Starting phenix.real_space_refine on Tue Aug 26 18:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.map" model { file = "/net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rtd_19488/08_2025/8rtd_19488.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.027 sd= 0.091 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: 3 Type Number sf(0) Gaussians C 23570 2.51 5 N 8254 2.21 5 O 8254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40078 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 969 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 2, 'TRANS': 194} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 13, 'PHE:plan': 2, 'GLN:plan1': 21, 'ARG:plan': 21, 'GLU:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 364 Chain: "D" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 183 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 34} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'TYR:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 969 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 2, 'TRANS': 194} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 13, 'PHE:plan': 2, 'GLN:plan1': 21, 'ARG:plan': 21, 'GLU:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 364 Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 138 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 969 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 2, 'TRANS': 194} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 13, 'PHE:plan': 2, 'GLN:plan1': 21, 'ARG:plan': 21, 'GLU:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 364 Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 64 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 969 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 2, 'TRANS': 194} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 13, 'PHE:plan': 2, 'GLN:plan1': 21, 'ARG:plan': 21, 'GLU:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 364 Chain: "a" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 242 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 969 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 2, 'TRANS': 194} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 13, 'PHE:plan': 2, 'GLN:plan1': 21, 'ARG:plan': 21, 'GLU:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 364 Chain: "L" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1311 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 718 Unresolved non-hydrogen angles: 941 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'PHE:plan': 18, 'GLU:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 9, 'GLN:plan1': 12, 'TYR:plan': 7, 'ARG:plan': 7, 'TRP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 349 Chain: "M" Number of atoms: 1330 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1330 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 724 Unresolved non-hydrogen angles: 949 Unresolved non-hydrogen dihedrals: 587 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'PHE:plan': 18, 'GLU:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 7, 'ARG:plan': 7, 'TRP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 353 Chain: "j" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 515 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 6, 'ARG:plan': 7, 'TRP:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 212 Chain: "H" Number of atoms: 1087 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 222, 1087 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 772 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 6, 'ARG:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 299 Chain: "O" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 3947 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 692} Link IDs: {'PTRANS': 37, 'TRANS': 761} Chain breaks: 2 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2625 Unresolved non-hydrogen angles: 3369 Unresolved non-hydrogen dihedrals: 2215 Unresolved non-hydrogen chiralities: 213 Planarities with less than four sites: {'GLU:plan': 58, 'ARG:plan': 49, 'GLN:plan1': 33, 'PHE:plan': 47, 'TYR:plan': 27, 'HIS:plan': 19, 'ASP:plan': 51, 'ASN:plan1': 30, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 1526 Chain: "I" Number of atoms: 1062 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 217, 1062 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 584 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'PHE:plan': 16, 'GLU:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 6, 'ARG:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 299 Chain: "P" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 3754 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 658} Link IDs: {'PTRANS': 35, 'TRANS': 724} Chain breaks: 5 Unresolved chain link angles: 35 Unresolved non-hydrogen bonds: 2516 Unresolved non-hydrogen angles: 3235 Unresolved non-hydrogen dihedrals: 2126 Unresolved non-hydrogen chiralities: 203 Planarities with less than four sites: {'GLN:plan1': 33, 'PHE:plan': 45, 'TYR:plan': 27, 'HIS:plan': 19, 'ASP:plan': 48, 'ASN:plan1': 30, 'GLU:plan': 54, 'TRP:plan': 12, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1474 Chain: "J" Number of atoms: 1330 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1330 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 724 Unresolved non-hydrogen angles: 949 Unresolved non-hydrogen dihedrals: 587 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'PHE:plan': 18, 'GLU:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 9, 'GLN:plan1': 13, 'TYR:plan': 7, 'ARG:plan': 7, 'TRP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 353 Chain: "Q" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 855 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 120, 'truncation_to_alanine': 56} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 741 Unresolved non-hydrogen angles: 1047 Unresolved non-hydrogen dihedrals: 509 Unresolved non-hydrogen chiralities: 178 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 12, 'GLU:plan': 6, 'ARG:plan': 16, 'ASP:plan': 11, 'PHE:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 12, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 408 Chain: "R" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 515 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 6, 'ARG:plan': 7, 'TRP:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 212 Chain: "S" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 973 Classifications: {'peptide': 223} Incomplete info: {'backbone_only': 125, 'truncation_to_alanine': 73} Link IDs: {'PTRANS': 11, 'TRANS': 211} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 816 Unresolved non-hydrogen angles: 1146 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 14, 'GLU:plan': 11, 'TYR:plan': 13, 'ARG:plan': 17, 'ASP:plan': 11, 'PHE:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 445 Chain: "T" Number of atoms: 3992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 3992 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 700} Link IDs: {'PTRANS': 37, 'TRANS': 770} Chain breaks: 1 Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2652 Unresolved non-hydrogen angles: 3403 Unresolved non-hydrogen dihedrals: 2235 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLU:plan': 61, 'ARG:plan': 49, 'GLN:plan1': 33, 'PHE:plan': 47, 'TYR:plan': 27, 'HIS:plan': 19, 'ASP:plan': 54, 'ASN:plan1': 30, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 1547 Chain: "U" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 839 Classifications: {'peptide': 193} Incomplete info: {'backbone_only': 112, 'truncation_to_alanine': 59} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 723 Unresolved non-hydrogen angles: 1017 Unresolved non-hydrogen dihedrals: 504 Unresolved non-hydrogen chiralities: 169 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 12, 'TYR:plan': 12, 'ARG:plan': 16, 'ASP:plan': 10, 'PHE:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 392 Chain: "V" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 3512 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 615} Link IDs: {'PTRANS': 32, 'TRANS': 678} Chain breaks: 9 Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 2371 Unresolved non-hydrogen angles: 3050 Unresolved non-hydrogen dihedrals: 2012 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'GLN:plan1': 31, 'PHE:plan': 44, 'TYR:plan': 27, 'HIS:plan': 17, 'ASP:plan': 41, 'ASN:plan1': 27, 'GLU:plan': 51, 'TRP:plan': 12, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1393 Chain: "X" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 297 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "Y" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 814 Classifications: {'peptide': 188} Incomplete info: {'backbone_only': 112, 'truncation_to_alanine': 57} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 717 Unresolved non-hydrogen angles: 1015 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 171 Planarities with less than four sites: {'TYR:plan': 13, 'GLU:plan': 10, 'ARG:plan': 15, 'ASP:plan': 9, 'PHE:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 3, 'GLN:plan1': 11} Unresolved non-hydrogen planarities: 411 Chain: "Z" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 306 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'TYR:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "b" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 912 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 123, 'truncation_to_alanine': 66} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1107 Unresolved non-hydrogen dihedrals: 544 Unresolved non-hydrogen chiralities: 186 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 11, 'TYR:plan': 13, 'ARG:plan': 17, 'ASP:plan': 11, 'PHE:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 427 Chain: "c" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 287 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'TRANS': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "d" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 184 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "e" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 193 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 38} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "f" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 475 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 7, 'TRANS': 88} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 6, 'ARG:plan': 7, 'TRP:plan': 9, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 195 Chain: "g" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 3719 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 654} Link IDs: {'PTRANS': 36, 'TRANS': 716} Chain breaks: 5 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2488 Unresolved non-hydrogen angles: 3198 Unresolved non-hydrogen dihedrals: 2103 Unresolved non-hydrogen chiralities: 203 Planarities with less than four sites: {'GLU:plan': 56, 'ARG:plan': 44, 'GLN:plan1': 32, 'PHE:plan': 44, 'TYR:plan': 27, 'HIS:plan': 18, 'ASP:plan': 46, 'ASN:plan1': 28, 'TRP:plan': 12} Unresolved non-hydrogen planarities: 1445 Chain: "h" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 2259 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 397} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 7 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1502 Unresolved non-hydrogen angles: 1938 Unresolved non-hydrogen dihedrals: 1270 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 21, 'PHE:plan': 25, 'TYR:plan': 18, 'HIS:plan': 15, 'ASP:plan': 23, 'ASN:plan1': 19, 'GLU:plan': 29, 'TRP:plan': 7, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 875 Chain: "i" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 138 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 12.03, per 1000 atoms: 0.30 Number of scatterers: 40078 At special positions: 0 Unit cell: (195.261, 243.276, 321.167, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 8254 8.00 N 8254 7.00 C 23570 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 - 3.00 Amino acid : True - 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: 4.37 Conformation dependent library (CDL) restraints added in 2.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14124 Finding SS restraints... Secondary structure from input PDB file: 325 helices and 67 sheets defined 58.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 33 through 65 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.505A pdb=" N GLU A 81 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.748A pdb=" N SER A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.784A pdb=" N GLY A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 163 Processing helix chain 'A' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 41 removed outlier: 3.643A pdb=" N TYR D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 65 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU B 81 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 83 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.746A pdb=" N SER B 93 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.782A pdb=" N GLY B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 165 removed outlier: 3.512A pdb=" N SER B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 23 through 43 Processing helix chain 'C' and resid 34 through 65 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.746A pdb=" N SER C 93 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 4.016A pdb=" N GLY C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 163 removed outlier: 3.601A pdb=" N SER C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'K' and resid 34 through 65 Processing helix chain 'K' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU K 81 " --> pdb=" O GLN K 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 83 " --> pdb=" O ARG K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER K 93 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.533A pdb=" N GLY K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 164 removed outlier: 3.689A pdb=" N SER K 163 " --> pdb=" O MET K 159 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 69 Processing helix chain 'E' and resid 34 through 65 Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.506A pdb=" N GLU E 81 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 83 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER E 93 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.501A pdb=" N GLY E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 163 removed outlier: 3.716A pdb=" N SER E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 22 Processing helix chain 'L' and resid 22 through 53 Proline residue: L 34 - end of helix Processing helix chain 'L' and resid 61 through 80 Processing helix chain 'L' and resid 82 through 101 removed outlier: 3.733A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Proline residue: L 95 - end of helix removed outlier: 3.948A pdb=" N SER L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 137 removed outlier: 4.043A pdb=" N VAL L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 185 Proline residue: L 181 - end of helix Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'L' and resid 189 through 191 No H-bonds generated for 'chain 'L' and resid 189 through 191' Processing helix chain 'L' and resid 192 through 231 removed outlier: 3.806A pdb=" N PHE L 196 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 271 removed outlier: 3.582A pdb=" N LEU L 260 " --> pdb=" O LEU L 256 " (cutoff:3.500A) Proline residue: L 261 - end of helix Processing helix chain 'M' and resid 5 through 20 Processing helix chain 'M' and resid 20 through 53 removed outlier: 3.513A pdb=" N SER M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Proline residue: M 34 - end of helix Processing helix chain 'M' and resid 61 through 79 Processing helix chain 'M' and resid 82 through 101 removed outlier: 3.794A pdb=" N GLU M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) Proline residue: M 95 - end of helix removed outlier: 4.084A pdb=" N SER M 100 " --> pdb=" O ASP M 96 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 101 " --> pdb=" O GLU M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 137 removed outlier: 3.598A pdb=" N LEU M 115 " --> pdb=" O SER M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 185 Proline residue: M 181 - end of helix Processing helix chain 'M' and resid 186 through 188 No H-bonds generated for 'chain 'M' and resid 186 through 188' Processing helix chain 'M' and resid 192 through 231 removed outlier: 3.793A pdb=" N PHE M 196 " --> pdb=" O ATHR M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 271 removed outlier: 3.589A pdb=" N LEU M 260 " --> pdb=" O LEU M 256 " (cutoff:3.500A) Proline residue: M 261 - end of helix Processing helix chain 'j' and resid 28 through 45 Processing helix chain 'j' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP j 50 " --> pdb=" O ILE j 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA j 51 " --> pdb=" O TRP j 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 47 through 51' Processing helix chain 'j' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU j 56 " --> pdb=" O LEU j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE j 73 " --> pdb=" O LYS j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 91 removed outlier: 4.071A pdb=" N TRP j 90 " --> pdb=" O ASN j 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 31 removed outlier: 4.556A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 101 removed outlier: 4.138A pdb=" N VAL H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Proline residue: H 95 - end of helix removed outlier: 4.029A pdb=" N SER H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 137 Processing helix chain 'H' and resid 141 through 185 Proline residue: H 181 - end of helix Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 192 through 231 removed outlier: 3.810A pdb=" N PHE H 196 " --> pdb=" O ATHR H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 271 Proline residue: H 261 - end of helix Processing helix chain 'O' and resid 4 through 12 removed outlier: 3.792A pdb=" N SER O 12 " --> pdb=" O LYS O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 20 Processing helix chain 'O' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY O 70 " --> pdb=" O ASN O 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE O 71 " --> pdb=" O THR O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 110 Processing helix chain 'O' and resid 132 through 140 removed outlier: 3.821A pdb=" N PHE O 138 " --> pdb=" O VAL O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 171 Processing helix chain 'O' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY O 175 " --> pdb=" O LYS O 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 172 through 175' Processing helix chain 'O' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU O 194 " --> pdb=" O SER O 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 218 removed outlier: 3.946A pdb=" N TYR O 217 " --> pdb=" O ARG O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 266 removed outlier: 4.300A pdb=" N VAL O 262 " --> pdb=" O GLN O 259 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU O 263 " --> pdb=" O LEU O 260 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU O 265 " --> pdb=" O VAL O 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER O 266 " --> pdb=" O LEU O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 297 Processing helix chain 'O' and resid 305 through 318 removed outlier: 4.066A pdb=" N ILE O 309 " --> pdb=" O GLN O 305 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL O 354 " --> pdb=" O ALA O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 370 Processing helix chain 'O' and resid 387 through 395 Processing helix chain 'O' and resid 456 through 468 Processing helix chain 'O' and resid 469 through 472 Processing helix chain 'O' and resid 484 through 491 Processing helix chain 'O' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN O 510 " --> pdb=" O ASN O 507 " (cutoff:3.500A) Processing helix chain 'O' and resid 514 through 529 Processing helix chain 'O' and resid 536 through 551 Processing helix chain 'O' and resid 556 through 560 Processing helix chain 'O' and resid 561 through 566 Processing helix chain 'O' and resid 584 through 588 Processing helix chain 'O' and resid 589 through 591 No H-bonds generated for 'chain 'O' and resid 589 through 591' Processing helix chain 'O' and resid 596 through 601 removed outlier: 4.381A pdb=" N PHE O 600 " --> pdb=" O TYR O 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP O 601 " --> pdb=" O GLY O 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 596 through 601' Processing helix chain 'O' and resid 620 through 625 removed outlier: 3.534A pdb=" N LEU O 623 " --> pdb=" O THR O 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 624 " --> pdb=" O GLU O 621 " (cutoff:3.500A) Processing helix chain 'O' and resid 628 through 642 removed outlier: 3.607A pdb=" N SER O 642 " --> pdb=" O TYR O 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 