Starting phenix.real_space_refine on Sat Jul 27 17:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_19488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_19488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_19488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_19488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtd_19488/07_2024/8rtd_19488.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 21, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} 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, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 21, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} 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, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} 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: {'GLN:plan1': 21, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} 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: {'PHE:plan': 1, 'GLU: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: {'GLN:plan1': 21, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} 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, 'HIS:plan': 1, 'ARG:plan': 4, 'TYR:plan': 3} 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: {'GLN:plan1': 21, 'TYR:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 21} 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: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 18, 'GLU:plan': 8, 'ARG:plan': 7} 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: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 18, 'GLU:plan': 8, 'ARG:plan': 7} 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, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 9, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 7} 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: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 16, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 33, 'ASP:plan': 51, 'TYR:plan': 27, 'ASN:plan1': 30, 'TRP:plan': 12, 'HIS:plan': 19, 'PHE:plan': 47, 'GLU:plan': 58, 'ARG:plan': 49} 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: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 16, 'GLU:plan': 6, 'ARG:plan': 4} 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, 'ARG:plan': 46, 'TYR:plan': 27, 'ASN:plan1': 30, 'TRP:plan': 12, 'HIS:plan': 19, 'PHE:plan': 45, 'GLU:plan': 54, 'ASP:plan': 48} 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: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 18, 'GLU:plan': 8, 'ARG:plan': 7} 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, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 16} 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, 'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 9, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 7} 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, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 17} 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: {'GLN:plan1': 33, 'ASP:plan': 54, 'TYR:plan': 27, 'ASN:plan1': 30, 'TRP:plan': 12, 'HIS:plan': 19, 'PHE:plan': 47, 'GLU:plan': 61, 'ARG:plan': 49} 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: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 16} 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, 'ARG:plan': 43, 'TYR:plan': 27, 'ASN:plan1': 27, 'TRP:plan': 12, 'HIS:plan': 17, 'PHE:plan': 44, 'GLU:plan': 51, 'ASP:plan': 41} 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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 15} 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, 'HIS:plan': 1, 'ARG:plan': 6, 'TYR:plan': 4} 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, 'HIS:plan': 3, 'TYR:plan': 13, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 17} 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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'PHE:plan': 2, 'GLU:plan': 1, '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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 9, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 7} 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: {'GLN:plan1': 32, 'ASP:plan': 46, 'TYR:plan': 27, 'ASN:plan1': 28, 'TRP:plan': 12, 'HIS:plan': 18, 'PHE:plan': 44, 'GLU:plan': 56, 'ARG:plan': 44} 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, 'ARG:plan': 27, 'TYR:plan': 18, 'ASN:plan1': 19, 'TRP:plan': 7, 'HIS:plan': 15, 'PHE:plan': 25, 'GLU:plan': 29, 'ASP:plan': 23} 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, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 23.76, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 10.5 seconds 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: 6.34 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: 24.30 Time building geometry restraints manager: 17.43 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: 72.64 - 90.35: 2 90.35 - 108.05: 725 108.05 - 125.75: 54308 125.75 - 143.45: 110 143.45 - 161.15: 9 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 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: 0.000 Normalize map: mean=0, sd=1: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.430 Check model and map are aligned: 0.270 Set scattering table: 0.360 Process input model: 122.150 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.990 ------------------------------------------------------------------------------- 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= 0.484 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.547 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3379 time to fit residues: 130.4232 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 1.9990 chunk 611 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 208 optimal weight: 40.0000 chunk 412 optimal weight: 30.0000 chunk 326 optimal weight: 30.0000 chunk 632 optimal weight: 0.0970 chunk 244 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 470 optimal weight: 8.9990 chunk 732 optimal weight: 50.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5676 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39998 Z= 0.160 Angle : 0.454 6.207 55154 Z= 0.287 Chirality : 0.038 0.149 7062 Planarity : 0.003 0.030 8174 Dihedral : 4.018 24.475 8174 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.10), residues: 8094 helix: 2.45 (0.08), residues: 4478 sheet: -1.49 (0.17), residues: 997 loop : -0.95 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3466 time to fit residues: 133.0727 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 609 optimal weight: 5.9990 chunk 499 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 734 optimal weight: 120.0000 chunk 793 optimal weight: 0.0010 chunk 653 optimal weight: 40.0000 chunk 728 optimal weight: 8.9990 chunk 250 optimal weight: 50.0000 chunk 588 optimal weight: 20.0000 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 39998 Z= 0.109 Angle : 0.353 4.987 55154 Z= 0.224 Chirality : 0.038 0.138 7062 Planarity : 0.002 0.016 8174 Dihedral : 3.261 19.622 8174 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.10), residues: 8094 helix: 3.46 (0.08), residues: 4419 sheet: -1.17 (0.16), residues: 1020 loop : -0.64 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3423 time to fit residues: 131.4348 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 