 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6751 time to fit residues: 265.6795 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1111 optimal weight: 1.9990 chunk 997 optimal weight: 10.0000 chunk 553 optimal weight: 30.0000 chunk 340 optimal weight: 50.0000 chunk 672 optimal weight: 9.9990 chunk 532 optimal weight: 20.0000 chunk 1031 optimal weight: 8.9990 chunk 399 optimal weight: 3.9990 chunk 627 optimal weight: 10.0000 chunk 767 optimal weight: 6.9990 chunk 1195 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.5242 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 93130 Z= 0.333 Angle : 0.921 17.679 135266 Z= 0.488 Chirality : 0.050 0.390 18464 Planarity : 0.005 0.046 13240 Dihedral : 21.734 179.308 34043 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.91 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.07), residues: 11702 helix: -0.19 (0.08), residues: 4079 sheet: -0.85 (0.11), residues: 2198 loop : -1.73 (0.08), residues: 5425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.873 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7572 time to fit residues: 298.4289 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 6.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 664 optimal weight: 20.0000 chunk 370 optimal weight: 50.0000 chunk 994 optimal weight: 4.9990 chunk 813 optimal weight: 10.0000 chunk 329 optimal weight: 40.0000 chunk 1197 optimal weight: 7.9990 chunk 1293 optimal weight: 10.0000 chunk 1066 optimal weight: 20.0000 chunk 1187 optimal weight: 5.9990 chunk 408 optimal weight: 0.9990 chunk 960 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.5433 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 93130 Z= 0.258 Angle : 0.762 11.188 135266 Z= 0.406 Chirality : 0.046 0.360 18464 Planarity : 0.004 0.038 13240 Dihedral : 21.689 179.826 34043 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.85 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.79 (0.08), residues: 11702 helix: 1.03 (0.08), residues: 4118 sheet: -0.78 (0.11), residues: 2144 loop : -1.66 (0.08), residues: 5440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 6.433 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7298 time to fit residues: 287.4604 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 7.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1182 optimal weight: 0.0470 chunk 900 optimal weight: 0.0010 chunk 621 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 571 optimal weight: 6.9990 chunk 803 optimal weight: 50.0000 chunk 1201 optimal weight: 20.0000 chunk 1272 optimal weight: 20.0000 chunk 627 optimal weight: 0.8980 chunk 1138 optimal weight: 20.0000 chunk 342 optimal weight: 30.0000 overall best weight: 1.7486 ------------------------------------------------------------------------------- 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: 0.5386 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 93130 Z= 0.115 Angle : 0.528 11.741 135266 Z= 0.289 Chirality : 0.040 0.305 18464 Planarity : 0.002 0.023 13240 Dihedral : 21.206 178.662 34043 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.75 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.03 (0.08), residues: 11702 helix: 1.99 (0.08), residues: 4104 sheet: -0.53 (0.11), residues: 2180 loop : -1.42 (0.08), residues: 5418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6933 time to fit residues: 273.2937 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1059 optimal weight: 20.0000 chunk 722 optimal weight: 0.8980 chunk 18 optimal weight: 30.0000 chunk 947 optimal weight: 30.0000 chunk 524 optimal weight: 20.0000 chunk 1085 optimal weight: 9.9990 chunk 879 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 649 optimal weight: 8.9990 chunk 1141 optimal weight: 20.0000 chunk 320 optimal weight: 50.0000 overall best weight: 11.9792 ------------------------------------------------------------------------------- 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: 0.5673 moved from start: 0.8802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.177 93130 Z= 0.552 Angle : 1.121 18.644 135266 Z= 0.585 Chirality : 0.059 0.576 18464 Planarity : 0.005 0.042 13240 Dihedral : 22.589 179.477 34043 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 32.11 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.02 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.22 % Twisted General : 0.08 % 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: -1.89 (0.07), residues: 11702 helix: 0.07 (0.08), residues: 4041 sheet: -1.20 (0.11), residues: 1939 loop : -2.30 (0.08), residues: 5722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.855 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7166 time to fit residues: 284.3191 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 427 optimal weight: 50.0000 chunk 1145 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 746 optimal weight: 20.0000 chunk 314 optimal weight: 50.0000 chunk 1273 optimal weight: 30.0000 chunk 1056 optimal weight: 0.9990 chunk 589 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 421 optimal weight: 50.0000 chunk 668 optimal weight: 50.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- 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: 0.5684 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 93130 Z= 0.398 Angle : 0.884 16.686 135266 Z= 0.472 Chirality : 0.052 0.618 18464 Planarity : 0.004 0.032 13240 Dihedral : 22.515 178.894 34043 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.82 % Favored : 88.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % 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: -1.87 (0.08), residues: 11702 helix: 0.36 (0.08), residues: 4051 sheet: -1.23 (0.12), residues: 1925 loop : -2.50 (0.08), residues: 5726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.827 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7041 time to fit residues: 276.9966 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1227 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 725 optimal weight: 50.0000 chunk 929 optimal weight: 40.0000 chunk 720 optimal weight: 50.0000 chunk 1071 optimal weight: 20.0000 chunk 711 optimal weight: 30.0000 chunk 1268 optimal weight: 20.0000 chunk 793 optimal weight: 100.0000 chunk 773 optimal weight: 0.9980 chunk 585 optimal weight: 9.9990 overall best weight: 10.1994 ------------------------------------------------------------------------------- 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: 0.5756 moved from start: 1.