Starting phenix.real_space_refine on Mon Nov 20 13:32:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znk_14804/11_2023/7znk_14804.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.146 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 492 5.16 5 C 56143 2.51 5 N 15329 2.21 5 O 16291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B ARG 985": "NH1" <-> "NH2" Residue "B GLU 1035": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "E ARG 660": "NH1" <-> "NH2" Residue "E ARG 663": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "I ARG 145": "NH1" <-> "NH2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "I ARG 495": "NH1" <-> "NH2" Residue "I ARG 498": "NH1" <-> "NH2" Residue "I ARG 503": "NH1" <-> "NH2" Residue "J ARG 268": "NH1" <-> "NH2" Residue "J GLU 350": "OE1" <-> "OE2" Residue "J ARG 396": "NH1" <-> "NH2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "J ARG 429": "NH1" <-> "NH2" Residue "J ARG 520": "NH1" <-> "NH2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "J GLU 942": "OE1" <-> "OE2" Residue "J ARG 985": "NH1" <-> "NH2" Residue "J GLU 1035": "OE1" <-> "OE2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K ARG 319": "NH1" <-> "NH2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ARG 663": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N ARG 258": "NH1" <-> "NH2" Residue "N ARG 335": "NH1" <-> "NH2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ARG 116": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "a ARG 145": "NH1" <-> "NH2" Residue "a ARG 165": "NH1" <-> "NH2" Residue "a GLU 379": "OE1" <-> "OE2" Residue "a ARG 495": "NH1" <-> "NH2" Residue "a ARG 498": "NH1" <-> "NH2" Residue "a ARG 503": "NH1" <-> "NH2" Residue "b ARG 268": "NH1" <-> "NH2" Residue "b GLU 350": "OE1" <-> "OE2" Residue "b ARG 396": "NH1" <-> "NH2" Residue "b ARG 428": "NH1" <-> "NH2" Residue "b ARG 429": "NH1" <-> "NH2" Residue "b ARG 520": "NH1" <-> "NH2" Residue "b ARG 555": "NH1" <-> "NH2" Residue "b GLU 942": "OE1" <-> "OE2" Residue "b ARG 985": "NH1" <-> "NH2" Residue "b GLU 1035": "OE1" <-> "OE2" Residue "c ARG 49": "NH1" <-> "NH2" Residue "c GLU 303": "OE1" <-> "OE2" Residue "c ARG 319": "NH1" <-> "NH2" Residue "e ARG 660": "NH1" <-> "NH2" Residue "e ARG 663": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 221": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 335": "NH1" <-> "NH2" Residue "f PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 145": "NH1" <-> "NH2" Residue "i ARG 165": "NH1" <-> "NH2" Residue "i ARG 495": "NH1" <-> "NH2" Residue "i ARG 498": "NH1" <-> "NH2" Residue "i ARG 503": "NH1" <-> "NH2" Residue "j ARG 268": "NH1" <-> "NH2" Residue "j GLU 350": "OE1" <-> "OE2" Residue "j ARG 396": "NH1" <-> "NH2" Residue "j ARG 428": "NH1" <-> "NH2" Residue "j ARG 429": "NH1" <-> "NH2" Residue "j ARG 520": "NH1" <-> "NH2" Residue "j ARG 555": "NH1" <-> "NH2" Residue "j GLU 942": "OE1" <-> "OE2" Residue "j ARG 985": "NH1" <-> "NH2" Residue "j GLU 1035": "OE1" <-> "OE2" Residue "k ARG 49": "NH1" <-> "NH2" Residue "k GLU 303": "OE1" <-> "OE2" Residue "k ARG 319": "NH1" <-> "NH2" Residue "m ARG 113": "NH1" <-> "NH2" Residue "m ARG 663": "NH1" <-> "NH2" Residue "n ARG 115": "NH1" <-> "NH2" Residue "n ARG 221": "NH1" <-> "NH2" Residue "n ARG 258": "NH1" <-> "NH2" Residue "n ARG 335": "NH1" <-> "NH2" Residue "o ARG 52": "NH1" <-> "NH2" Residue "o ARG 116": "NH1" <-> "NH2" Residue "o ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 88261 Number of models: 1 Model: "" Number of chains: 32 Chain: "2" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "4" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2889 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 342} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7012 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 30, 'TRANS': 888} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 611 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 292 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2433 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 3765 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 24, 'TRANS': 513} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 776 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 360 Chain: "F" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 800 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 315 Chain: "H" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2935 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 13, 'TRANS': 349} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "J" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 6956 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 30, 'TRANS': 883} Chain breaks: 24 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 623 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 301 Chain: "K" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2433 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4136 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 26, 'TRANS': 522} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 191 Chain: "N" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1129 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 136 Chain: "P" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2974 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain breaks: 2 Chain: "a" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2889 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 342} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "b" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7012 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 30, 'TRANS': 888} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 611 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 292 Chain: "c" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2433 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3676 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 772 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 360 Chain: "f" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2537 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "g" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 800 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 464 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 315 Chain: "h" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1398 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain: "i" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2936 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 349} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "j" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 6956 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 30, 'TRANS': 883} Chain breaks: 24 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 623 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 301 Chain: "k" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2433 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "l" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4136 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 26, 'TRANS': 522} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 191 Chain: "n" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain: "o" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1129 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 136 Chain: "p" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2974 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain breaks: 2 Time building chain proxies: 33.28, per 1000 atoms: 0.38 Number of scatterers: 88261 At special positions: 0 Unit cell: (344.04, 290.46, 310.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 492 16.00 P 6 15.00 O 16291 8.00 N 15329 7.00 C 56143 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: 26.34 Conformation dependent library (CDL) restraints added in 12.4 seconds 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22206 Finding SS restraints... Secondary structure from input PDB file: 432 helices and 74 sheets defined 57.1% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.507A pdb=" N ARG A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 45 through 65 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.725A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.897A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 253 through 275 removed outlier: 3.701A pdb=" N LYS A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.537A pdb=" N ASP A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.576A pdb=" N ARG A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.653A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.661A pdb=" N ARG A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 503 removed outlier: 4.213A pdb=" N ARG A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.619A pdb=" N LYS A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.729A pdb=" N ILE B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.694A pdb=" N MET B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 100 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.819A pdb=" N SER B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.500A pdb=" N TYR B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.225A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 4.519A pdb=" N CYS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.689A pdb=" N TYR B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 288 removed outlier: 3.995A pdb=" N LEU B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 308 removed outlier: 3.524A pdb=" N ALA B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.530A pdb=" N ALA B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.650A pdb=" N GLN B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 399 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 441 through 444 removed outlier: 3.641A pdb=" N HIS B 444 " --> pdb=" O HIS B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.785A pdb=" N PHE B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 496 removed outlier: 5.071A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.898A pdb=" N TRP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.747A pdb=" N LYS B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 575 through 591 Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 605 through 622 Processing helix chain 'B' and resid 636 through 653 Processing helix chain 'B' and resid 658 through 670 Processing helix chain 'B' and resid 675 through 686 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 724 through 736 removed outlier: 3.650A pdb=" N HIS B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.775A pdb=" N GLN B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN B 751 " --> pdb=" O ALA B 747 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 788 Processing helix chain 'B' and resid 789 through 797 removed outlier: 3.524A pdb=" N LYS B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 removed outlier: 3.648A pdb=" N CYS B 804 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 805 " --> pdb=" O ASP B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 878 through 887 Processing helix chain 'B' and resid 900 through 908 Processing helix chain 'B' and resid 929 through 962 removed outlier: 3.679A pdb=" N LEU B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS B 957 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 959 " --> pdb=" O ARG B 955 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 989 removed outlier: 4.109A pdb=" N PHE B 977 " --> pdb=" O THR B 973 " (cutoff:3.500A) Proline residue: B 984 - end of helix removed outlier: 3.985A pdb=" N SER B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1006 removed outlier: 3.540A pdb=" N VAL B1000 " --> pdb=" O CYS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 removed outlier: 3.617A pdb=" N ASP B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1030 removed outlier: 4.168A pdb=" N THR B1027 " --> pdb=" O ASP B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1053 removed outlier: 3.735A pdb=" N PHE B1042 " --> pdb=" O ARG B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1113 Processing helix chain 'B' and resid 1116 through 1130 removed outlier: 3.919A pdb=" N ILE B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1154 removed outlier: 3.673A pdb=" N GLU B1154 " --> pdb=" O LYS B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1176 Processing helix chain 'C' and resid 32 through 45 removed outlier: 3.611A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 53 through 75 Processing helix chain 'E' and resid 81 through 144 Processing helix chain 'E' and resid 190 through 247 Proline residue: E 231 - end of helix Proline residue: E 242 - end of helix Processing helix chain 