661 Processing helix chain 'O' and resid 665 through 677 Processing helix chain 'O' and resid 678 through 680 No H-bonds generated for 'chain 'O' and resid 678 through 680' Processing helix chain 'O' and resid 689 through 695 removed outlier: 3.520A pdb=" N ALA O 693 " --> pdb=" O GLU O 689 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU O 695 " --> pdb=" O SER O 691 " (cutoff:3.500A) Processing helix chain 'O' and resid 696 through 705 removed outlier: 3.833A pdb=" N LYS O 700 " --> pdb=" O SER O 696 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR O 701 " --> pdb=" O ASN O 697 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O 702 " --> pdb=" O ILE O 698 " (cutoff:3.500A) Processing helix chain 'O' and resid 718 through 725 removed outlier: 3.636A pdb=" N TYR O 722 " --> pdb=" O ASP O 718 " (cutoff:3.500A) Processing helix chain 'O' and resid 729 through 738 Processing helix chain 'O' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL O 783 " --> pdb=" O ASP O 779 " (cutoff:3.500A) Processing helix chain 'O' and resid 787 through 801 removed outlier: 3.782A pdb=" N SER O 796 " --> pdb=" O GLU O 792 " (cutoff:3.500A) Processing helix chain 'O' and resid 804 through 820 Proline residue: O 810 - end of helix Processing helix chain 'I' and resid 5 through 27 removed outlier: 3.806A pdb=" N THR I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 101 Proline residue: I 95 - end of helix removed outlier: 3.936A pdb=" N SER I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 137 Processing helix chain 'I' and resid 141 through 186 Proline residue: I 181 - end of helix Processing helix chain 'I' and resid 187 through 191 removed outlier: 5.275A pdb=" N GLN I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Proline residue: I 191 - end of helix No H-bonds generated for 'chain 'I' and resid 187 through 191' Processing helix chain 'I' and resid 192 through 230 removed outlier: 3.949A pdb=" N PHE I 196 " --> pdb=" O ATHR I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 271 Proline residue: I 261 - end of helix Processing helix chain 'P' and resid 53 through 71 removed outlier: 3.927A pdb=" N VAL P 57 " --> pdb=" O SER P 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE P 58 " --> pdb=" O GLU P 54 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 71 " --> pdb=" O THR P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 110 Processing helix chain 'P' and resid 148 through 171 Processing helix chain 'P' and resid 191 through 202 removed outlier: 4.061A pdb=" N PHE P 195 " --> pdb=" O ALA P 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU P 196 " --> pdb=" O PRO P 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL P 200 " --> pdb=" O LEU P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR P 217 " --> pdb=" O ARG P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 265 Processing helix chain 'P' and resid 280 through 297 Processing helix chain 'P' and resid 305 through 320 removed outlier: 3.858A pdb=" N ASN P 314 " --> pdb=" O ASP P 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE P 317 " --> pdb=" O LEU P 313 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER P 318 " --> pdb=" O ASN P 314 " (cutoff:3.500A) Processing helix chain 'P' and resid 336 through 353 Processing helix chain 'P' and resid 364 through 371 Processing helix chain 'P' and resid 387 through 395 Processing helix chain 'P' and resid 456 through 468 Processing helix chain 'P' and resid 469 through 472 Processing helix chain 'P' and resid 484 through 491 Processing helix chain 'P' and resid 507 through 511 Processing helix chain 'P' and resid 514 through 531 removed outlier: 3.672A pdb=" N ALA P 531 " --> pdb=" O LYS P 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 538 through 550 Processing helix chain 'P' and resid 561 through 566 Processing helix chain 'P' and resid 584 through 588 Processing helix chain 'P' and resid 589 through 591 No H-bonds generated for 'chain 'P' and resid 589 through 591' Processing helix chain 'P' and resid 596 through 601 removed outlier: 4.381A pdb=" N PHE P 600 " --> pdb=" O TYR P 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP P 601 " --> pdb=" O GLY P 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 596 through 601' Processing helix chain 'P' and resid 628 through 643 removed outlier: 3.584A pdb=" N MET P 643 " --> pdb=" O ARG P 639 " (cutoff:3.500A) Processing helix chain 'P' and resid 656 through 661 Processing helix chain 'P' and resid 662 through 677 removed outlier: 4.195A pdb=" N ASP P 667 " --> pdb=" O GLU P 663 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 668 " --> pdb=" O TYR P 664 " (cutoff:3.500A) Processing helix chain 'P' and resid 689 through 695 removed outlier: 3.803A pdb=" N ALA P 693 " --> pdb=" O GLU P 689 " (cutoff:3.500A) Processing helix chain 'P' and resid 696 through 705 removed outlier: 3.920A pdb=" N LYS P 700 " --> pdb=" O SER P 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR P 701 " --> pdb=" O ASN P 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN P 705 " --> pdb=" O THR P 701 " (cutoff:3.500A) Processing helix chain 'P' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR P 722 " --> pdb=" O ASP P 718 " (cutoff:3.500A) Processing helix chain 'P' and resid 729 through 739 removed outlier: 3.607A pdb=" N LEU P 739 " --> pdb=" O LEU P 735 " (cutoff:3.500A) Processing helix chain 'P' and resid 777 through 785 Processing helix chain 'P' and resid 787 through 802 Processing helix chain 'P' and resid 804 through 821 removed outlier: 4.283A pdb=" N TRP P 808 " --> pdb=" O ASP P 804 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU P 809 " --> pdb=" O PRO P 805 " (cutoff:3.500A) Proline residue: P 810 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 21 through 53 Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 61 through 80 Processing helix chain 'J' and resid 82 through 101 removed outlier: 4.036A pdb=" N GLU J 86 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Proline residue: J 95 - end of helix removed outlier: 3.991A pdb=" N SER J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 137 removed outlier: 3.957A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 186 Proline residue: J 181 - end of helix Processing helix chain 'J' and resid 192 through 230 removed outlier: 3.975A pdb=" N PHE J 196 " --> pdb=" O ATHR J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 271 Proline residue: J 261 - end of helix Processing helix chain 'Q' and resid 16 through 25 Processing helix chain 'Q' and resid 27 through 62 removed outlier: 3.823A pdb=" N SER Q 62 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 111 Processing helix chain 'Q' and resid 116 through 127 Processing helix chain 'Q' and resid 129 through 138 Processing helix chain 'Q' and resid 139 through 141 No H-bonds generated for 'chain 'Q' and resid 139 through 141' Processing helix chain 'Q' and resid 145 through 150 Processing helix chain 'Q' and resid 206 through 211 Processing helix chain 'R' and resid 28 through 45 Processing helix chain 'R' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP R 50 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA R 51 " --> pdb=" O TRP R 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 47 through 51' Processing helix chain 'R' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 91 removed outlier: 4.072A pdb=" N TRP R 90 " --> pdb=" O ASN R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 60 removed outlier: 3.644A pdb=" N TYR S 17 " --> pdb=" O GLN S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.845A pdb=" N ARG S 87 " --> pdb=" O THR S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 111 Processing helix chain 'S' and resid 116 through 127 Processing helix chain 'S' and resid 129 through 138 Processing helix chain 'S' and resid 139 through 141 No H-bonds generated for 'chain 'S' and resid 139 through 141' Processing helix chain 'S' and resid 145 through 150 Processing helix chain 'S' and resid 206 through 211 Processing helix chain 'T' and resid 4 through 12 removed outlier: 3.790A pdb=" N SER T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 20 Processing helix chain 'T' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE T 58 " --> pdb=" O GLU T 54 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY T 70 " --> pdb=" O ASN T 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE T 71 " --> pdb=" O THR T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 110 Processing helix chain 'T' and resid 132 through 140 removed outlier: 3.821A pdb=" N PHE T 138 " --> pdb=" O VAL T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 171 Processing helix chain 'T' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY T 175 " --> pdb=" O LYS T 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 172 through 175' Processing helix chain 'T' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU T 194 " --> pdb=" O SER T 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE T 195 " --> pdb=" O ALA T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 218 removed outlier: 3.946A pdb=" N TYR T 217 " --> pdb=" O ARG T 213 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 266 removed outlier: 4.301A pdb=" N VAL T 262 " --> pdb=" O GLN T 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU T 263 " --> pdb=" O LEU T 260 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU T 265 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER T 266 " --> pdb=" O LEU T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 280 through 297 Processing helix chain 'T' and resid 305 through 318 removed outlier: 4.066A pdb=" N ILE T 309 " --> pdb=" O GLN T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL T 354 " --> pdb=" O ALA T 350 " (cutoff:3.500A) Processing helix chain 'T' and resid 364 through 370 Processing helix chain 'T' and resid 387 through 395 Processing helix chain 'T' and resid 456 through 468 Processing helix chain 'T' and resid 469 through 472 Processing helix chain 'T' and resid 484 through 491 Processing helix chain 'T' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN T 510 " --> pdb=" O ASN T 507 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 529 Processing helix chain 'T' and resid 536 through 551 Processing helix chain 'T' and resid 556 through 560 Processing helix chain 'T' and resid 561 through 566 Processing helix chain 'T' and resid 584 through 588 Processing helix chain 'T' and resid 589 through 591 No H-bonds generated for 'chain 'T' and resid 589 through 591' Processing