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 93130 Z= 0.465 Angle : 0.993 14.073 135266 Z= 0.527 Chirality : 0.054 0.577 18464 Planarity : 0.005 0.032 13240 Dihedral : 22.942 179.662 34043 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.27 % Favored : 86.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.22 % 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: -2.32 (0.08), residues: 11702 helix: 0.10 (0.08), residues: 4048 sheet: -1.64 (0.12), residues: 1830 loop : -2.79 (0.07), residues: 5824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.763 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6920 time to fit residues: 271.9601 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 784 optimal weight: 30.0000 chunk 506 optimal weight: 40.0000 chunk 757 optimal weight: 7.9990 chunk 382 optimal weight: 30.0000 chunk 249 optimal weight: 30.0000 chunk 245 optimal weight: 50.0000 chunk 806 optimal weight: 20.0000 chunk 864 optimal weight: 30.0000 chunk 627 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 997 optimal weight: 8.9990 overall best weight: 12.1994 ------------------------------------------------------------------------------- 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: 0.5790 moved from start: 1.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 93130 Z= 0.497 Angle : 1.005 15.073 135266 Z= 0.536 Chirality : 0.056 0.629 18464 Planarity : 0.005 0.041 13240 Dihedral : 23.321 179.976 34043 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 30.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.79 % Favored : 84.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.43 % Twisted General : 0.09 % 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: -2.66 (0.07), residues: 11702 helix: -0.14 (0.08), residues: 4005 sheet: -1.80 (0.12), residues: 1703 loop : -3.02 (0.07), residues: 5994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.782 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7057 time to fit residues: 278.5068 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1153 optimal weight: 50.0000 chunk 1215 optimal weight: 5.9990 chunk 1108 optimal weight: 9.9990 chunk 1181 optimal weight: 6.9990 chunk 1214 optimal weight: 6.9990 chunk 711 optimal weight: 0.0670 chunk 514 optimal weight: 40.0000 chunk 928 optimal weight: 50.0000 chunk 362 optimal weight: 30.0000 chunk 1068 optimal weight: 7.9990 chunk 1117 optimal weight: 9.9990 overall best weight: 5.6126 ------------------------------------------------------------------------------- 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: 0.5732 moved from start: 1.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 93130 Z= 0.253 Angle : 0.723 10.306 135266 Z= 0.390 Chirality : 0.046 0.424 18464 Planarity : 0.003 0.028 13240 Dihedral : 22.684 179.035 34043 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.31 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.22 % 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: -2.07 (0.08), residues: 11702 helix: 0.63 (0.08), residues: 4050 sheet: -1.85 (0.12), residues: 1774 loop : -2.79 (0.08), residues: 5878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.724 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.6904 time to fit residues: 272.9205 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 1177 optimal weight: 30.0000 chunk 776 optimal weight: 50.0000 chunk 1249 optimal weight: 20.0000 chunk 762 optimal weight: 0.0070 chunk 592 optimal weight: 10.0000 chunk 868 optimal weight: 30.0000 chunk 1311 optimal weight: 20.0000 chunk 1206 optimal weight: 30.0000 chunk 1044 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 806 optimal weight: 40.0000 overall best weight: 12.0014 ------------------------------------------------------------------------------- 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: 0.5815 moved from start: 1.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.145 93130 Z= 0.507 Angle : 1.014 14.249 135266 Z= 0.537 Chirality : 0.055 0.452 18464 Planarity : 0.005 0.033 13240 Dihedral : 23.344 179.224 34043 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 17.13 % Favored : 82.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.22 % Twisted General : 0.06 % 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: -2.74 (0.08), residues: 11702 helix: -0.05 (0.08), residues: 4008 sheet: -2.05 (0.12), residues: 1715 loop : -3.12 (0.07), residues: 5979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23404 Ramachandran restraints generated. 11702 Oldfield, 0 Emsley, 11702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 7.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.7559 time to fit residues: 295.6256 Evaluate side-chains 202 residues out of total 10480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1316 random chunks: chunk 640 optimal weight: 20.0000 chunk 829 optimal weight: 10.0000 chunk 1112 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 962 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 290 optimal weight: 50.0000 chunk 1045 optimal weight: 10.0000 chunk 437 optimal weight: 2.9990 chunk 1073 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.117033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093236 restraints weight = 616489.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091228 restraints weight = 1013053.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090825 restraints weight = 789457.751| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 1.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 93130 Z= 0.274 Angle : 0.728 10.789 135266 Z= 0.393 Chirality : 0.047 0.421 18464 Planarity : 0.003 0.028 13240 Dihedral : 22.799 179.549 34043 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.25 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.06 % Twisted Proline : 0.22 % 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: -2.18 (0.08), residues: 11702 helix: 0.62 (0.08), residues: 4039 sheet: -1.95 (0.12), residues: 1686 loop : -2.90 (0.07), residues: 5977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRPUA 122 PHE 0.000 0.000 PHEUA 5 TYR 0.000 0.000 TYRUA 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9981.58 seconds wall clock time: 179 minutes 6.47 seconds (10746.47 seconds total)