'E' and resid 253 through 262 Processing helix chain 'E' and resid 265 through 282 Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.613A pdb=" N ALA E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 415 through 424 removed outlier: 3.623A pdb=" N GLN E 419 " --> pdb=" O ASN E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 Processing helix chain 'E' and resid 441 through 449 removed outlier: 3.960A pdb=" N GLN E 445 " --> pdb=" O TYR E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 497 removed outlier: 4.661A pdb=" N SER E 470 " --> pdb=" O SER E 466 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN E 484 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 removed outlier: 4.350A pdb=" N TYR E 509 " --> pdb=" O ASP E 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 511 " --> pdb=" O GLN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 532 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.754A pdb=" N VAL E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 607 removed outlier: 4.054A pdb=" N ARG E 599 " --> pdb=" O ASP E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 612 removed outlier: 3.503A pdb=" N GLU E 611 " --> pdb=" O CYS E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 639 Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.696A pdb=" N LYS F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 4.084A pdb=" N LEU F 106 " --> pdb=" O TRP F 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 7 through 13 Processing helix chain 'G' and resid 24 through 41 Processing helix chain 'G' and resid 46 through 128 Processing helix chain 'G' and resid 134 through 181 removed outlier: 3.881A pdb=" N LEU G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 296 through 309 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 367 through 376 Processing helix chain 'H' and resid 393 through 408 removed outlier: 3.784A pdb=" N ALA H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 Processing helix chain 'I' and resid 30 through 37 Processing helix chain 'I' and resid 45 through 65 Processing helix chain 'I' and resid 71 through 84 Processing helix chain 'I' and resid 92 through 104 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'I' and resid 134 through 147 Processing helix chain 'I' and resid 152 through 167 Processing helix chain 'I' and resid 231 through 247 removed outlier: 3.613A pdb=" N TYR I 235 " --> pdb=" O ASP I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 251 removed outlier: 3.537A pdb=" N CYS I 251 " --> pdb=" O PRO I 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 248 through 251' Processing helix chain 'I' and resid 254 through 275 removed outlier: 4.166A pdb=" N LYS I 275 " --> pdb=" O PHE I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 333 Processing helix chain 'I' and resid 346 through 366 Processing helix chain 'I' and resid 370 through 392 removed outlier: 3.694A pdb=" N TRP I 391 " --> pdb=" O ASN I 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 392 " --> pdb=" O TRP I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 443 removed outlier: 3.662A pdb=" N ARG I 440 " --> pdb=" O GLU I 436 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU I 441 " --> pdb=" O GLU I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 503 removed outlier: 4.213A pdb=" N ARG I 495 " --> pdb=" O ASN I 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 501 " --> pdb=" O LEU I 497 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG I 502 " --> pdb=" O ARG I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 528 removed outlier: 3.618A pdb=" N LYS I 528 " --> pdb=" O ASN I 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 23 Processing helix chain 'J' and resid 40 through 57 removed outlier: 3.732A pdb=" N ILE J 57 " --> pdb=" O SER J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.698A pdb=" N MET J 80 " --> pdb=" O PHE J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 100 Processing helix chain 'J' and resid 108 through 119 removed outlier: 3.816A pdb=" N SER J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 156 Processing helix chain 'J' and resid 168 through 180 removed outlier: 3.578A pdb=" N TYR J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 204 Processing helix chain 'J' and resid 206 through 221 Processing helix chain 'J' and resid 225 through 237 Processing helix chain 'J' and resid 241 through 254 removed outlier: 4.520A pdb=" N CYS J 245 " --> pdb=" O PRO J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 276 removed outlier: 3.689A pdb=" N TYR J 267 " --> pdb=" O PRO J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 288 removed outlier: 3.996A pdb=" N LEU J 284 " --> pdb=" O ASP J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 308 removed outlier: 3.525A pdb=" N ALA J 306 " --> pdb=" O GLU J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 353 removed outlier: 3.531A pdb=" N ALA J 351 " --> pdb=" O GLY J 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 367 removed outlier: 3.650A pdb=" N GLN J 367 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 399 Proline residue: J 393 - end of helix Processing helix chain 'J' and resid 425 through 436 Processing helix chain 'J' and resid 441 through 444 removed outlier: 3.640A pdb=" N HIS J 444 " --> pdb=" O HIS J 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 441 through 444' Processing helix chain 'J' and resid 445 through 464 removed outlier: 3.788A pdb=" N PHE J 449 " --> pdb=" O ASP J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 496 removed outlier: 5.073A pdb=" N LEU J 492 " --> pdb=" O ASP J 488 " (cutoff:3.500A) Proline residue: J 493 - end of helix Processing helix chain 'J' and resid 503 through 513 removed outlier: 3.898A pdb=" N TRP J 509 " --> pdb=" O SER J 505 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY J 510 " --> pdb=" O GLU J 506 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET J 511 " --> pdb=" O GLU J 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS J 513 " --> pdb=" O TRP J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 530 Processing helix chain 'J' and resid 535 through 554 removed outlier: 3.745A pdb=" N LYS J 554 " --> pdb=" O LYS J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 575 Processing helix chain 'J' and resid 575 through 591 Processing helix chain 'J' and resid 593 through 601 Processing helix chain 'J' and resid 605 through 622 Processing helix chain 'J' and resid 636 through 653 Processing helix chain 'J' and resid 658 through 670 Processing helix chain 'J' and resid 675 through 686 Processing helix chain 'J' and resid 696 through 703 Processing helix chain 'J' and resid 708 through 713 Processing helix chain 'J' and resid 724 through 736 removed outlier: 3.650A pdb=" N HIS J 736 " --> pdb=" O ALA J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 756 removed outlier: 3.774A pdb=" N GLN J 748 " --> pdb=" O LEU J 744 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN J 751 " --> pdb=" O ALA J 747 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE J 754 " --> pdb=" O ARG J 750 " (cutoff:3.500A) Processing helix chain 'J' and resid 764 through 788 Processing helix chain 'J' and resid 789 through 797 removed outlier: 3.524A pdb=" N LYS J 795 " --> pdb=" O GLU J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 799 through 807 removed outlier: 3.650A pdb=" N CYS J 804 " --> pdb=" O ILE J 800 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN J 805 " --> pdb=" O ASP J 801 " (cutoff:3.500A) Processing helix chain 'J' and resid 810 through 823 Proline residue: J 820 - end of helix Processing helix chain 'J' and resid 861 through 869 Processing helix chain 'J' and resid 878 through 887 Processing helix chain 'J' and resid 900 through 908 Processing helix chain 'J' and resid 929 through 962 removed outlier: 3.681A pdb=" N LEU J 956 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS J 957 " --> pdb=" O LEU J 953 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU J 958 " --> pdb=" O GLN J 954 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU J 959 " --> pdb=" O ARG J 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN J 962 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing helix chain 'J' and resid 972 through 989 removed outlier: 4.106A pdb=" N PHE J 977 " --> pdb=" O THR J 973 " (cutoff:3.500A) Proline residue: J 984 - end of helix removed outlier: 3.986A pdb=" N SER J 989 " --> pdb=" O ARG J 985 " (cutoff:3.500A) Processing helix chain 'J' and resid 989 through 1006 removed outlier: 3.538A pdb=" N VAL J1000 " --> pdb=" O CYS J 996 " (cutoff:3.500A) Processing helix chain 'J' and resid 1013 through 1023 removed outlier: 3.617A pdb=" N ASP J1023 " --> pdb=" O ARG J1019 " (cutoff:3.500A) Processing helix chain 'J' and resid 1023 through 1030 removed outlier: 4.166A pdb=" N THR J1027 " --> pdb=" O ASP J1023 " (cutoff:3.500A) Processing helix chain 'J' and resid 1034 through 1053 removed outlier: 3.735A pdb=" N PHE J1042 " --> pdb=" O ARG J1038 " (cutoff:3.500A) Processing helix chain 'J' and resid 1091 through 1113 Processing helix chain 'J' and resid 1116 through 1130 removed outlier: 3.919A pdb=" N ILE J1120 " --> pdb=" O GLU J1116 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1154 removed outlier: 3.673A pdb=" N GLU J1154 " --> pdb=" O LYS J1150 " (cutoff:3.500A) Processing helix chain 'J' and resid 1161 through 1176 Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.612A pdb=" N LEU K 36 " --> pdb=" O SER K 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 255 removed outlier: 4.031A pdb=" N MET L 254 " --> pdb=" O TYR L 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP L 255 " --> pdb=" O ASN L 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 76 Processing helix chain 'M' and resid 81 through 148 removed outlier: 3.852A pdb=" N ALA M 119 " --> pdb=" O GLN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 170 through 175 Processing helix chain 'M' and resid 176 through 179 Processing helix chain 'M' and resid 183 through 240 Proline residue: M 231 - end of helix Processing helix chain 'M' and resid 244 through 248 Processing helix chain 'M' and resid 260 through 264 removed outlier: 3.597A pdb=" N HIS M 263 " --> pdb=" O THR M 260 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 264 " --> pdb=" O ALA M 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 260 through 264' Processing helix chain 'M' and resid 265 through 282 removed outlier: 3.555A pdb=" N CYS M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 299 removed outlier: 3.845A pdb=" N ALA M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 415 through 425 removed outlier: 3.863A pdb=" N GLN M 419 " --> pdb=" O ASN M 415 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL M 425 " --> pdb=" O GLN M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 438 Processing helix chain 'M' and resid 441 through 449 removed outlier: 3.918A pdb=" N GLN M 445 " --> pdb=" O TYR M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 471 through 497 Processing helix chain 'M' and resid 506 through 511 removed outlier: 4.352A pdb=" N TYR M 509 " --> pdb=" O ASP M 506 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE M 511 " --> pdb=" O GLN M 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 526 through 532 Processing helix chain 'M' and resid 536 through 543 removed outlier: 3.752A pdb=" N VAL M 540 " --> pdb=" O THR M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 595 through 607 removed outlier: 4.055A pdb=" N ARG M 599 " --> pdb=" O ASP M 595 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 612 Processing helix chain 'M' and resid 620 through 639 Processing helix chain 'N' and resid 12 through 24 Processing helix chain 'N' and resid 53 through 57 Processing helix chain 'N' and resid 62 through 66 removed outlier: 3.694A pdb=" N LYS N 66 " --> pdb=" O GLU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 106 removed outlier: 4.080A pdb=" N LEU N 106 " --> pdb=" O TRP N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 102 through 106' Processing helix chain 'O' and resid 7 through 13 Processing helix chain 'O' and resid 24 through 41 Processing helix chain 'O' and resid 47 through 127 removed outlier: 3.904A pdb=" N LEU O 68 " --> pdb=" O MET O 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU O 69 " --> pdb=" O GLY O 65 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 181 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 69 through 80 Proline residue: P 77 - end of helix Processing helix chain 'P' and resid 94 through 107 removed outlier: 3.887A pdb=" N VAL P 98 " --> pdb=" O GLY P 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE P 99 " --> pdb=" O LYS P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 