helix chain 'T' and resid 596 through 601 removed outlier: 4.381A pdb=" N PHE T 600 " --> pdb=" O TYR T 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP T 601 " --> pdb=" O GLY T 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 596 through 601' Processing helix chain 'T' and resid 620 through 625 removed outlier: 3.534A pdb=" N LEU T 623 " --> pdb=" O THR T 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP T 624 " --> pdb=" O GLU T 621 " (cutoff:3.500A) Processing helix chain 'T' and resid 628 through 642 removed outlier: 3.606A pdb=" N SER T 642 " --> pdb=" O TYR T 638 " (cutoff:3.500A) Processing helix chain 'T' and resid 656 through 661 Processing helix chain 'T' and resid 665 through 677 Processing helix chain 'T' and resid 678 through 680 No H-bonds generated for 'chain 'T' and resid 678 through 680' Processing helix chain 'T' and resid 689 through 695 removed outlier: 3.519A pdb=" N ALA T 693 " --> pdb=" O GLU T 689 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU T 695 " --> pdb=" O SER T 691 " (cutoff:3.500A) Processing helix chain 'T' and resid 696 through 705 removed outlier: 3.833A pdb=" N LYS T 700 " --> pdb=" O SER T 696 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR T 701 " --> pdb=" O ASN T 697 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU T 702 " --> pdb=" O ILE T 698 " (cutoff:3.500A) Processing helix chain 'T' and resid 718 through 725 removed outlier: 3.635A pdb=" N TYR T 722 " --> pdb=" O ASP T 718 " (cutoff:3.500A) Processing helix chain 'T' and resid 729 through 738 Processing helix chain 'T' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL T 783 " --> pdb=" O ASP T 779 " (cutoff:3.500A) Processing helix chain 'T' and resid 787 through 801 removed outlier: 3.782A pdb=" N SER T 796 " --> pdb=" O GLU T 792 " (cutoff:3.500A) Processing helix chain 'T' and resid 804 through 820 Proline residue: T 810 - end of helix Processing helix chain 'U' and resid 10 through 21 removed outlier: 3.807A pdb=" N LEU U 14 " --> pdb=" O LYS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 61 Processing helix chain 'U' and resid 97 through 111 Processing helix chain 'U' and resid 116 through 127 Processing helix chain 'U' and resid 129 through 138 Processing helix chain 'U' and resid 206 through 211 Processing helix chain 'V' and resid 53 through 71 removed outlier: 3.926A pdb=" N VAL V 57 " --> pdb=" O SER V 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE V 71 " --> pdb=" O THR V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 110 Processing helix chain 'V' and resid 151 through 171 Processing helix chain 'V' and resid 191 through 202 removed outlier: 4.062A pdb=" N PHE V 195 " --> pdb=" O ALA V 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU V 196 " --> pdb=" O PRO V 192 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL V 200 " --> pdb=" O LEU V 196 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR V 217 " --> pdb=" O ARG V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 265 Processing helix chain 'V' and resid 280 through 297 Processing helix chain 'V' and resid 305 through 320 removed outlier: 3.859A pdb=" N ASN V 314 " --> pdb=" O ASP V 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE V 317 " --> pdb=" O LEU V 313 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER V 318 " --> pdb=" O ASN V 314 " (cutoff:3.500A) Processing helix chain 'V' and resid 336 through 353 Processing helix chain 'V' and resid 364 through 371 Processing helix chain 'V' and resid 387 through 395 Processing helix chain 'V' and resid 456 through 468 Processing helix chain 'V' and resid 469 through 472 Processing helix chain 'V' and resid 484 through 491 Processing helix chain 'V' and resid 516 through 531 removed outlier: 3.672A pdb=" N ALA V 531 " --> pdb=" O LYS V 527 " (cutoff:3.500A) Processing helix chain 'V' and resid 538 through 550 Processing helix chain 'V' and resid 564 through 568 Processing helix chain 'V' and resid 584 through 588 Processing helix chain 'V' and resid 589 through 591 No H-bonds generated for 'chain 'V' and resid 589 through 591' Processing helix chain 'V' and resid 628 through 643 removed outlier: 3.584A pdb=" N MET V 643 " --> pdb=" O ARG V 639 " (cutoff:3.500A) Processing helix chain 'V' and resid 656 through 661 Processing helix chain 'V' and resid 662 through 677 removed outlier: 4.195A pdb=" N ASP V 667 " --> pdb=" O GLU V 663 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU V 668 " --> pdb=" O TYR V 664 " (cutoff:3.500A) Processing helix chain 'V' and resid 689 through 695 removed outlier: 3.802A pdb=" N ALA V 693 " --> pdb=" O GLU V 689 " (cutoff:3.500A) Processing helix chain 'V' and resid 696 through 705 removed outlier: 3.921A pdb=" N LYS V 700 " --> pdb=" O SER V 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR V 701 " --> pdb=" O ASN V 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN V 705 " --> pdb=" O THR V 701 " (cutoff:3.500A) Processing helix chain 'V' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR V 722 " --> pdb=" O ASP V 718 " (cutoff:3.500A) Processing helix chain 'V' and resid 729 through 739 removed outlier: 3.607A pdb=" N LEU V 739 " --> pdb=" O LEU V 735 " (cutoff:3.500A) Processing helix chain 'V' and resid 777 through 785 Processing helix chain 'V' and resid 787 through 798 Processing helix chain 'V' and resid 808 through 821 Processing helix chain 'X' and resid 23 through 61 Processing helix chain 'Y' and resid 18 through 25 Processing helix chain 'Y' and resid 27 through 61 Processing helix chain 'Y' and resid 96 through 111 Processing helix chain 'Y' and resid 116 through 127 Processing helix chain 'Y' and resid 129 through 138 Processing helix chain 'Y' and resid 146 through 150 Processing helix chain 'Z' and resid 43 through 69 Processing helix chain 'b' and resid 13 through 59 removed outlier: 3.643A pdb=" N TYR b 17 " --> pdb=" O GLN b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 89 removed outlier: 3.846A pdb=" N ARG b 87 " --> pdb=" O THR b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 111 Processing helix chain 'b' and resid 116 through 127 Processing helix chain 'b' and resid 129 through 138 Processing helix chain 'b' and resid 139 through 141 No H-bonds generated for 'chain 'b' and resid 139 through 141' Processing helix chain 'b' and resid 145 through 150 Processing helix chain 'b' and resid 206 through 211 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 23 through 58 Processing helix chain 'd' and resid 29 through 60 Processing helix chain 'e' and resid 47 through 68 Processing helix chain 'f' and resid 28 through 45 Processing helix chain 'f' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP f 50 " --> pdb=" O ILE f 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA f 51 " --> pdb=" O TRP f 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 47 through 51' Processing helix chain 'f' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU f 56 " --> pdb=" O LEU f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE f 73 " --> pdb=" O LYS f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 86 through 91 removed outlier: 4.071A pdb=" N TRP f 90 " --> pdb=" O ASN f 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 6 through 12 removed outlier: 3.792A pdb=" N SER g 12 " --> pdb=" O LYS g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 20 Processing helix chain 'g' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE g 58 " --> pdb=" O GLU g 54 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY g 70 " --> pdb=" O ASN g 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE g 71 " --> pdb=" O THR g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 110 Processing helix chain 'g' and resid 147 through 171 Processing helix chain 'g' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY g 175 " --> pdb=" O LYS g 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 172 through 175' Processing helix chain 'g' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU g 194 " --> pdb=" O SER g 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE g 195 " --> pdb=" O ALA g 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 218 removed outlier: 3.945A pdb=" N TYR g 217 " --> pdb=" O ARG g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 258 through 266 removed outlier: 4.300A pdb=" N VAL g 262 " --> pdb=" O GLN g 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU g 263 " --> pdb=" O LEU g 260 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU g 265 " --> pdb=" O VAL g 262 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER g 266 " --> pdb=" O LEU g 263 " (cutoff:3.500A) Processing helix chain 'g' and resid 280 through 296 Processing helix chain 'g' and resid 307 through 318 Processing helix chain 'g' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL g 354 " --> pdb=" O ALA g 350 " (cutoff:3.500A) Processing helix chain 'g' and resid 364 through 370 Processing helix chain 'g' and resid 387 through 395 Processing helix chain 'g' and resid 456 through 468 Processing helix chain 'g' and resid 469 through 472 Processing helix chain 'g' and resid 484 through 491 Processing helix chain 'g' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN g 510 " --> pdb=" O ASN g 507 " (cutoff:3.500A) Processing helix chain 'g' and resid 514 through 529 Processing helix chain 'g' and resid 536 through 551 Processing helix chain 'g' and resid 556 through 560 Processing helix chain 'g' and resid 561 through 566 Processing helix chain 'g' and resid 584 through 588 Processing helix chain 'g' and resid 589 through 591 No H-bonds generated for 'chain 'g' and resid 589 through 591' Processing helix chain 'g' and resid 596 through 601 removed outlier: 4.381A pdb=" N PHE g 600 " --> pdb=" O TYR g 596 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP g 601 " --> pdb=" O GLY g 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 596 through 601' Processing helix chain 'g' and resid 620 through 625 removed outlier: 3.533A pdb=" N LEU g 623 " --> pdb=" O THR g 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP g 624 " --> pdb=" O GLU g 621 " (cutoff:3.500A) Processing helix chain 'g' and resid 628 through 642 removed outlier: 3.607A pdb=" N SER g 642 " --> pdb=" O TYR g 638 " (cutoff:3.500A) Processing helix chain 'g' and resid 656 through 661 Processing helix chain 'g' and resid 665 through 677 Processing helix chain 'g' and resid 678 through 680 No H-bonds generated for 'chain 'g' and resid 678 through 680' Processing helix chain 'g' and resid 689 through 695 removed outlier: 