2.9990 chunk 551 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 350 optimal weight: 5.9990 chunk 492 optimal weight: 30.0000 chunk 736 optimal weight: 20.0000 chunk 780 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 698 optimal weight: 50.0000 chunk 210 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 39998 Z= 0.187 Angle : 0.446 6.827 55154 Z= 0.287 Chirality : 0.038 0.133 7062 Planarity : 0.003 0.017 8174 Dihedral : 3.839 20.972 8174 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 8094 helix: 3.10 (0.08), residues: 4463 sheet: -0.95 (0.16), residues: 1016 loop : -0.67 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3452 time to fit residues: 132.4421 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 40.0000 chunk 442 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 580 optimal weight: 50.0000 chunk 321 optimal weight: 30.0000 chunk 665 optimal weight: 10.0000 chunk 539 optimal weight: 20.0000 chunk 0 optimal weight: 220.0000 chunk 398 optimal weight: 8.9990 chunk 700 optimal weight: 2.9990 chunk 196 optimal weight: 30.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39998 Z= 0.218 Angle : 0.473 7.301 55154 Z= 0.309 Chirality : 0.039 0.138 7062 Planarity : 0.003 0.016 8174 Dihedral : 4.193 23.357 8174 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.10), residues: 8094 helix: 2.88 (0.08), residues: 4437 sheet: -0.84 (0.17), residues: 958 loop : -0.77 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.341 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3650 time to fit residues: 138.3785 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 40.0000 chunk 702 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 780 optimal weight: 50.0000 chunk 648 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 64 optimal weight: 50.0000 chunk 258 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39998 Z= 0.191 Angle : 0.426 6.086 55154 Z= 0.278 Chirality : 0.038 0.132 7062 Planarity : 0.002 0.022 8174 Dihedral : 4.079 29.405 8174 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.10), residues: 8094 helix: 2.98 (0.08), residues: 4472 sheet: -0.77 (0.17), residues: 963 loop : -0.81 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.070 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3461 time to fit residues: 133.0175 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 444 optimal weight: 0.9990 chunk 570 optimal weight: 30.0000 chunk 441 optimal weight: 1.9990 chunk 657 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 chunk 777 optimal weight: 50.0000 chunk 486 optimal weight: 20.0000 chunk 474 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 39998 Z= 0.118 Angle : 0.349 5.582 55154 Z= 0.225 Chirality : 0.037 0.130 7062 Planarity : 0.002 0.013 8174 Dihedral : 3.629 17.066 8174 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.10), residues: 8094 helix: 3.48 (0.08), residues: 4460 sheet: -0.68 (0.17), residues: 969 loop : -0.66 (0.13), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3656 time to fit residues: 140.6442 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 chunk 464 optimal weight: 20.0000 chunk 234 optimal weight: 0.0030 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 chunk 494 optimal weight: 50.0000 chunk 529 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 611 optimal weight: 50.0000 overall best weight: 11.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39998 Z= 0.238 Angle : 0.471 6.122 55154 Z= 0.311 Chirality : 0.038 0.154 7062 Planarity : 0.003 0.019 8174 Dihedral : 4.349 26.769 8174 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.10), residues: 8094 helix: 2.71 (0.08), residues: 4459 sheet: -0.74 (0.18), residues: 918 loop : -0.95 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3653 time to fit residues: 141.1936 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 50.0000 chunk 745 optimal weight: 8.9990 chunk 679 optimal weight: 50.0000 chunk 724 optimal weight: 8.9990 chunk 744 optimal weight: 50.0000 chunk 436 optimal weight: 40.0000 chunk 315 optimal weight: 20.0000 chunk 569 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 654 optimal weight: 8.9990 chunk 685 optimal weight: 2.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 39998 Z= 0.157 Angle : 0.381 6.087 55154 Z= 0.251 Chirality : 0.038 0.131 7062 Planarity : 0.002 0.012 8174 Dihedral : 3.877 20.042 8174 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.10), residues: 8094 helix: 3.20 (0.08), residues: 4469 sheet: -0.77 (0.18), residues: 924 loop : -0.87 (0.13), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 *********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 5.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3660 time to fit residues: 141.6940 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 30.0000 chunk 475 optimal weight: 7.9990 chunk 766 optimal weight: 50.0000 chunk 467 optimal weight: 30.0000 chunk 363 optimal weight: 50.0000 chunk 532 optimal weight: 6.9990 chunk 803 optimal weight: 30.0000 chunk 739 optimal weight: 20.0000 chunk 640 optimal weight: 8.9990 chunk 66 optimal weight: 50.0000 chunk 494 optimal weight: 50.0000 overall best weight: 14.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.9030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 39998 Z= 0.296 Angle : 0.527 7.363 55154 Z= 0.355 Chirality : 0.039 0.134 7062 Planarity : 0.003 0.022 8174 Dihedral : 4.783 30.379 8174 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.66 % Favored : 92.28 % 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 : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.10), residues: 8094 helix: 2.14 (0.08), residues: 4449 sheet: -0.83 (0.19), residues: 858 loop : -1.22 (0.12), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 ********************** 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3636 time to fit residues: 139.7926 Evaluate side-chains 194 residues out of total 6886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 5.9990 chunk 508 optimal weight: 50.0000 chunk 681 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 590 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 641 optimal weight: 20.0000 chunk 268 optimal weight: 1.9990 chunk 658 optimal weight: 50.0000 chunk 81 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.2982 r_free = 0.2982 target = 0.036674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.030021 restraints weight = 868134.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.029891 restraints weight = 965339.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.029831 restraints weight = 1045239.219| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.8910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 39998 Z= 0.116 Angle : 0.356 5.688 55154 Z= 0.231 Chirality : 0.038 0.135 7062 Planarity : 0.002 0.012 8174 Dihedral : 3.889 20.213 8174 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.10), residues: 8094 helix: 3.27 (0.08), residues: 4481 sheet: -0.93 (0.18), residues: 897 loop : -0.95 (0.13), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP D 40 PHE 0.000 0.000 PHE A 36 TYR 0.000 0.000 TYR A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5942.74 seconds wall clock time: 105 minutes 43.47 seconds (6343.47 seconds total)