137 Processing helix chain 'P' and resid 153 through 163 removed outlier: 3.730A pdb=" N ASP P 157 " --> pdb=" O SER P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 Processing helix chain 'P' and resid 197 through 204 Processing helix chain 'P' and resid 204 through 218 removed outlier: 3.546A pdb=" N MET P 217 " --> pdb=" O GLU P 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR P 218 " --> pdb=" O ILE P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 241 removed outlier: 4.425A pdb=" N VAL P 238 " --> pdb=" O GLU P 234 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS P 241 " --> pdb=" O PRO P 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 296 through 309 Processing helix chain 'P' and resid 322 through 335 Processing helix chain 'P' and resid 367 through 376 Processing helix chain 'P' and resid 393 through 408 removed outlier: 3.784A pdb=" N ALA P 397 " --> pdb=" O ASP P 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.584A pdb=" N ARG a 22 " --> pdb=" O THR a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 37 Processing helix chain 'a' and resid 45 through 65 Processing helix chain 'a' and resid 72 through 84 Processing helix chain 'a' and resid 92 through 104 Processing helix chain 'a' and resid 106 through 120 removed outlier: 3.726A pdb=" N VAL a 120 " --> pdb=" O VAL a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 147 Processing helix chain 'a' and resid 152 through 167 removed outlier: 3.898A pdb=" N PHE a 167 " --> pdb=" O LEU a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 247 Processing helix chain 'a' and resid 248 through 251 Processing helix chain 'a' and resid 253 through 275 removed outlier: 3.703A pdb=" N LYS a 275 " --> pdb=" O PHE a 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 309 through 314 removed outlier: 3.537A pdb=" N ASP a 314 " --> pdb=" O LEU a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 334 removed outlier: 3.574A pdb=" N ARG a 318 " --> pdb=" O ASP a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 366 Processing helix chain 'a' and resid 370 through 389 removed outlier: 3.653A pdb=" N ASN a 387 " --> pdb=" O ASN a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 443 removed outlier: 3.662A pdb=" N ARG a 440 " --> pdb=" O GLU a 436 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU a 441 " --> pdb=" O GLU a 437 " (cutoff:3.500A) Processing helix chain 'a' and resid 489 through 503 removed outlier: 4.212A pdb=" N ARG a 495 " --> pdb=" O ASN a 491 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA a 501 " --> pdb=" O LEU a 497 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG a 502 " --> pdb=" O ARG a 498 " (cutoff:3.500A) Processing helix chain 'a' and resid 517 through 528 removed outlier: 3.620A pdb=" N LYS a 528 " --> pdb=" O ASN a 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 23 Processing helix chain 'b' and resid 40 through 57 removed outlier: 3.730A pdb=" N ILE b 57 " --> pdb=" O SER b 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 80 removed outlier: 3.695A pdb=" N MET b 80 " --> pdb=" O PHE b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 100 Processing helix chain 'b' and resid 108 through 119 removed outlier: 3.819A pdb=" N SER b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 156 Processing helix chain 'b' and resid 168 through 180 Processing helix chain 'b' and resid 189 through 204 Processing helix chain 'b' and resid 206 through 221 Processing helix chain 'b' and resid 224 through 237 removed outlier: 4.223A pdb=" N PHE b 228 " --> pdb=" O HIS b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 254 removed outlier: 4.520A pdb=" N CYS b 245 " --> pdb=" O PRO b 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 276 removed outlier: 3.689A pdb=" N TYR b 267 " --> pdb=" O PRO b 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 280 through 288 removed outlier: 3.995A pdb=" N LEU b 284 " --> pdb=" O ASP b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 308 removed outlier: 3.525A pdb=" N ALA b 306 " --> pdb=" O GLU b 302 " (cutoff:3.500A) Processing helix chain 'b' and resid 344 through 353 removed outlier: 3.530A pdb=" N ALA b 351 " --> pdb=" O GLY b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 358 through 367 removed outlier: 3.649A pdb=" N GLN b 367 " --> pdb=" O ASN b 363 " (cutoff:3.500A) Processing helix chain 'b' and resid 376 through 399 Proline residue: b 393 - end of helix Processing helix chain 'b' and resid 425 through 436 Processing helix chain 'b' and resid 441 through 444 removed outlier: 3.642A pdb=" N HIS b 444 " --> pdb=" O HIS b 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 441 through 444' Processing helix chain 'b' and resid 445 through 464 removed outlier: 3.785A pdb=" N PHE b 449 " --> pdb=" O ASP b 445 " (cutoff:3.500A) Processing helix chain 'b' and resid 474 through 496 removed outlier: 5.072A pdb=" N LEU b 492 " --> pdb=" O ASP b 488 " (cutoff:3.500A) Proline residue: b 493 - end of helix Processing helix chain 'b' and resid 503 through 513 removed outlier: 3.898A pdb=" N TRP b 509 " --> pdb=" O SER b 505 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET b 511 " --> pdb=" O GLU b 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS b 513 " --> pdb=" O TRP b 509 " (cutoff:3.500A) Processing helix chain 'b' and resid 516 through 530 Processing helix chain 'b' and resid 535 through 554 removed outlier: 3.746A pdb=" N LYS b 554 " --> pdb=" O LYS b 550 " (cutoff:3.500A) Processing helix chain 'b' and resid 564 through 575 Processing helix chain 'b' and resid 575 through 591 Processing helix chain 'b' and resid 593 through 601 Processing helix chain 'b' and resid 605 through 622 Processing helix chain 'b' and resid 636 through 653 Processing helix chain 'b' and resid 658 through 670 Processing helix chain 'b' and resid 675 through 686 Processing helix chain 'b' and resid 696 through 703 Processing helix chain 'b' and resid 708 through 713 Processing helix chain 'b' and resid 724 through 736 removed outlier: 3.648A pdb=" N HIS b 736 " --> pdb=" O ALA b 732 " (cutoff:3.500A) Processing helix chain 'b' and resid 738 through 756 removed outlier: 3.775A pdb=" N GLN b 748 " --> pdb=" O LEU b 744 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN b 751 " --> pdb=" O ALA b 747 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE b 754 " --> pdb=" O ARG b 750 " (cutoff:3.500A) Processing helix chain 'b' and resid 764 through 788 Processing helix chain 'b' and resid 789 through 797 removed outlier: 3.526A pdb=" N LYS b 795 " --> pdb=" O GLU b 791 " (cutoff:3.500A) Processing helix chain 'b' and resid 799 through 807 removed outlier: 3.649A pdb=" N CYS b 804 " --> pdb=" O ILE b 800 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN b 805 " --> pdb=" O ASP b 801 " (cutoff:3.500A) Processing helix chain 'b' and resid 810 through 823 Proline residue: b 820 - end of helix Processing helix chain 'b' and resid 861 through 869 Processing helix chain 'b' and resid 878 through 887 Processing helix chain 'b' and resid 900 through 908 Processing helix chain 'b' and resid 929 through 962 removed outlier: 3.679A pdb=" N LEU b 956 " --> pdb=" O VAL b 952 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS b 957 " --> pdb=" O LEU b 953 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU b 958 " --> pdb=" O GLN b 954 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU b 959 " --> pdb=" O ARG b 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN b 962 " --> pdb=" O LEU b 958 " (cutoff:3.500A) Processing helix chain 'b' and resid 972 through 989 removed outlier: 4.107A pdb=" N PHE b 977 " --> pdb=" O THR b 973 " (cutoff:3.500A) Proline residue: b 984 - end of helix removed outlier: 3.988A pdb=" N SER b 989 " --> pdb=" O ARG b 985 " (cutoff:3.500A) Processing helix chain 'b' and resid 989 through 1006 removed outlier: 3.542A pdb=" N VAL b1000 " --> pdb=" O CYS b 996 " (cutoff:3.500A) Processing helix chain 'b' and resid 1013 through 1023 removed outlier: 3.617A pdb=" N ASP b1023 " --> pdb=" O ARG b1019 " (cutoff:3.500A) Processing helix chain 'b' and resid 1023 through 1030 removed outlier: 4.166A pdb=" N THR b1027 " --> pdb=" O ASP b1023 " (cutoff:3.500A) Processing helix chain 'b' and resid 1034 through 1053 removed outlier: 3.734A pdb=" N PHE b1042 " --> pdb=" O ARG b1038 " (cutoff:3.500A) Processing helix chain 'b' and resid 1091 through 1113 Processing helix chain 'b' and resid 1116 through 1130 removed outlier: 3.919A pdb=" N ILE b1120 " --> pdb=" O GLU b1116 " (cutoff:3.500A) Processing helix chain 'b' and resid 1138 through 1154 removed outlier: 3.671A pdb=" N GLU b1154 " --> pdb=" O LYS b1150 " (cutoff:3.500A) Processing helix chain 'b' and resid 1161 through 1176 Processing helix chain 'c' and resid 32 through 45 removed outlier: 3.612A pdb=" N LEU c 36 " --> pdb=" O SER c 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 47 Processing helix chain 'e' and resid 53 through 75 Processing helix chain 'e' and resid 81 through 144 Processing helix chain 'e' and resid 190 through 247 Proline residue: e 231 - end of helix Proline residue: e 242 - end of helix Processing helix chain 'e' and resid 253 through 262 Processing helix chain 'e' and resid 265 through 282 Processing helix chain 'e' and resid 293 through 299 removed outlier: 3.618A pdb=" N ALA e 299 " --> pdb=" O ASP e 295 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 341 Processing helix chain 'e' and resid 415 through 425 removed outlier: 3.623A pdb=" N GLN e 419 " --> pdb=" O ASN e 415 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL e 425 " --> pdb=" O GLN e 421 " (cutoff:3.500A) Processing helix chain 'e' and resid 431 through 438 Processing helix chain 'e' and resid 441 through 449 removed outlier: 3.961A pdb=" N GLN e 445 " --> pdb=" O TYR e 441 " (cutoff:3.500A) Processing helix chain 'e' and resid 464 through 497 removed outlier: 4.663A pdb=" N SER e 470 " --> pdb=" O SER e 466 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS e 471 " --> pdb=" O LEU e 467 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU e 473 " --> pdb=" O ALA e 469 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN e 484 " --> pdb=" O LYS e 480 " (cutoff:3.500A) Processing helix chain 'e' and resid 506 through 511 removed outlier: 4.353A pdb=" N TYR e 509 " --> pdb=" O ASP e 506 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE e 511 " --> pdb=" O GLN e 508 " (cutoff:3.500A) Processing helix chain 'e' and resid 526 through 532 Processing helix chain 'e' and resid 536 through 543 removed outlier: 3.755A pdb=" N VAL e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 595 through 607 removed outlier: 4.057A pdb=" N ARG e 599 " --> pdb=" O ASP e 595 " (cutoff:3.500A) Processing helix chain 'e' and resid 608 through 612 removed outlier: 3.500A pdb=" N GLU e 611 " --> pdb=" O CYS e 608 " (cutoff:3.500A) Processing helix chain 'e' and resid 620 through 639 Processing helix chain 'f' and resid 12 through 24 Processing helix chain 'f' and resid 53 through 57 Processing helix chain 'f' and resid 62 through 66 removed outlier: 3.698A pdb=" N LYS f 66 " --> pdb=" O GLU f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 106 removed outlier: 4.081A pdb=" N LEU f 106 " --> pdb=" O TRP f 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 102 through 106' Processing helix chain 'g' and resid 7 through 13 Processing helix chain 'g' and resid 24 through 41 Processing helix chain 'g' and resid 46 through 128 Processing helix chain 'g' and resid 134 through 181 removed outlier: 3.878A pdb=" N LEU g 162 " --> pdb=" O ASP g 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 273 through 285 Processing helix chain 'h' and resid 296 through 309 Processing helix chain 'h' and resid 322 through 335 Processing helix chain 'h' and resid 367 through 376 Processing helix chain 'h' and resid 393 through 408 removed outlier: 3.781A pdb=" N ALA h 397 " --> pdb=" O ASP h 393 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 22 Processing helix chain 'i' and resid 30 through 37 Processing helix chain 'i' and resid 45 through 65 Processing helix chain 'i' and resid 71 through 84 Processing helix chain 'i' and resid 92 through 104 Processing helix chain 'i' and resid 106 through 119 Processing helix chain 'i' and resid 134 through 147 Processing helix chain 'i' and resid 152 through 167 Processing helix chain 'i' and resid 231 through 247 removed outlier: 3.611A pdb=" N TYR i 235 " --> pdb=" O ASP i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 248 through 251 removed outlier: 3.538A pdb=" N CYS i 251 " --> pdb=" O PRO i 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 248 through 251' Processing helix chain 'i' and resid 254 through 275 removed outlier: 4.169A pdb=" N