3.519A pdb=" N ALA g 693 " --> pdb=" O GLU g 689 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU g 695 " --> pdb=" O SER g 691 " (cutoff:3.500A) Processing helix chain 'g' and resid 696 through 705 removed outlier: 3.833A pdb=" N LYS g 700 " --> pdb=" O SER g 696 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR g 701 " --> pdb=" O ASN g 697 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU g 702 " --> pdb=" O ILE g 698 " (cutoff:3.500A) Processing helix chain 'g' and resid 718 through 725 removed outlier: 3.635A pdb=" N TYR g 722 " --> pdb=" O ASP g 718 " (cutoff:3.500A) Processing helix chain 'g' and resid 729 through 738 Processing helix chain 'g' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL g 783 " --> pdb=" O ASP g 779 " (cutoff:3.500A) Processing helix chain 'g' and resid 787 through 801 removed outlier: 3.781A pdb=" N SER g 796 " --> pdb=" O GLU g 792 " (cutoff:3.500A) Processing helix chain 'g' and resid 804 through 820 Proline residue: g 810 - end of helix Processing helix chain 'h' and resid 53 through 71 removed outlier: 3.926A pdb=" N VAL h 57 " --> pdb=" O SER h 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE h 58 " --> pdb=" O GLU h 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN h 59 " --> pdb=" O ALA h 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE h 71 " --> pdb=" O THR h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 110 Processing helix chain 'h' and resid 148 through 171 Processing helix chain 'h' and resid 191 through 202 removed outlier: 4.061A pdb=" N PHE h 195 " --> pdb=" O ALA h 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU h 196 " --> pdb=" O PRO h 192 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL h 200 " --> pdb=" O LEU h 196 " (cutoff:3.500A) Processing helix chain 'h' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR h 217 " --> pdb=" O ARG h 213 " (cutoff:3.500A) Processing helix chain 'h' and resid 260 through 265 Processing helix chain 'h' and resid 280 through 297 Processing helix chain 'h' and resid 305 through 320 removed outlier: 3.858A pdb=" N ASN h 314 " --> pdb=" O ASP h 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE h 317 " --> pdb=" O LEU h 313 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER h 318 " --> pdb=" O ASN h 314 " (cutoff:3.500A) Processing helix chain 'h' and resid 336 through 353 Processing helix chain 'h' and resid 364 through 371 Processing helix chain 'h' and resid 387 through 395 Processing helix chain 'h' and resid 456 through 468 Processing helix chain 'h' and resid 469 through 471 No H-bonds generated for 'chain 'h' and resid 469 through 471' Processing helix chain 'h' and resid 689 through 694 removed outlier: 3.801A pdb=" N ALA h 693 " --> pdb=" O GLU h 689 " (cutoff:3.500A) Processing helix chain 'h' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR h 722 " --> pdb=" O ASP h 718 " (cutoff:3.500A) Processing helix chain 'h' and resid 729 through 738 Processing helix chain 'i' and resid 16 through 25 Processing helix chain 'i' and resid 27 through 40 Processing sheet with id=AA1, first strand: chain 'j' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'j' and resid 93 through 94 removed outlier: 3.587A pdb=" N ARG O 222 " --> pdb=" O ARG O 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 25 through 27 removed outlier: 6.754A pdb=" N ILE O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 124 through 127 removed outlier: 3.534A pdb=" N SER O 40 " --> pdb=" O VAL O 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR O 38 " --> pdb=" O TYR O 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'O' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'O' and resid 242 through 245 Processing sheet with id=AA8, first strand: chain 'O' and resid 248 through 250 removed outlier: 3.524A pdb=" N ARG O 249 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU O 357 " --> pdb=" O ARG O 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS O 326 " --> pdb=" O ALA O 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 415 through 417 Processing sheet with id=AB2, first strand: chain 'O' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE O 475 " --> pdb=" O TYR O 615 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE O 617 " --> pdb=" O ILE O 475 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA O 477 " --> pdb=" O PHE O 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR O 474 " --> pdb=" O MET O 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL O 652 " --> pdb=" O THR O 474 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL O 476 " --> pdb=" O VAL O 652 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL O 684 " --> pdb=" O PHE O 649 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR O 651 " --> pdb=" O VAL O 684 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR O 447 " --> pdb=" O PHE O 685 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET O 448 " --> pdb=" O ILE O 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR O 709 " --> pdb=" O LYS O 749 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL O 768 " --> pdb=" O GLU O 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS P 24 " --> pdb=" O SER P 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE P 30 " --> pdb=" O VAL P 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR P 38 " --> pdb=" O TYR P 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU P 121 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR P 331 " --> pdb=" O VAL P 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'P' and resid 277 through 278 Processing sheet with id=AB8, first strand: chain 'P' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR P 415 " --> pdb=" O PHE P 427 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 684 through 687 removed outlier: 6.002A pdb=" N THR P 447 " --> pdb=" O PHE P 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR P 687 " --> pdb=" O THR P 447 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU P 449 " --> pdb=" O THR P 687 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET P 448 " --> pdb=" O ILE P 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 615 through 618 removed outlier: 6.269A pdb=" N ALA P 477 " --> pdb=" O PHE P 617 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL P 476 " --> pdb=" O VAL P 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 764 through 768 Processing sheet with id=AC3, first strand: chain 'Q' and resid 70 through 73 Processing sheet with id=AC4, first strand: chain 'Q' and resid 155 through 165 removed outlier: 5.394A pdb=" N ILE Q 156 " --> pdb=" O HIS Q 180 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS Q 180 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL Q 158 " --> pdb=" O GLN Q 178 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLN Q 178 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL Q 160 " --> pdb=" O THR Q 176 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR Q 176 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS Q 191 " --> pdb=" O PRO Q 226 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE Q 193 " --> pdb=" O ALA Q 224 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA Q 224 " --> pdb=" O ILE Q 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR Q 195 " --> pdb=" O TYR Q 222 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR Q 222 " --> pdb=" O THR Q 195 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY Q 197 " --> pdb=" O THR Q 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 22 through 23 Processing sheet with id=AC6, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.587A pdb=" N ARG T 222 " --> pdb=" O ARG T 235 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 154 through 165 removed outlier: 5.392A pdb=" N ILE S 156 " --> pdb=" O HIS S 180 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS S 180 " --> pdb=" O ILE S 156 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL S 158 " --> pdb=" O GLN S 178 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN S 178 " --> pdb=" O VAL S 158 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL S 160 " --> pdb=" O THR S 176 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR S 176 " --> pdb=" O VAL S 160 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR S 199 " --> pdb=" O VAL S 219 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL S 219 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 25 through 27 removed outlier: 6.753A pdb=" N ILE T 30 " --> pdb=" O VAL T 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 124 through 127 removed outlier: 3.534A pdb=" N SER T 40 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR T 38 " --> pdb=" O TYR T 127 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 85 through 86 Processing sheet with id=AD2, first strand: chain 'T' and resid 182 through 183 Processing sheet with id=AD3, first strand: chain 'T' and resid 242 through 245 Processing sheet with id=AD4, first strand: chain 'T' and resid 248 through 250 removed outlier: 3.523A pdb=" N ARG T 249 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU T 357 " --> pdb=" O ARG T 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'T' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS T 326 " --> pdb=" O ALA T 384 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 415 through 417 Processing sheet with id=AD7, first strand: chain 'T' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE T 475 " --> pdb=" O TYR T 615 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE T 617 " --> pdb=" O ILE T 475 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA T 477 " --> pdb=" O PHE T 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR T 474 " --> pdb=" O MET T 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL T 652 " --> pdb=" O THR T 474 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL T 476 " --> pdb=" O VAL T 652 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL T 684 " --> pdb=" O PHE T 649 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR T 651 " --> pdb=" O VAL T 684 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR T 447 " --> pdb=" O PHE T 685 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N MET T 448 " --> pdb=" O ILE T 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR T 709 " --> pdb=" O LYS T 749 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL T 768 " --> pdb=" O GLU T 771 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 80 through 81 removed outlier: 3.673A pdb=" N VAL X 73 " --> pdb=" O LEU U 71 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL U 73 " --> pdb=" O VAL X 73 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 155 through 165 removed outlier: 5.394A pdb=" N ILE U 156 " --> pdb=" O HIS U 180 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS U 180 " --> pdb=" O ILE U 156 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL U 158 " --> pdb=" O GLN U 178 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN U 178 " --> pdb=" O VAL U 158 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL U 160 " --> pdb=" O THR U 176 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR U 176 " --> pdb=" O VAL U 160 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR U 199 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL U 219 " --> pdb=" O THR U 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS V 24 " --> pdb=" O SER V 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE V 30 " --> pdb=" O VAL V 26 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR V 38 " --> pdb=" O TYR V 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU V 121 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR V 331 " --> pdb=" O VAL V 271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 183 through 184 Processing sheet with id=AE5, first strand: chain 'V' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR V 415 " --> pdb=" O PHE V 427 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 685 through 687 removed outlier: 6.305A pdb=" N LEU V 449 " --> pdb=" O THR V 687 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET V 448 " --> pdb=" O ILE V 710 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 616 through 618 removed outlier: 6.269A pdb=" N ALA V 477 " --> pdb=" O PHE V 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL V 476 " --> pdb=" O VAL V 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'V' and resid 764 through 765 Processing sheet with id=AE9, first strand: chain 'Y' and resid 70 through 73 Processing sheet with id=AF1, first strand: chain 'Y' and resid 154 through 165 removed outlier: 5.393A pdb=" N ILE Y 156 " --> pdb=" O HIS Y 180 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS Y 180 " --> pdb=" O ILE Y 156 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL Y 158 " --> pdb=" O GLN Y 178 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLN Y 178 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL Y 160 " --> pdb=" O THR Y 176 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR Y 176 " --> pdb=" O VAL Y 160 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS Y 191 " --> pdb=" O PRO Y 226 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE Y 193 " --> pdb=" O ALA Y 224 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA Y 224 " --> pdb=" O ILE Y 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR Y 195 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR Y 222 " --> pdb=" O THR Y 195 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY Y 197 " --> pdb=" O THR Y 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 155 through 165 removed outlier: 5.392A pdb=" N ILE b 156 " --> pdb=" O HIS b 180 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS b 180 " --> pdb=" O ILE b 156 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL b 158 " --> pdb=" O GLN b 178 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLN b 178 " --> pdb=" O VAL b 158 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL b 160 " --> pdb=" O THR b 176 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR b 176 " --> pdb=" O VAL b 160 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR b 199 " --> pdb=" O VAL b 219 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL b 219 " --> pdb=" O THR b 199 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 80 through 82 removed outlier: 3.674A pdb=" N VAL d 73 " --> pdb=" O LEU c 71 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL c 73 " --> pdb=" O VAL d 73 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 22 through 23 Processing sheet with id=AF5, first strand: chain 'f' and resid 93 through 94 removed outlier: 3.588A pdb=" N ARG g 222 " --> pdb=" O ARG g 235 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 25 through 27 removed outlier: 6.753A pdb=" N ILE g 30 " --> pdb=" O VAL g 26 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 124 through 127 removed outlier: 3.533A pdb=" N SER g 40 " --> pdb=" O VAL g 125 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR g 38 " --> pdb=" O TYR g 127 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 85 through 86 Processing sheet with id=AF9, first strand: chain 'g' and resid 182 through 183 Processing sheet with id=AG1, first strand: chain 'g' and resid 242 through 245 Processing sheet with id=AG2, first strand: chain 'g' and resid 248 through 250 removed outlier: 3.523A pdb=" N ARG g 249 " --> pdb=" O LEU g 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU g 357 " --> pdb=" O ARG g 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'g' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS g 326 " --> pdb=" O ALA g 384 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 415 through 417 Processing sheet with id=AG5, first strand: chain 'g' and resid 448 through 450 removed outlier: 6.127A pdb=" N MET g 448 " --> pdb=" O ILE g 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR g 709 " --> pdb=" O LYS g 749 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE g 475 " --> pdb=" O TYR g 615 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE g 617 " --> pdb=" O ILE g 475 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA g 477 " --> pdb=" O PHE g 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR g 474 " --> pdb=" O MET g 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL g 652 " --> pdb=" O THR g 474 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL g 476 " --> pdb=" O VAL g 652 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL g 684 " --> pdb=" O PHE g 649 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR g 651 " --> pdb=" O VAL g 684 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL g 768 " --> pdb=" O GLU g 771 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS h 24 " --> pdb=" O SER h 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE h 30 " --> pdb=" O VAL h 26 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'h' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR h 38 " --> pdb=" O TYR h 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU h 121 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR h 331 " --> pdb=" O VAL h 271 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 183 through 184 Processing sheet with id=AH2, first strand: chain 'h' and resid 277 through 278 Processing sheet with id=AH3, first strand: chain 'h' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR h 415 " --> pdb=" O PHE h 427 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 685 through 687 removed outlier: 6.002A pdb=" N THR h 447 " --> pdb=" O PHE h 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR h 687 " --> pdb=" O THR h 447 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU h 449 " --> pdb=" O THR h 687 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET h 448 " --> pdb=" O ILE h 710 " (cutoff:3.500A) 3679 hydrogen bonds defined for protein. 10626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.47 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 8286 1.28 - 1.35: 7991 1.35 - 1.42: 142 1.42 - 1.49: 8149 1.49 - 1.56: 15430 Bond restraints: 39998 Sorted by residual: bond pdb=" C LEU V 599 " pdb=" N PHE V 600 " ideal model delta sigma weight residual 1.329 1.478 -0.149 1.40e-02 5.10e+03 1.13e+02 bond pdb=" C LEU O 599 " pdb=" N PHE O 600 " ideal model delta sigma weight residual 1.333 1.477 -0.144 1.51e-02 4.39e+03 9.14e+01 bond pdb=" C LEU g 599 " pdb=" N PHE g 600 " ideal model delta sigma weight residual 1.333 1.477 -0.144 1.51e-02 4.39e+03 9.12e+01 bond pdb=" C LEU P 599 " pdb=" N PHE P 600 " ideal model delta sigma weight residual 1.333 1.477 -0.144 1.51e-02 4.39e+03 9.11e+01 bond pdb=" C LEU T 599 " pdb=" N PHE T 600 " ideal model delta sigma weight residual 1.333 1.477 -0.144 1.51e-02 4.39e+03 9.09e+01 ... (remaining 39993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.08: 55137 10.08 - 20.16: 2 20.16 - 30.24: 4 30.24 - 40.32: 7 40.32 - 50.40: 4 Bond angle restraints: 55154 Sorted by residual: angle pdb=" O MET P 759 " pdb=" C MET P 759 " pdb=" N ASN P 760 " ideal model delta sigma weight residual 123.04 72.64 50.40 1.17e+00 7.31e-01 1.86e+03 angle pdb=" O MET V 759 " pdb=" C MET V 759 " pdb=" N ASN V 760 " ideal model delta sigma weight residual 123.04 72.70 50.34 1.17e+00 7.31e-01 1.85e+03 angle pdb=" CA MET V 759 " pdb=" C MET V 759 " pdb=" N ASN V 760 " ideal model delta sigma weight residual 116.23 161.15 -44.92 1.30e+00 5.92e-01 1.19e+03 angle pdb=" CA MET P 759 " pdb=" C MET P 759 " pdb=" N ASN P 760 " ideal model delta sigma weight residual 116.23 161.14 -44.91 1.30e+00 5.92e-01 1.19e+03 angle pdb=" C MET V 759 " pdb=" N ASN V 760 " pdb=" CA ASN V 760 " ideal model delta sigma weight residual 122.95 154.11 -31.16 1.44e+00 4.82e-01 4.68e+02 ... (remaining 55149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.23: 21204 7.23 - 14.47: 974 14.47 - 21.70: 97 21.70 - 28.94: 18 28.94 - 36.17: 5 Dihedral angle restraints: 22298 sinusoidal: 0 harmonic: 22298 Sorted by residual: dihedral pdb=" CA GLY K 71 " pdb=" C GLY K 71 " pdb=" N ASP K 72 " pdb=" CA ASP K 72 " ideal model delta harmonic sigma weight residual -180.00 -143.83 -36.17 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA GLY C 71 " pdb=" C GLY C 71 " pdb=" N ASP C 72 " pdb=" CA ASP C 72 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA GLY E 71 " pdb=" C GLY E 71 " pdb=" N ASP E 72 " pdb=" CA ASP E 72 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.21e+01 ... (remaining 22295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 6143 0.074 - 0.147: 820 0.147 - 0.221: 85 0.221 - 0.295: 11 0.295 - 0.369: 3 Chirality restraints: 7062 Sorted by residual: chirality pdb=" CA ASP O 605 " pdb=" N ASP O 605 " pdb=" C ASP O 605 " pdb=" CB ASP O 605 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA LEU H 82 " pdb=" N LEU H 82 " pdb=" C LEU H 82 " pdb=" CB LEU H 82 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA LEU Q 69 " pdb=" N LEU Q 69 " pdb=" C LEU Q 69 " pdb=" CB LEU Q 69 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 7059 not shown) Planarity restraints: 8174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 498 " 0.116 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" C LEU P 498 " -0.365 2.00e-02 2.50e+03 pdb=" O LEU P 498 " 0.156 2.00e-02 2.50e+03 pdb=" N LYS P 499 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 498 " 0.116 2.00e-02 2.50e+03 2.12e-01 4.50e+02 pdb=" C LEU V 498 " -0.365 2.00e-02 2.50e+03 pdb=" O LEU V 498 " 0.156 2.00e-02 2.50e+03 pdb=" N LYS V 499 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Z 88 " -0.028 2.00e-02 2.50e+03 5.50e-02 3.03e+01 pdb=" C ILE Z 88 " 0.095 2.00e-02 2.50e+03 pdb=" O ILE Z 88 " -0.035 2.00e-02 2.50e+03 pdb=" N PRO Z 89 " -0.032 2.00e-02 2.50e+03 ... (remaining 8171 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 2 2.11 - 2.81: 12587 2.81 - 3.51: 57214 3.51 - 4.20: 68756 4.20 - 4.90: 122209 Nonbonded interactions: 260768 Sorted by model distance: nonbonded pdb=" CB THR a 46 " pdb=" CB PHE O 138 " model vdw 1.418 3.870 nonbonded pdb=" CA GLY a 43 " pdb=" CB LEU O 135 " model vdw 2.045 3.840 nonbonded pdb=" O SER O 821 " pdb=" CB ALA T 516 " model vdw 2.145 3.460 nonbonded pdb=" O LEU V 498 " pdb=" CB LYS V 499 " model vdw 2.154 3.440 nonbonded pdb=" O LEU P 498 " pdb=" CB LYS P 499 " model vdw 2.155 3.440 ... (remaining 260763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 16 through 40) selection = (chain 'i' and resid 16 through 40) } ncs_group { reference = (chain 'H' and (resid 2 through 27 or resid 83 through 273)) selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 2 through 106 or resid 111 through 273)) selection = chain 'L' selection = (chain 'M' and (resid 2 through 106 or resid 111 through 273)) } ncs_group { reference = (chain 'O' and (resid 15 through 127 or resid 150 through 296 or resid 306 throu \ gh 427 or resid 447 through 510 or resid 515 through 532 or resid 537 through 55 \ 0 or resid 562 through 600 or resid 615 through 766 or resid 772 through 798 or \ resid 805 through 820)) selection = (chain 'P' and (resid 15 through 127 or resid 150 through 296 or resid 306 throu \ gh 427 or resid 447 through 510 or resid 515 through 550 or resid 562 through 60 \ 0 or resid 615 through 766 or resid 772 through 798 or resid 805 through 820)) selection = (chain 'T' and (resid 15 through 127 or resid 150 through 296 or resid 306 throu \ gh 427 or resid 447 through 510 or resid 515 through 532 or resid 537 through 55 \ 0 or resid 562 through 600 or resid 615 through 766 or resid 772 through 798 or \ resid 805 through 820)) selection = (chain 'V' and (resid 15 through 127 or resid 150 through 296 or resid 306 throu \ gh 820)) selection = (chain 'g' and (resid 15 through 127 or resid 150 through 510 or resid 515 throu \ gh 532 or resid 537 through 550 or resid 562 through 600 or resid 615 through 76 \ 6 or resid 772 through 798 or resid 805 through 820)) } ncs_group { reference = (chain 'Q' and (resid 13 through 59 or resid 70 through 82 or (resid 83 through \ 140 and (name N or name CA or name C or name O )) or resid 146 through 180 or re \ sid 191 through 226)) selection = (chain 'S' and (resid 13 through 59 or resid 70 through 82 or (resid 83 and (nam \ e N or name CA or name C or name O )) or resid 97 through 140 or resid 146 throu \ gh 180 or resid 191 through 226)) selection = (chain 'U' and (resid 13 through 59 or resid 70 through 82 or resid 96 through 1 \ 80 or resid 191 through 226)) selection = (chain 'b' and (resid 13 through 82 or (resid 83 and (name N or name CA or name \ C or name O )) or resid 97 through 140 or resid 146 through 180 or resid 191 thr \ ough 226)) } ncs_group { reference = (chain 'R' and resid 9 through 104) selection = chain 'f' selection = (chain 'j' and resid 9 through 104) } ncs_group { reference = (chain 'X' and (resid 22 through 60 or resid 70 through 82)) selection = (chain 'c' and resid 22 through 82) } 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: 0.010 Normalize map: mean=0, sd=1: 12.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.900 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 47.970 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 39998 Z= 0.491 Angle : 1.127 50.396 55154 Z= 0.821 Chirality : 0.052 0.369 7062 Planarity : 0.006 0.212 8174 Dihedral : 5.166 36.170 8174 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.09), residues: 8094 helix: 1.25 (0.08), residues: 4355 sheet: -1.92 (0.17), residues: 994 loop : -1.56 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00659 (39998) covalent geometry : angle 1.12656 (55154) hydrogen bonds : bond 0.14161 ( 3679) hydrogen bonds : angle 6.07958 (10626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1755 time to fit residues: 66.6191 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 394 optimal weight: 50.0000 chunk 776 optimal weight: 50.0000 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 802 optimal weight: 40.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.054433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.033534 restraints weight = 518303.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.033663 restraints weight = 490848.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.033619 restraints weight = 420940.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.033674 restraints weight = 411181.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.033686 restraints weight = 387229.335| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39998 Z= 0.138 Angle : 0.421 6.334 55154 Z= 0.266 Chirality : 0.038 0.143 7062 Planarity : 0.002 0.020 8174 Dihedral : 3.933 25.373 8174 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.10), residues: 8094 helix: 2.57 (0.08), residues: 4485 sheet: -1.51 (0.17), residues: 1015 loop : -0.98 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00186 (39998) covalent geometry : angle 0.42123 (55154) hydrogen bonds : bond 0.04018 ( 3679) hydrogen bonds : angle 4.33440 (10626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1607 time to fit residues: 61.1108 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 261 optimal weight: 30.0000 chunk 427 optimal weight: 40.0000 chunk 186 optimal weight: 3.9990 chunk 757 optimal weight: 50.0000 chunk 368 optimal weight: 50.0000 chunk 749 optimal weight: 0.8980 chunk 31 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 768 optimal weight: 6.9990 chunk 726 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.053020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.032292 restraints weight = 523204.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.032364 restraints weight = 484506.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.032281 restraints weight = 450244.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.032302 restraints weight = 439074.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.032333 restraints weight = 410264.002| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 39998 Z= 0.126 Angle : 0.365 4.793 55154 Z= 0.233 Chirality : 0.038 0.132 7062 Planarity : 0.002 0.014 8174 Dihedral : 3.217 19.366 8174 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.10), residues: 8094 helix: 3.49 (0.08), residues: 4431 sheet: -1.19 (0.17), residues: 1025 loop : -0.68 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00163 (39998) covalent geometry : angle 0.36534 (55154) hydrogen bonds : bond 0.03270 ( 3679) hydrogen bonds : angle 3.67006 (10626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1571 time to fit residues: 59.7459 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 657 optimal weight: 8.9990 chunk 741 optimal weight: 30.0000 chunk 509 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 780 optimal weight: 50.0000 chunk 457 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 694 optimal weight: 40.0000 chunk 80 optimal weight: 40.0000 chunk 400 optimal weight: 3.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.051872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.031314 restraints weight = 526193.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.031252 restraints weight = 522302.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.031153 restraints weight = 479268.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.031193 restraints weight = 472716.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.031279 restraints weight = 426710.396| |-----------------------------------------------------------------------------| r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 39998 Z= 0.139 Angle : 0.378 6.534 55154 Z= 0.241 Chirality : 0.038 0.129 7062 Planarity : 0.002 0.014 8174 Dihedral : 3.340 19.779 8174 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.10), residues: 8094 helix: 3.42 (0.08), residues: 4506 sheet: -1.12 (0.16), residues: 1009 loop : -0.59 (0.13), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00187 (39998) covalent geometry : angle 0.37780 (55154) hydrogen bonds : bond 0.03282 ( 3679) hydrogen bonds : angle 3.75594 (10626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1568 time to fit residues: 60.0336 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 131 optimal weight: 30.0000 chunk 672 optimal weight: 7.9990 chunk 735 optimal weight: 30.0000 chunk 494 optimal weight: 50.0000 chunk 782 optimal weight: 50.0000 chunk 404 optimal weight: 0.9990 chunk 508 optimal weight: 30.0000 chunk 706 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 600 optimal weight: 60.0000 chunk 541 optimal weight: 8.9990 overall best weight: 15.5994 ------------------------------------------------------------------------------- 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 = 0.2976 r_free = 0.2976 target = 0.036252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030002 restraints weight = 987387.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030000 restraints weight = 1082857.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030000 restraints weight = 1085113.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030000 restraints weight = 1085113.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030000 restraints weight = 1085113.715| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 39998 Z= 0.337 Angle : 0.619 9.692 55154 Z= 0.409 Chirality : 0.040 0.167 7062 Planarity : 0.004 0.025 8174 Dihedral : 5.117 31.827 8174 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.09), residues: 8094 helix: 1.75 (0.08), residues: 4478 sheet: -1.25 (0.17), residues: 954 loop : -1.06 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00457 (39998) covalent geometry : angle 0.61865 (55154) hydrogen bonds : bond 0.05261 ( 3679) hydrogen bonds : angle 5.41988 (10626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1535 time to fit residues: 58.6566 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 194 optimal weight: 20.0000 chunk 681 optimal weight: 6.9990 chunk 23 optimal weight: 50.0000 chunk 805 optimal weight: 40.0000 chunk 671 optimal weight: 50.0000 chunk 81 optimal weight: 30.0000 chunk 509 optimal weight: 6.9990 chunk 264 optimal weight: 40.0000 chunk 427 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 549 optimal weight: 40.0000 overall best weight: 20.7996 ------------------------------------------------------------------------------- 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 = 0.2949 r_free = 0.2949 target = 0.036097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029607 restraints weight = 845460.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029607 restraints weight = 939412.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029607 restraints weight = 939427.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029607 restraints weight = 939478.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029607 restraints weight = 939478.558| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.8310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 39998 Z= 0.406 Angle : 0.645 7.154 55154 Z= 0.436 Chirality : 0.040 0.151 7062 Planarity : 0.004 0.034 8174 Dihedral : 5.556 36.655 8174 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.09), residues: 8094 helix: 0.77 (0.08), residues: 4452 sheet: -1.53 (0.18), residues: 850 loop : -1.54 (0.12), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00549 (39998) covalent geometry : angle 0.64480 (55154) hydrogen bonds : bond 0.05656 ( 3679) hydrogen bonds : angle 6.00932 (10626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1742 time to fit residues: 65.9703 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 448 optimal weight: 50.0000 chunk 439 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 652 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 731 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 293 optimal weight: 50.0000 chunk 642 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- 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 = 0.2964 r_free = 0.2964 target = 0.035833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029445 restraints weight = 969346.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029445 restraints weight = 1033655.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029445 restraints weight = 1033712.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029445 restraints weight = 1033727.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029445 restraints weight = 1033728.682| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.8374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 39998 Z= 0.218 Angle : 0.455 6.873 55154 Z= 0.300 Chirality : 0.038 0.141 7062 Planarity : 0.002 0.020 8174 Dihedral : 4.667 25.261 8174 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.10), residues: 8094 helix: 1.76 (0.08), residues: 4449 sheet: -1.43 (0.18), residues: 863 loop : -1.32 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00293 (39998) covalent geometry : angle 0.45478 (55154) hydrogen bonds : bond 0.04351 ( 3679) hydrogen bonds : angle 5.09091 (10626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.657 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1501 time to fit residues: 57.4181 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 434 optimal weight: 50.0000 chunk 399 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 603 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 chunk 643 optimal weight: 0.0570 chunk 711 optimal weight: 50.0000 chunk 606 optimal weight: 50.0000 chunk 724 optimal weight: 30.0000 chunk 722 optimal weight: 0.0670 overall best weight: 9.4246 ------------------------------------------------------------------------------- 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 = 0.2970 r_free = 0.2970 target = 0.035974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.029486 restraints weight = 938803.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029324 restraints weight = 1054833.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.029259 restraints weight = 1195418.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.029240 restraints weight = 1237088.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.029237 restraints weight = 1240136.107| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.8770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 39998 Z= 0.194 Angle : 0.415 5.915 55154 Z= 0.273 Chirality : 0.038 0.132 7062 Planarity : 0.002 0.019 8174 Dihedral : 4.076 23.384 8174 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.10), residues: 8094 helix: 2.63 (0.08), residues: 4499 sheet: -1.49 (0.18), residues: 888 loop : -1.23 (0.13), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00260 (39998) covalent geometry : angle 0.41538 (55154) hydrogen bonds : bond 0.03853 ( 3679) hydrogen bonds : angle 4.51147 (10626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.084 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1521 time to fit residues: 57.4305 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 386 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 455 optimal weight: 4.9990 chunk 422 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 749 optimal weight: 50.0000 chunk 170 optimal weight: 30.0000 chunk 435 optimal weight: 40.0000 chunk 212 optimal weight: 40.0000 chunk 526 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.2974 r_free = 0.2974 target = 0.035997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029548 restraints weight = 959133.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029393 restraints weight = 1072504.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029336 restraints weight = 1201115.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029336 restraints weight = 1228214.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029336 restraints weight = 1228214.945| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.8871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 39998 Z= 0.149 Angle : 0.374 5.812 55154 Z= 0.243 Chirality : 0.038 0.132 7062 Planarity : 0.002 0.012 8174 Dihedral : 3.898 21.813 8174 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.10), residues: 8094 helix: 2.95 (0.08), residues: 4514 sheet: -1.45 (0.18), residues: 867 loop : -1.14 (0.13), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00199 (39998) covalent geometry : angle 0.37369 (55154) hydrogen bonds : bond 0.03554 ( 3679) hydrogen bonds : angle 4.29089 (10626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.499 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1650 time to fit residues: 62.7355 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 271 optimal weight: 9.9990 chunk 567 optimal weight: 50.0000 chunk 274 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 233 optimal weight: 50.0000 chunk 596 optimal weight: 50.0000 chunk 509 optimal weight: 5.9990 chunk 300 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 522 optimal weight: 0.9990 chunk 504 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- 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 = 0.2964 r_free = 0.2964 target = 0.036016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029480 restraints weight = 886649.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029323 restraints weight = 990404.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029244 restraints weight = 1110077.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029244 restraints weight = 1157029.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029244 restraints weight = 1157029.724| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.9211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 39998 Z= 0.190 Angle : 0.407 5.682 55154 Z= 0.267 Chirality : 0.038 0.131 7062 Planarity : 0.002 0.015 8174 Dihedral : 3.988 24.670 8174 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.10), residues: 8094 helix: 2.91 (0.08), residues: 4489 sheet: -1.54 (0.18), residues: 893 loop : -1.12 (0.13), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00255 (39998) covalent geometry : angle 0.40671 (55154) hydrogen bonds : bond 0.03773 ( 3679) hydrogen bonds : angle 4.41896 (10626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16188 Ramachandran restraints generated. 8094 Oldfield, 0 Emsley, 8094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.518 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1616 time to fit residues: 61.4640 Evaluate side-chains 194 residues out of total 6886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 187 optimal weight: 5.9990 chunk 347 optimal weight: 120.0000 chunk 254 optimal weight: 50.0000 chunk 415 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 232 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 729 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 575 optimal weight: 20.0000 chunk 516 optimal weight: 50.0000 overall best weight: 14.1994 ------------------------------------------------------------------------------- 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 = 0.2955 r_free = 0.2955 target = 0.038767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.031401 restraints weight = 476900.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031335 restraints weight = 596278.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031335 restraints weight = 629411.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031335 restraints weight = 629417.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031335 restraints weight = 629417.507| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39998 Z= 0.286 Angle : 0.494 6.044 55154 Z= 0.332 Chirality : 0.039 0.137 7062 Planarity : 0.003 0.018 8174 Dihedral : 4.569 28.728 8174 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.15 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.10), residues: 8094 helix: 2.20 (0.08), residues: 4476 sheet: -1.67 (0.18), residues: 848 loop : -1.39 (0.12), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 61 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP D 40 Details of bonding type rmsd covalent geometry : bond 0.00386 (39998) covalent geometry : angle 0.49381 (55154) hydrogen bonds : bond 0.04480 ( 3679) hydrogen bonds : angle 5.03470 (10626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8314.12 seconds wall clock time: 141 minutes 45.85 seconds (8505.85 seconds total)