LYS i 275 " --> pdb=" O PHE i 271 " (cutoff:3.500A) Processing helix chain 'i' and resid 315 through 333 Processing helix chain 'i' and resid 346 through 366 Processing helix chain 'i' and resid 370 through 392 removed outlier: 3.697A pdb=" N TRP i 391 " --> pdb=" O ASN i 387 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS i 392 " --> pdb=" O TRP i 388 " (cutoff:3.500A) Processing helix chain 'i' and resid 435 through 443 removed outlier: 3.661A pdb=" N ARG i 440 " --> pdb=" O GLU i 436 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU i 441 " --> pdb=" O GLU i 437 " (cutoff:3.500A) Processing helix chain 'i' and resid 489 through 503 removed outlier: 4.213A pdb=" N ARG i 495 " --> pdb=" O ASN i 491 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA i 501 " --> pdb=" O LEU i 497 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG i 502 " --> pdb=" O ARG i 498 " (cutoff:3.500A) Processing helix chain 'i' and resid 517 through 528 removed outlier: 3.620A pdb=" N LYS i 528 " --> pdb=" O ASN i 524 " (cutoff:3.500A) Processing helix chain 'j' and resid 15 through 23 Processing helix chain 'j' and resid 40 through 57 removed outlier: 3.731A pdb=" N ILE j 57 " --> pdb=" O SER j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 73 through 80 removed outlier: 3.696A pdb=" N MET j 80 " --> pdb=" O PHE j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 100 Processing helix chain 'j' and resid 108 through 119 removed outlier: 3.818A pdb=" N SER j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 143 through 156 Processing helix chain 'j' and resid 168 through 180 removed outlier: 3.579A pdb=" N TYR j 172 " --> pdb=" O GLU j 168 " (cutoff:3.500A) Processing helix chain 'j' and resid 189 through 204 Processing helix chain 'j' and resid 206 through 221 Processing helix chain 'j' and resid 225 through 237 Processing helix chain 'j' and resid 241 through 254 removed outlier: 4.518A pdb=" N CYS j 245 " --> pdb=" O PRO j 241 " (cutoff:3.500A) Processing helix chain 'j' and resid 263 through 276 removed outlier: 3.689A pdb=" N TYR j 267 " --> pdb=" O PRO j 263 " (cutoff:3.500A) Processing helix chain 'j' and resid 280 through 288 removed outlier: 3.995A pdb=" N LEU j 284 " --> pdb=" O ASP j 280 " (cutoff:3.500A) Processing helix chain 'j' and resid 293 through 308 removed outlier: 3.523A pdb=" N ALA j 306 " --> pdb=" O GLU j 302 " (cutoff:3.500A) Processing helix chain 'j' and resid 344 through 353 removed outlier: 3.530A pdb=" N ALA j 351 " --> pdb=" O GLY j 347 " (cutoff:3.500A) Processing helix chain 'j' and resid 358 through 367 removed outlier: 3.651A pdb=" N GLN j 367 " --> pdb=" O ASN j 363 " (cutoff:3.500A) Processing helix chain 'j' and resid 376 through 399 Proline residue: j 393 - end of helix Processing helix chain 'j' and resid 425 through 436 Processing helix chain 'j' and resid 441 through 444 removed outlier: 3.641A pdb=" N HIS j 444 " --> pdb=" O HIS j 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 441 through 444' Processing helix chain 'j' and resid 445 through 464 removed outlier: 3.786A pdb=" N PHE j 449 " --> pdb=" O ASP j 445 " (cutoff:3.500A) Processing helix chain 'j' and resid 474 through 496 removed outlier: 5.073A pdb=" N LEU j 492 " --> pdb=" O ASP j 488 " (cutoff:3.500A) Proline residue: j 493 - end of helix Processing helix chain 'j' and resid 503 through 513 removed outlier: 3.898A pdb=" N TRP j 509 " --> pdb=" O SER j 505 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY j 510 " --> pdb=" O GLU j 506 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET j 511 " --> pdb=" O GLU j 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS j 513 " --> pdb=" O TRP j 509 " (cutoff:3.500A) Processing helix chain 'j' and resid 516 through 530 Processing helix chain 'j' and resid 535 through 554 removed outlier: 3.746A pdb=" N LYS j 554 " --> pdb=" O LYS j 550 " (cutoff:3.500A) Processing helix chain 'j' and resid 564 through 575 Processing helix chain 'j' and resid 575 through 591 Processing helix chain 'j' and resid 593 through 601 Processing helix chain 'j' and resid 605 through 622 Processing helix chain 'j' and resid 636 through 653 Processing helix chain 'j' and resid 658 through 670 Processing helix chain 'j' and resid 675 through 686 Processing helix chain 'j' and resid 696 through 703 Processing helix chain 'j' and resid 708 through 713 Processing helix chain 'j' and resid 724 through 736 removed outlier: 3.650A pdb=" N HIS j 736 " --> pdb=" O ALA j 732 " (cutoff:3.500A) Processing helix chain 'j' and resid 738 through 756 removed outlier: 3.776A pdb=" N GLN j 748 " --> pdb=" O LEU j 744 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN j 751 " --> pdb=" O ALA j 747 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE j 754 " --> pdb=" O ARG j 750 " (cutoff:3.500A) Processing helix chain 'j' and resid 764 through 788 Processing helix chain 'j' and resid 789 through 797 removed outlier: 3.526A pdb=" N LYS j 795 " --> pdb=" O GLU j 791 " (cutoff:3.500A) Processing helix chain 'j' and resid 799 through 807 removed outlier: 3.648A pdb=" N CYS j 804 " --> pdb=" O ILE j 800 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN j 805 " --> pdb=" O ASP j 801 " (cutoff:3.500A) Processing helix chain 'j' and resid 810 through 823 Proline residue: j 820 - end of helix Processing helix chain 'j' and resid 861 through 869 Processing helix chain 'j' and resid 878 through 887 Processing helix chain 'j' and resid 900 through 908 Processing helix chain 'j' and resid 929 through 962 removed outlier: 3.679A pdb=" N LEU j 956 " --> pdb=" O VAL j 952 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS j 957 " --> pdb=" O LEU j 953 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU j 958 " --> pdb=" O GLN j 954 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU j 959 " --> pdb=" O ARG j 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN j 962 " --> pdb=" O LEU j 958 " (cutoff:3.500A) Processing helix chain 'j' and resid 972 through 989 removed outlier: 4.109A pdb=" N PHE j 977 " --> pdb=" O THR j 973 " (cutoff:3.500A) Proline residue: j 984 - end of helix removed outlier: 3.986A pdb=" N SER j 989 " --> pdb=" O ARG j 985 " (cutoff:3.500A) Processing helix chain 'j' and resid 989 through 1006 removed outlier: 3.540A pdb=" N VAL j1000 " --> pdb=" O CYS j 996 " (cutoff:3.500A) Processing helix chain 'j' and resid 1013 through 1023 removed outlier: 3.617A pdb=" N ASP j1023 " --> pdb=" O ARG j1019 " (cutoff:3.500A) Processing helix chain 'j' and resid 1023 through 1030 removed outlier: 4.166A pdb=" N THR j1027 " --> pdb=" O ASP j1023 " (cutoff:3.500A) Processing helix chain 'j' and resid 1034 through 1053 removed outlier: 3.735A pdb=" N PHE j1042 " --> pdb=" O ARG j1038 " (cutoff:3.500A) Processing helix chain 'j' and resid 1091 through 1113 Processing helix chain 'j' and resid 1116 through 1130 removed outlier: 3.919A pdb=" N ILE j1120 " --> pdb=" O GLU j1116 " (cutoff:3.500A) Processing helix chain 'j' and resid 1138 through 1154 removed outlier: 3.672A pdb=" N GLU j1154 " --> pdb=" O LYS j1150 " (cutoff:3.500A) Processing helix chain 'j' and resid 1161 through 1176 Processing helix chain 'k' and resid 32 through 45 removed outlier: 3.612A pdb=" N LEU k 36 " --> pdb=" O SER k 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 255 removed outlier: 4.031A pdb=" N MET l 254 " --> pdb=" O TYR l 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP l 255 " --> pdb=" O ASN l 251 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 76 Processing helix chain 'm' and resid 81 through 148 removed outlier: 3.853A pdb=" N ALA m 119 " --> pdb=" O GLN m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 161 through 169 Processing helix chain 'm' and resid 170 through 175 Processing helix chain 'm' and resid 176 through 179 Processing helix chain 'm' and resid 183 through 240 Proline residue: m 231 - end of helix Processing helix chain 'm' and resid 244 through 248 Processing helix chain 'm' and resid 260 through 264 removed outlier: 3.597A pdb=" N HIS m 263 " --> pdb=" O THR m 260 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU m 264 " --> pdb=" O ALA m 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 260 through 264' Processing helix chain 'm' and resid 265 through 282 removed outlier: 3.556A pdb=" N CYS m 282 " --> pdb=" O TYR m 278 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 299 removed outlier: 3.848A pdb=" N ALA m 299 " --> pdb=" O ASP m 295 " (cutoff:3.500A) Processing helix chain 'm' and resid 335 through 342 Processing helix chain 'm' and resid 415 through 425 removed outlier: 3.864A pdb=" N GLN m 419 " --> pdb=" O ASN m 415 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL m 425 " --> pdb=" O GLN m 421 " (cutoff:3.500A) Processing helix chain 'm' and resid 431 through 438 Processing helix chain 'm' and resid 441 through 449 removed outlier: 3.916A pdb=" N GLN m 445 " --> pdb=" O TYR m 441 " (cutoff:3.500A) Processing helix chain 'm' and resid 471 through 497 Processing helix chain 'm' and resid 506 through 511 removed outlier: 4.351A pdb=" N TYR m 509 " --> pdb=" O ASP m 506 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE m 511 " --> pdb=" O GLN m 508 " (cutoff:3.500A) Processing helix chain 'm' and resid 526 through 532 Processing helix chain 'm' and resid 536 through 543 removed outlier: 3.756A pdb=" N VAL m 540 " --> pdb=" O THR m 536 " (cutoff:3.500A) Processing helix chain 'm' and resid 595 through 607 removed outlier: 4.057A pdb=" N ARG m 599 " --> pdb=" O ASP m 595 " (cutoff:3.500A) Processing helix chain 'm' and resid 608 through 612 Processing helix chain 'm' and resid 620 through 639 Processing helix chain 'n' and resid 12 through 24 Processing helix chain 'n' and resid 53 through 57 Processing helix chain 'n' and resid 62 through 66 removed outlier: 3.694A pdb=" N LYS n 66 " --> pdb=" O GLU n 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 102 through 106 removed outlier: 4.081A pdb=" N LEU n 106 " --> pdb=" O TRP n 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 106' Processing helix chain 'o' and resid 7 through 13 Processing helix chain 'o' and resid 24 through 41 Processing helix chain 'o' and resid 47 through 127 removed outlier: 3.900A pdb=" N LEU o 68 " --> pdb=" O MET o 64 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU o 69 " --> pdb=" O GLY o 65 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU o 87 " --> pdb=" O LYS o 83 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU o 97 " --> pdb=" O ALA o 93 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL o 125 " --> pdb=" O ALA o 121 " (cutoff:3.500A) Processing helix chain 'o' and resid 132 through 181 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 69 through 80 Proline residue: p 77 - end of helix Processing helix chain 'p' and resid 94 through 107 removed outlier: 3.887A pdb=" N VAL p 98 " --> pdb=" O GLY p 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE p 99 " --> pdb=" O LYS p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 122 through 137 Processing helix chain 'p' and resid 153 through 163 removed outlier: 3.730A pdb=" N ASP p 157 " --> pdb=" O SER p 153 " (cutoff:3.500A) Processing helix chain 'p' and resid 172 through 182 Processing helix chain 'p' and resid 197 through 204 Processing helix chain 'p' and resid 204 through 218 removed outlier: 3.548A pdb=" N MET p 217 " --> pdb=" O GLU p 213 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR p 218 " --> pdb=" O ILE p 214 " (cutoff:3.500A) Processing helix chain 'p' and resid 234 through 241 removed outlier: 4.423A pdb=" N VAL p 238 " --> pdb=" O GLU p 234 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS p 241 " --> pdb=" O PRO p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 273 through 285 Processing helix chain 'p' and resid 296 through 309 Processing helix chain 'p' and resid 322 through 335 Processing helix chain 'p' and resid 367 through 376 Processing helix chain 'p' and resid 393 through 408 removed outlier: 3.781A pdb=" N ALA p 397 " --> pdb=" O ASP p 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 54 removed outlier: 3.773A pdb=" N LYS C 47 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 346 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 53 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY C 340 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 312 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.511A pdb=" N SER C 60 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 79 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 83 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS C 91 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 107 removed outlier: 3.692A pdb=" N SER C 119 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 124 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR C 137 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 126 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 149 removed outlier: 6.766A pdb=" N GLY C 159 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE C 147 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 157 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP C 149 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 155 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 164 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 165 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 178 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C 167 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 185 through 190 removed outlier: 4.498A pdb=" N GLU C 187 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER C 210 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 227 through 232 removed outlier: 3.693A pdb=" N CYS C 229 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 260 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP C 252 " --> pdb=" O CYS C 258 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N CYS C 258 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 274 Processing sheet with id=AA8, first strand: chain 'E' and resid 286 through 291 removed outlier: 4.196A pdb=" N SER E 358 " --> pdb=" O CYS E 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 518 through 525 removed outlier: 5.897A pdb=" N LEU E 519 " --> pdb=" O GLU E 557 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU E 557 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS E 521 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR E 551 " --> pdb=" O ILE E 525 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS E 562 " --> pdb=" O ASN E 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 672 through 674 Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 32 removed outlier: 3.893A pdb=" N VAL F 70 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.687A pdb=" N SER F 81 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 129 through 135 removed outlier: 3.528A pdb=" N ALA F 144 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 135 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER F 140 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG F 162 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP F 154 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE F 160 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 171 through 174 removed outlier: 7.072A pdb=" N GLY F 186 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU F 174 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 184 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY F 187 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA F 191 " --> pdb=" O GLY F 187 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN F 204 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 223 through 225 removed outlier: 7.018A pdb=" N GLY F 236 " --> pdb=" O GLY F 224 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU F 241 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 253 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS F 245 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 261 through 266 removed outlier: 5.036A pdb=" N GLY F 275 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS F 279 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN F 284 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU F 289 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 300 through 305 removed outlier: 6.688A pdb=" N ALA F 320 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU F 303 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR F 318 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY F 321 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG F 325 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 337 " --> pdb=" O VAL F 328 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 314 through 317 removed outlier: 6.562A pdb=" N VAL H 290 " --> pdb=" O LEU H 341 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA H 343 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE H 292 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN H 289 " --> pdb=" O VAL H 356 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 358 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN H 263 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR H 389 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR H 265 " --> pdb=" O THR H 389 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL H 391 " --> pdb=" O TYR H 265 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL H 267 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N SER H 412 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN H 264 " --> pdb=" O SER H 412 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 47 through 54 removed outlier: 3.772A pdb=" N LYS K 47 " --> pdb=" O GLY K 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY K 346 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA K 53 " --> pdb=" O GLY K 340 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLY K 340 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR K 312 " --> pdb=" O ALA K 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 58 through 63 removed outlier: 3.512A pdb=" N SER K 60 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA K 79 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU K 83 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS K 91 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 102 through 107 removed outlier: 3.691A pdb=" N SER K 119 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE K 124 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR K 137 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE K 126 " --> pdb=" O ILE K 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 144 through 149 removed outlier: 6.764A pdb=" N GLY K 159 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE K 147 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA K 157 " --> pdb=" O ILE K 147 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP K 149 " --> pdb=" O THR K 155 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR K 155 " --> pdb=" O TRP K 149 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL K 164 " --> pdb=" O ASN K 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL K 165 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU K 178 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE K 167 " --> pdb=" O LYS K 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 185 through 190 removed outlier: 4.501A pdb=" N GLU K 187 " --> pdb=" O THR K 200 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER K 210 " --> pdb=" O PRO K 216 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 227 through 232 removed outlier: 3.691A pdb=" N CYS K 229 " --> pdb=" O GLY K 242 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG K 260 " --> pdb=" O LEU K 250 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP K 252 " --> pdb=" O CYS K 258 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N CYS K 258 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 269 through 274 Processing sheet with id=AC8, first strand: chain 'M' and resid 286 through 291 Processing sheet with id=AC9, first strand: chain 'M' and resid 518 through 525 removed outlier: 5.894A pdb=" N LEU M 519 " --> pdb=" O GLU M 557 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU M 557 " --> pdb=" O LEU M 519 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS M 521 " --> pdb=" O LEU M 555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR M 551 " --> pdb=" O ILE M 525 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS M 562 " --> pdb=" O ASN M 585 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 672 through 674 Processing sheet with id=AD2, first strand: chain 'N' and resid 30 through 32 removed outlier: 3.890A pdb=" N VAL N 70 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 81 through 84 removed outlier: 3.688A pdb=" N SER N 81 " --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 129 through 135 removed outlier: 3.529A pdb=" N ALA N 144 " --> pdb=" O ALA N 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL N 135 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER N 140 " --> pdb=" O VAL N 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG N 162 " --> pdb=" O THR N 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP N 154 " --> pdb=" O PHE N 160 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE N 160 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 171 through 174 removed outlier: 7.070A pdb=" N GLY N 186 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU N 174 " --> pdb=" O LEU N 184 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU N 184 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY N 187 " --> pdb=" O ALA N 191 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA N 191 " --> pdb=" O GLY N 187 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN N 204 " --> pdb=" O LEU N 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 223 through 225 removed outlier: 7.017A pdb=" N GLY N 236 " --> pdb=" O GLY N 224 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU N 241 " --> pdb=" O ILE N 254 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE N 254 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU N 243 " --> pdb=" O THR N 252 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR N 250 " --> pdb=" O HIS N 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 261 through 266 removed outlier: 5.037A pdb=" N GLY N 275 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS N 279 " --> pdb=" O GLY N 275 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN N 284 " --> pdb=" O LEU N 289 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU N 289 " --> pdb=" O GLN N 284 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 300 through 305 removed outlier: 6.689A pdb=" N ALA N 320 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU N 303 " --> pdb=" O THR N 318 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR N 318 " --> pdb=" O LEU N 303 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY N 321 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG N 325 " --> pdb=" O GLY N 321 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE N 337 " --> pdb=" O VAL N 328 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 145 through 148 removed outlier: 6.311A pdb=" N ALA P 146 " --> pdb=" O VAL P 170 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL P 116 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLY P 171 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL P 118 " --> pdb=" O GLY P 171 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU P 117 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP P 196 " --> pdb=" O LEU P 117 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET P 119 " --> pdb=" O ASP P 196 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 314 through 317 removed outlier: 6.562A pdb=" N VAL P 290 " --> pdb=" O LEU P 341 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA P 343 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE P 292 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN P 289 " --> pdb=" O VAL P 356 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE P 358 " --> pdb=" O GLN P 289 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN P 263 " --> pdb=" O ALA P 387 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR P 389 " --> pdb=" O GLN P 263 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR P 265 " --> pdb=" O THR P 389 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL P 391 " --> pdb=" O TYR P 265 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL P 267 " --> pdb=" O VAL P 391 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N SER P 412 " --> pdb=" O LEU P 262 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN P 264 " --> pdb=" O SER P 412 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 47 through 54 removed outlier: 3.771A pdb=" N LYS c 47 " --> pdb=" O GLY c 346 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY c 346 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA c 53 " --> pdb=" O GLY c 340 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY c 340 " --> pdb=" O ALA c 53 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR c 312 " --> pdb=" O ALA c 325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 58 through 63 removed outlier: 3.510A pdb=" N SER c 60 " --> pdb=" O GLY c 73 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR c 78 " --> pdb=" O SER c 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA c 79 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU c 83 " --> pdb=" O LYS c 91 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS c 91 " --> pdb=" O LEU c 83 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 102 through 107 removed outlier: 3.692A pdb=" N SER c 119 " --> pdb=" O THR c 123 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE c 124 " --> pdb=" O THR c 137 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR c 137 " --> pdb=" O ILE c 124 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE c 126 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 144 through 149 removed outlier: 6.766A pdb=" N GLY c 159 " --> pdb=" O ILE c 145 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE c 147 " --> pdb=" O ALA c 157 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA c 157 " --> pdb=" O ILE c 147 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP c 149 " --> pdb=" O THR c 155 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR c 155 " --> pdb=" O TRP c 149 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL c 164 " --> pdb=" O ASN c 160 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL c 165 " --> pdb=" O GLU c 178 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU c 178 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE c 167 " --> pdb=" O LYS c 176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 185 through 190 removed outlier: 4.498A pdb=" N GLU c 187 " --> pdb=" O THR c 200 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER c 210 " --> pdb=" O PRO c 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 227 through 232 removed outlier: 3.692A pdb=" N CYS c 229 " --> pdb=" O GLY c 242 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG c 260 " --> pdb=" O LEU c 250 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP c 252 " --> pdb=" O CYS c 258 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS c 258 " --> pdb=" O ASP c 252 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 269 through 274 Processing sheet with id=AE9, first strand: chain 'e' and resid 286 through 291 Processing sheet with id=AF1, first strand: chain 'e' and resid 518 through 525 removed outlier: 5.896A pdb=" N LEU e 519 " --> pdb=" O GLU e 557 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU e 557 " --> pdb=" O LEU e 519 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS e 521 " --> pdb=" O LEU e 555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR e 551 " --> pdb=" O ILE e 525 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS e 562 " --> pdb=" O ASN e 585 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'e' and resid 672 through 674 Processing sheet with id=AF3, first strand: chain 'f' and resid 30 through 32 removed outlier: 3.895A pdb=" N VAL f 70 " --> pdb=" O ILE f 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 81 through 84 removed outlier: 3.693A pdb=" N SER f 81 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 129 through 135 removed outlier: 3.529A pdb=" N ALA f 144 " --> pdb=" O ALA f 131 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL f 135 " --> pdb=" O SER f 140 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER f 140 " --> pdb=" O VAL f 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG f 162 " --> pdb=" O THR f 152 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP f 154 " --> pdb=" O PHE f 160 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE f 160 " --> pdb=" O ASP f 154 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 171 through 174 removed outlier: 7.072A pdb=" N GLY f 186 " --> pdb=" O HIS f 172 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU f 174 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU f 184 " --> pdb=" O LEU f 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY f 187 " --> pdb=" O ALA f 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA f 191 " --> pdb=" O GLY f 187 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN f 204 " --> pdb=" O LEU f 194 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 223 through 225 removed outlier: 7.022A pdb=" N GLY f 236 " --> pdb=" O GLY f 224 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU f 241 " --> pdb=" O PHE f 255 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR f 253 " --> pdb=" O LEU f 243 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS f 245 " --> pdb=" O PRO f 251 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'f' and resid 261 through 266 removed outlier: 5.037A pdb=" N GLY f 275 " --> pdb=" O CYS f 279 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS f 279 " --> pdb=" O GLY f 275 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN f 284 " --> pdb=" O LEU f 289 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU f 289 " --> pdb=" O GLN f 284 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'f' and resid 300 through 305 removed outlier: 6.688A pdb=" N ALA f 320 " --> pdb=" O LEU f 301 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU f 303 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR f 318 " --> pdb=" O LEU f 303 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY f 321 " --> pdb=" O ARG f 325 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG f 325 " --> pdb=" O GLY f 321 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE f 337 " --> pdb=" O VAL f 328 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 314 through 317 removed outlier: 6.564A pdb=" N VAL h 290 " --> pdb=" O LEU h 341 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA h 343 " --> pdb=" O VAL h 290 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE h 292 " --> pdb=" O ALA h 343 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN h 289 " --> pdb=" O VAL h 356 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE h 358 " --> pdb=" O GLN h 289 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN h 263 " --> pdb=" O ALA h 387 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR h 389 " --> pdb=" O GLN h 263 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR h 265 " --> pdb=" O THR h 389 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL h 391 " --> pdb=" O TYR h 265 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL h 267 " --> pdb=" O VAL h 391 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N SER h 412 " --> pdb=" O LEU h 262 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN h 264 " --> pdb=" O SER h 412 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 47 through 54 removed outlier: 3.772A pdb=" N LYS k 47 " --> pdb=" O GLY k 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY k 346 " --> pdb=" O LYS k 47 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA k 53 " --> pdb=" O GLY k 340 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLY k 340 " --> pdb=" O ALA k 53 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR k 312 " --> pdb=" O ALA k 325 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'k' and resid 58 through 63 removed outlier: 3.512A pdb=" N SER k 60 " --> pdb=" O GLY k 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR k 78 " --> pdb=" O SER k 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA k 79 " --> pdb=" O TYR k 95 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU k 83 " --> pdb=" O LYS k 91 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS k 91 " --> pdb=" O LEU k 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'k' and resid 102 through 107 removed outlier: 3.691A pdb=" N SER k 119 " --> pdb=" O THR k 123 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR k 123 " --> pdb=" O SER k 119 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE k 124 " --> pdb=" O THR k 137 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR k 137 " --> pdb=" O ILE k 124 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE k 126 " --> pdb=" O ILE k 135 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 144 through 149 removed outlier: 6.764A pdb=" N GLY k 159 " --> pdb=" O ILE k 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE k 147 " --> pdb=" O ALA k 157 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA k 157 " --> pdb=" O ILE k 147 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP k 149 " --> pdb=" O THR k 155 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR k 155 " --> pdb=" O TRP k 149 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL k 164 " --> pdb=" O ASN k 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL k 165 " --> pdb=" O GLU k 178 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU k 178 " --> pdb=" O VAL k 165 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE k 167 " --> pdb=" O LYS k 176 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 185 through 190 removed outlier: 4.499A pdb=" N GLU k 187 " --> pdb=" O THR k 200 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER k 210 " --> pdb=" O PRO k 216 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 227 through 232 removed outlier: 3.692A pdb=" N CYS k 229 " --> pdb=" O GLY k 242 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG k 260 " --> pdb=" O LEU k 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP k 252 " --> pdb=" O CYS k 258 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N CYS k 258 " --> pdb=" O ASP k 252 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 269 through 274 Processing sheet with id=AG9, first strand: chain 'm' and resid 286 through 291 Processing sheet with id=AH1, first strand: chain 'm' and resid 518 through 525 removed outlier: 5.896A pdb=" N LEU m 519 " --> pdb=" O GLU m 557 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU m 557 " --> pdb=" O LEU m 519 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS m 521 " --> pdb=" O LEU m 555 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR m 551 " --> pdb=" O ILE m 525 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS m 562 " --> pdb=" O ASN m 585 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 672 through 674 Processing sheet with id=AH3, first strand: chain 'n' and resid 30 through 32 removed outlier: 3.895A pdb=" N VAL n 70 " --> pdb=" O ILE n 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 81 through 84 removed outlier: 3.689A pdb=" N SER n 81 " --> pdb=" O ALA n 92 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 129 through 135 removed outlier: 3.529A pdb=" N ALA n 144 " --> pdb=" O ALA n 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL n 135 " --> pdb=" O SER n 140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER n 140 " --> pdb=" O VAL n 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG n 162 " --> pdb=" O THR n 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP n 154 " --> pdb=" O PHE n 160 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE n 160 " --> pdb=" O ASP n 154 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 171 through 174 removed outlier: 7.070A pdb=" N GLY n 186 " --> pdb=" O HIS n 172 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU n 174 " --> pdb=" O LEU n 184 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU n 184 " --> pdb=" O LEU n 174 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY n 187 " --> pdb=" O ALA n 191 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA n 191 " --> pdb=" O GLY n 187 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN n 204 " --> pdb=" O LEU n 194 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'n' and resid 223 through 225 removed outlier: 7.019A pdb=" N GLY n 236 " --> pdb=" O GLY n 224 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU n 241 " --> pdb=" O PHE n 255 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR n 253 " --> pdb=" O LEU n 243 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS n 245 " --> pdb=" O PRO n 251 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'n' and resid 261 through 266 removed outlier: 5.038A pdb=" N GLY n 275 " --> pdb=" O CYS n 279 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS n 279 " --> pdb=" O GLY n 275 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN n 284 " --> pdb=" O LEU n 289 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU n 289 " --> pdb=" O GLN n 284 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 300 through 305 removed outlier: 6.690A pdb=" N ALA n 320 " --> pdb=" O LEU n 301 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU n 303 " --> pdb=" O THR n 318 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR n 318 " --> pdb=" O LEU n 303 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY n 321 " --> pdb=" O ARG n 325 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG n 325 " --> pdb=" O GLY n 321 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE n 337 " --> pdb=" O VAL n 328 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'p' and resid 145 through 148 removed outlier: 6.309A pdb=" N ALA p 146 " --> pdb=" O VAL p 170 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL p 116 " --> pdb=" O VAL p 169 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY p 171 " --> pdb=" O VAL p 116 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL p 118 " --> pdb=" O GLY p 171 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU p 117 " --> pdb=" O ILE p 194 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP p 196 " --> pdb=" O LEU p 117 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET p 119 " --> pdb=" O ASP p 196 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'p' and resid 314 through 317 removed outlier: 6.561A pdb=" N VAL p 290 " --> pdb=" O LEU p 341 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA p 343 " --> pdb=" O VAL p 290 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE p 292 " --> pdb=" O ALA p 343 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN p 289 " --> pdb=" O VAL p 356 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE p 358 " --> pdb=" O GLN p 289 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN p 263 " --> pdb=" O ALA p 387 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR p 389 " --> pdb=" O GLN p 263 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR p 265 " --> pdb=" O THR p 389 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL p 391 " --> pdb=" O TYR p 265 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL p 267 " --> pdb=" O VAL p 391 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N SER p 412 " --> pdb=" O LEU p 262 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN p 264 " --> pdb=" O SER p 412 " (cutoff:3.500A) 5334 hydrogen bonds defined for protein. 15762 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: 44.20 Time building geometry restraints manager: 29.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 13436 1.25 - 1.39: 22717 1.39 - 1.53: 50650 1.53 - 1.68: 2364 1.68 - 1.82: 719 Bond restraints: 89886 Sorted by residual: bond pdb=" C GLU e 86 " pdb=" N ARG e 87 " ideal model delta sigma weight residual 1.334 1.105 0.229 1.27e-02 6.20e+03 3.26e+02 bond pdb=" C GLU E 86 " pdb=" N ARG E 87 " ideal model delta sigma weight residual 1.334 1.106 0.228 1.27e-02 6.20e+03 3.22e+02 bond pdb=" C ARG l 253 " pdb=" N MET l 254 " ideal model delta sigma weight residual 1.335 1.204 0.131 1.36e-02 5.41e+03 9.30e+01 bond pdb=" C ARG L 253 " pdb=" N MET L 254 " ideal model delta sigma weight residual 1.335 1.204 0.131 1.36e-02 5.41e+03 9.21e+01 bond pdb=" C SER j 234 " pdb=" N TYR j 235 " ideal model delta sigma weight residual 1.334 1.202 0.132 1.41e-02 5.03e+03 8.75e+01 ... (remaining 89881 not shown) Histogram of bond angle deviations from ideal: 94.19 - 102.28: 255 102.28 - 110.36: 21330 110.36 - 118.45: 49512 118.45 - 126.53: 49327 126.53 - 134.62: 1321 Bond angle restraints: 121745 Sorted by residual: angle pdb=" C ARG l 253 " pdb=" N MET l 254 " pdb=" CA MET l 254 " ideal model delta sigma weight residual 120.29 134.32 -14.03 1.42e+00 4.96e-01 9.77e+01 angle pdb=" C ARG L 253 " pdb=" N MET L 254 " pdb=" CA MET L 254 " ideal model delta sigma weight residual 120.29 134.29 -14.00 1.42e+00 4.96e-01 9.72e+01 angle pdb=" CA ASP P 199 " pdb=" CB ASP P 199 " pdb=" CG ASP P 199 " ideal model delta sigma weight residual 112.60 104.57 8.03 1.00e+00 1.00e+00 6.45e+01 angle pdb=" CA ASP p 199 " pdb=" CB ASP p 199 " pdb=" CG ASP p 199 " ideal model delta sigma weight residual 112.60 104.61 7.99 1.00e+00 1.00e+00 6.39e+01 angle pdb=" CA PHE P 242 " pdb=" CB PHE P 242 " pdb=" CG PHE P 242 " ideal model delta sigma weight residual 113.80 105.81 7.99 1.00e+00 1.00e+00 6.39e+01 ... (remaining 121740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.41: 51310 18.41 - 36.81: 2121 36.81 - 55.22: 492 55.22 - 73.62: 146 73.62 - 92.03: 32 Dihedral angle restraints: 54101 sinusoidal: 20177 harmonic: 33924 Sorted by residual: dihedral pdb=" CA LYS B 562 " pdb=" C LYS B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta harmonic sigma weight residual 180.00 130.96 49.04 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" CA LYS j 562 " pdb=" C LYS j 562 " pdb=" N PRO j 563 " pdb=" CA PRO j 563 " ideal model delta harmonic sigma weight residual 180.00 131.00 49.00 0 5.00e+00 4.00e-02 9.60e+01 dihedral pdb=" CA LYS b 562 " pdb=" C LYS b 562 " pdb=" N PRO b 563 " pdb=" CA PRO b 563 " ideal model delta harmonic sigma weight residual 180.00 131.02 48.98 0 5.00e+00 4.00e-02 9.60e+01 ... (remaining 54098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 13545 0.112 - 0.224: 407 0.224 - 0.337: 20 0.337 - 0.449: 14 0.449 - 0.561: 4 Chirality restraints: 13990 Sorted by residual: chirality pdb=" CA PRO p 166 " pdb=" N PRO p 166 " pdb=" C PRO p 166 " pdb=" CB PRO p 166 " both_signs ideal model delta sigma weight residual False 2.72 2.16 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA PRO P 166 " pdb=" N PRO P 166 " pdb=" C PRO P 166 " pdb=" CB PRO P 166 " both_signs ideal model delta sigma weight residual False 2.72 2.16 0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" CA PRO p 109 " pdb=" N PRO p 109 " pdb=" C PRO p 109 " pdb=" CB PRO p 109 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 13987 not shown) Planarity restraints: 15581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS P 67 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO P 68 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO P 68 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO P 68 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS p 67 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO p 68 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO p 68 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO p 68 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU j 788 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LEU j 788 " 0.067 2.00e-02 2.50e+03 pdb=" O LEU j 788 " -0.025 2.00e-02 2.50e+03 pdb=" N SER j 789 " -0.023 2.00e-02 2.50e+03 ... (remaining 15578 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 118 2.35 - 2.98: 42688 2.98 - 3.62: 129294 3.62 - 4.26: 191527 4.26 - 4.90: 323513 Nonbonded interactions: 687140 Sorted by model distance: nonbonded pdb=" O2 U 2 1 " pdb=" OD2 ASP P 206 " model vdw 1.707 3.040 nonbonded pdb=" O2 U 4 1 " pdb=" OD2 ASP p 206 " model vdw 1.708 3.040 nonbonded pdb=" N ASP B 426 " pdb=" OD1 ASP B 426 " model vdw 2.171 2.520 nonbonded pdb=" N ASP j 426 " pdb=" OD1 ASP j 426 " model vdw 2.171 2.520 nonbonded pdb=" N ASP b 426 " pdb=" OD1 ASP b 426 " model vdw 2.172 2.520 ... (remaining 687135 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 '2' selection = chain '4' } ncs_group { reference = (chain 'A' and (resid 10 through 392 or resid 418 through 528)) selection = (chain 'I' and (resid 10 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 120 or resid 133 through 278 or re \ sid 296 through 528)) selection = (chain 'a' and (resid 10 through 392 or resid 418 through 528)) selection = (chain 'i' and (resid 10 through 37 or (resid 38 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 64 or (resid 65 and (na \ me N or name CA or name C or name O or name CB )) or resid 71 through 120 or res \ id 133 through 278 or resid 296 through 528)) } ncs_group { reference = (chain 'B' and (resid 14 through 158 or resid 164 through 165 or (resid 166 thro \ ugh 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 1177)) selection = chain 'J' selection = (chain 'b' and (resid 14 through 158 or resid 164 through 165 or (resid 166 thro \ ugh 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 1177)) selection = chain 'j' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'E' and (resid 46 through 240 or resid 243 through 247 or resid 253 or re \ sid 258 through 299 or resid 334 through 453 or resid 466 or resid 471 through 6 \ 42 or resid 659 through 675 or resid 678 through 683)) selection = (chain 'M' and (resid 50 through 75 or (resid 80 through 111 and (name N or name \ CA or name C or name O or name CB )) or resid 112 or (resid 113 through 144 and \ (name N or name CA or name C or name O or name CB )) or (resid 189 through 247 \ and (name N or name CA or name C or name O or name CB )) or (resid 257 and (name \ N or name CA or name C or name O or name CB )) or resid 258 through 425 or resi \ d 430 through 453 or resid 470 through 675 or resid 678 through 683)) selection = (chain 'e' and (resid 46 through 240 or resid 243 through 247 or resid 253 or re \ sid 258 through 299 or resid 334 through 453 or resid 466 or resid 471 through 6 \ 83)) selection = (chain 'm' and (resid 50 through 75 or (resid 80 through 111 and (name N or name \ CA or name C or name O or name CB )) or resid 112 or (resid 113 through 144 and \ (name N or name CA or name C or name O or name CB )) or (resid 189 through 247 \ and (name N or name CA or name C or name O or name CB )) or (resid 257 and (name \ N or name CA or name C or name O or name CB )) or resid 258 through 425 or resi \ d 430 through 453 or resid 470 through 675 or resid 678 through 683)) } ncs_group { reference = (chain 'F' and (resid 5 through 119 or resid 128 through 341)) selection = (chain 'N' and (resid 5 through 119 or resid 128 through 341)) selection = chain 'f' selection = (chain 'n' and (resid 5 through 119 or resid 128 through 341)) } ncs_group { reference = (chain 'G' and (resid 6 through 41 or resid 46 through 181)) selection = (chain 'O' and ((resid 6 through 64 and (name N or name CA or name C or name O o \ r name CB )) or resid 65 or (resid 66 through 93 and (name N or name CA or name \ C or name O or name CB )) or (resid 94 through 129 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 134 through 142 and (name N or name CA or \ name C or name O or name CB )) or resid 143 through 181)) selection = (chain 'g' and (resid 6 through 41 or resid 46 through 181)) selection = (chain 'o' and ((resid 6 through 64 and (name N or name CA or name C or name O o \ r name CB )) or resid 65 or (resid 66 through 93 and (name N or name CA or name \ C or name O or name CB )) or (resid 94 through 129 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 134 through 142 and (name N or name CA or \ name C or name O or name CB )) or resid 143 through 181)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'P' selection = chain 'p' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 18.090 Check model and map are aligned: 0.990 Set scattering table: 0.600 Process input model: 188.370 Find NCS groups from input model: 5.560 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4791 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 : 0.006 0.229 89886 Z= 0.384 Angle : 0.884 14.034 121745 Z= 0.535 Chirality : 0.048 0.561 13990 Planarity : 0.006 0.106 15581 Dihedral : 11.830 92.027 31895 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.43 % Favored : 93.29 % Rotamer: Outliers : 5.83 % Allowed : 6.01 % Favored : 88.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.18 % 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 (0.07), residues: 11143 helix: -0.52 (0.06), residues: 6138 sheet: -0.60 (0.13), residues: 1400 loop : -3.23 (0.08), residues: 3605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2697 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 515 poor density : 2182 time to evaluate : 7.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 515 outliers final: 76 residues processed: 2548 average time/residue: 0.8834 time to fit residues: 3840.7271 Evaluate side-chains 1451 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1375 time to evaluate : 7.609 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 76 outliers final: 1 residues processed: 76 average time/residue: 0.7443 time to fit residues: 112.0124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 965 optimal weight: 6.9990 chunk 866 optimal weight: 7.9990 chunk 480 optimal weight: 5.9990 chunk 295 optimal weight: 0.0060 chunk 584 optimal weight: 0.9990 chunk 462 optimal weight: 20.0000 chunk 895 optimal weight: 0.6980 chunk 346 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 666 optimal weight: 6.9990 chunk 1037 optimal weight: 2.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 514 GLN A 524 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 224 HIS B 246 HIS ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN B 376 HIS ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 526 GLN ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 575 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 640 GLN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 ASN B 805 ASN B 945 GLN B1054 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 HIS C 349 ASN E 274 GLN E 361 HIS E 369 ASN E 492 GLN F 18 GLN F 44 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 HIS F 261 GLN ** H 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 HIS ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 141 ASN I 242 GLN I 387 ASN I 512 ASN J 145 ASN J 204 ASN J 224 HIS J 256 GLN ** J 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN J 441 HIS J 489 GLN J 526 GLN J 535 HIS J 567 GLN J 575 ASN ** J 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 608 ASN J 640 GLN J 727 GLN ** J 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 749 GLN ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 779 GLN J 787 ASN J 805 ASN J 945 GLN K 195 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 HIS K 305 GLN K 316 HIS M 186 GLN M 369 ASN M 492 GLN M 597 ASN N 149 GLN N 172 HIS N 261 GLN N 263 HIS P 67 HIS ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 GLN ** P 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 GLN P 192 HIS P 323 GLN P 331 GLN ** P 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 GLN P 361 ASN P 404 GLN ** a 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 320 HIS a 367 ASN a 389 ASN ** a 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 512 ASN a 524 ASN b 224 HIS b 246 HIS ** b 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 367 GLN b 441 HIS b 464 GLN b 489 GLN b 526 GLN ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 575 ASN ** b 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 640 GLN ** b 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 787 ASN b 805 ASN ** b 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 945 GLN ** b1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1054 HIS ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 201 ASN ** c 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 316 HIS c 349 ASN e 274 GLN e 369 ASN e 492 GLN ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 HIS f 172 HIS f 261 GLN h 264 GLN ** h 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 318 HIS ** h 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 395 ASN i 53 GLN i 141 ASN ** i 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 387 ASN i 512 ASN j 145 ASN j 204 ASN j 224 HIS j 246 HIS j 256 GLN j 362 GLN j 367 GLN j 441 HIS j 489 GLN j 526 GLN j 535 HIS j 567 GLN ** j 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 608 ASN j 630 HIS j 727 GLN j 756 GLN j 787 ASN j 805 ASN j 945 GLN k 59 HIS k 146 ASN k 173 HIS k 191 ASN ** k 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 HIS ** k 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 492 GLN m 675 HIS ** n 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 149 GLN n 172 HIS n 261 GLN n 263 HIS p 67 HIS ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 113 GLN p 128 GLN p 192 HIS p 323 GLN p 331 GLN p 404 GLN Total number of N/Q/H flips: 147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 89886 Z= 0.270 Angle : 0.806 15.428 121745 Z= 0.405 Chirality : 0.044 0.335 13990 Planarity : 0.006 0.124 15581 Dihedral : 5.464 88.497 12259 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 3.62 % Allowed : 14.75 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.13 % 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: -0.48 (0.08), residues: 11143 helix: 0.99 (0.06), residues: 6248 sheet: -0.29 (0.13), residues: 1437 loop : -2.83 (0.09), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1736 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1416 time to evaluate : 7.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 320 outliers final: 158 residues processed: 1631 average time/residue: 0.8521 time to fit residues: 2403.4326 Evaluate side-chains 1370 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1212 time to evaluate : 7.780 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 158 outliers final: 1 residues processed: 158 average time/residue: 0.7371 time to fit residues: 222.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 576 optimal weight: 0.7980 chunk 322 optimal weight: 20.0000 chunk 863 optimal weight: 0.8980 chunk 706 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 1039 optimal weight: 3.9990 chunk 1123 optimal weight: 20.0000 chunk 926 optimal weight: 9.9990 chunk 1031 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 834 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 HIS ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 524 ASN ** J 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 684 GLN J 772 GLN J 779 GLN J 979 GLN K 186 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 ASN M 508 GLN N 149 GLN N 151 HIS ** P 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 361 ASN a 349 GLN ** a 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 592 ASN ** b 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1110 HIS ** b1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** c 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 18 GLN ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 242 GLN i 524 ASN ** j 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 684 GLN j 774 HIS ** k 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 186 ASN ** k 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 HIS k 226 ASN ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 88 HIS n 149 GLN o 128 HIS p 332 GLN ** p 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5169 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 89886 Z= 0.231 Angle : 0.758 15.831 121745 Z= 0.375 Chirality : 0.043 0.294 13990 Planarity : 0.005 0.145 15581 Dihedral : 5.320 85.155 12259 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 2.51 % Allowed : 16.92 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.08), residues: 11143 helix: 1.48 (0.07), residues: 6156 sheet: -0.12 (0.13), residues: 1445 loop : -2.49 (0.10), residues: 3542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1269 time to evaluate : 7.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 222 outliers final: 107 residues processed: 1426 average time/residue: 0.8148 time to fit residues: 2017.4455 Evaluate side-chains 1243 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1136 time to evaluate : 7.831 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.6851 time to fit residues: 147.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 1027 optimal weight: 9.9990 chunk 781 optimal weight: 30.0000 chunk 539 optimal weight: 9.9990 chunk 115 optimal weight: 0.0030 chunk 496 optimal weight: 9.9990 chunk 698 optimal weight: 0.6980 chunk 1043 optimal weight: 0.0070 chunk 1104 optimal weight: 6.9990 chunk 545 optimal weight: 7.9990 chunk 989 optimal weight: 10.0000 chunk 297 optimal weight: 0.9980 overall best weight: 1.7410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 HIS ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 640 GLN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 606 ASN N 88 HIS a 443 ASN ** a 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 413 GLN ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 305 GLN ** h 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 361 ASN j 684 GLN ** k 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 HIS ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 361 HIS m 369 ASN m 508 GLN o 128 HIS p 318 HIS ** p 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 89886 Z= 0.232 Angle : 0.756 15.427 121745 Z= 0.374 Chirality : 0.043 0.417 13990 Planarity : 0.005 0.118 15581 Dihedral : 5.282 83.177 12259 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 2.33 % Allowed : 18.18 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.08), residues: 11143 helix: 1.66 (0.07), residues: 6159 sheet: -0.21 (0.13), residues: 1485 loop : -2.33 (0.10), residues: 3499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1231 time to evaluate : 7.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 206 outliers final: 114 residues processed: 1369 average time/residue: 0.8150 time to fit residues: 1944.9773 Evaluate side-chains 1220 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1106 time to evaluate : 7.896 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.7066 time to fit residues: 159.1309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 920 optimal weight: 5.9990 chunk 627 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 822 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 942 optimal weight: 6.9990 chunk 763 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 564 optimal weight: 0.7980 chunk 991 optimal weight: 7.9990 chunk 278 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN E 606 ASN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 HIS J 362 GLN ** J 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 ASN a 367 ASN a 514 GLN ** b 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 HIS ** h 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 684 GLN ** k 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 223 HIS ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 606 ASN n 151 HIS o 128 HIS p 331 GLN ** p 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 89886 Z= 0.266 Angle : 0.805 19.617 121745 Z= 0.401 Chirality : 0.044 0.379 13990 Planarity : 0.005 0.120 15581 Dihedral : 5.389 81.182 12259 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 2.17 % Allowed : 19.81 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.08), residues: 11143 helix: 1.62 (0.07), residues: 6131 sheet: -0.30 (0.13), residues: 1515 loop : -2.20 (0.10), residues: 3497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1210 time to evaluate : 7.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 192 outliers final: 104 residues processed: 1342 average time/residue: 0.8058 time to fit residues: 1913.2238 Evaluate side-chains 1235 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1131 time to evaluate : 7.750 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 0.7102 time to fit residues: 145.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 371 optimal weight: 3.9990 chunk 994 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 648 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 1105 optimal weight: 5.9990 chunk 918 optimal weight: 3.9990 chunk 512 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 chunk 580 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 HIS ** B 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS C 98 HIS C 144 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 527 HIS ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 151 HIS ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 GLN ** J 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 756 GLN ** J 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 ASN N 306 ASN O 74 ASN O 128 HIS ** P 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 242 GLN a 324 GLN a 367 ASN ** b 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 359 GLN ** b 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 HIS ** h 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 979 GLN j1054 HIS ** k 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 331 ASN o 128 HIS p 78 GLN p 186 ASN p 332 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 89886 Z= 0.328 Angle : 0.860 19.154 121745 Z= 0.439 Chirality : 0.046 0.623 13990 Planarity : 0.006 0.110 15581 Dihedral : 5.641 82.437 12259 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.39 % Favored : 92.51 % Rotamer: Outliers : 2.70 % Allowed : 21.16 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.13 % 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: 0.10 (0.08), residues: 11143 helix: 1.41 (0.07), residues: 6133 sheet: -0.28 (0.13), residues: 1461 loop : -2.23 (0.10), residues: 3549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22286 Ramachandran restraints generated. 11143 Oldfield, 0 Emsley, 11143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1167 time to evaluate : 7.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 155 residues processed: 1311 average time/residue: 0.7811 time to fit residues: 1806.8213 Evaluate side-chains 1244 residues out of total 10413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1089 time to evaluate : 9.540 Switching outliers to nearest non-outliers outliers start: 155 outliers final: 0 residues processed: 155 average time/residue: 0.7079 time to fit residues: 213.2505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1143 random chunks: chunk 1066 optimal weight: 8.9990 chunk 124 optimal weight: 0.0870 chunk 630 optimal weight: 5.9990 chunk 807 optimal weight: 7.9990 chunk 625 optimal weight: 2.9990 chunk 930 optimal weight: 0.9990 chunk 617 optimal weight: 0.7980 chunk 1101 optimal weight: 6.9990 chunk 689 optimal weight: 0.9980 chunk 671 optimal weight: 0.7980 chunk 508 optimal weight: 20.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: