Starting phenix.real_space_refine on Sun Sep 29 22:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/09_2024/5m32_4146.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 12 5.49 5 S 400 5.16 5 C 47773 2.51 5 N 13346 2.21 5 O 14554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76085 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1836 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1771 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1757 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1805 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1818 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1663 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1590 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "J" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1545 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1637 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1660 Chain: "M" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1513 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 194} Chain: "O" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "P" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1785 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1834 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 228} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1877 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1841 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 1627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1643 Chain: "W" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1586 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1563 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "Z" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1519 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 21, 'TRANS': 325} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "e" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2776 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "f" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2692 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 330} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "g" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2777 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2518 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 314} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "i" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1145 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 12, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 348 Chain: "j" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 779 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 283 Chain: "k" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 1819 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 331} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 357} Chain breaks: 4 Unresolved non-hydrogen bonds: 1186 Unresolved non-hydrogen angles: 1496 Unresolved non-hydrogen dihedrals: 962 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 19, 'PHE:plan': 9, 'GLU:plan': 35, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 617 Chain: "l" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2572 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 10, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 16, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 374 Chain: "m" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2421 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 365} Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 426 Chain: "n" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1030 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 370 Chain: "o" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 377 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "p" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 504 Classifications: {'peptide': 101} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 85} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 Chain: "q" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1311 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 755 Unresolved non-hydrogen angles: 961 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 404 Chain: "r" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "s" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "t" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {'6V9': 1, '7C9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7C9:plan-1': 2, '6V9:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'6VA': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {'6V9': 1, '7C9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7C9:plan-1': 2, '6V9:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "u" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'6VA': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 36.62, per 1000 atoms: 0.48 Number of scatterers: 76085 At special positions: 0 Unit cell: (186.69, 172.72, 304.8, 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 400 16.00 P 12 15.00 O 14554 8.00 N 13346 7.00 C 47773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 61 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 43 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 61 " distance=2.02 Simple disulfide: pdb=" SG CYS c 236 " - pdb=" SG CYS c 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM76026 O3A ADP g 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75948 O5' ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM76026 O3A ADP g 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75947 O4' ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75999 O3A ADP e 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75975 O5' ADP d 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75975 O5' ADP d 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75974 O4' ADP d 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.91 Conformation dependent library (CDL) restraints added in 8.7 seconds 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19560 Finding SS restraints... Secondary structure from input PDB file: 350 helices and 88 sheets defined 40.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 removed outlier: 3.582A pdb=" N GLU A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 101 removed outlier: 3.860A pdb=" N ARG A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.618A pdb=" N GLY A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 221 through 231 removed outlier: 3.583A pdb=" N VAL A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 31 removed outlier: 3.756A pdb=" N ALA B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.866A pdb=" N ALA B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.890A pdb=" N LEU B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.636A pdb=" N ALA B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.128A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 15 removed outlier: 4.032A pdb=" N GLY C 14 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.525A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 4.377A pdb=" N LEU C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.757A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 98 removed outlier: 3.879A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.518A pdb=" N ILE C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 184 through 197 Processing helix chain 'C' and resid 221 through 235 removed outlier: 3.569A pdb=" N GLU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 29 removed outlier: 3.545A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 104 Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.564A pdb=" N ASN D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.845A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.726A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 31 Processing helix chain 'E' and resid 77 through 98 Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 165 through 174 removed outlier: 4.098A pdb=" N ARG E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 4.154A pdb=" N LYS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA E 194 " --> pdb=" O HIS E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.688A pdb=" N GLU F 24 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 103 Processing helix chain 'F' and resid 107 through 122 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.733A pdb=" N THR F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.852A pdb=" N ALA F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 235 through 239 Processing helix chain 'G' and resid 24 through 30 Processing helix chain 'G' and resid 83 through 105 removed outlier: 4.085A pdb=" N ARG G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.819A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 182 removed outlier: 3.721A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 removed outlier: 4.276A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 241 Processing helix chain 'H' and resid 48 through 71 removed outlier: 3.999A pdb=" N ASP H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.597A pdb=" N ARG H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 136 removed outlier: 4.512A pdb=" N ALA H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 147 through 164 removed outlier: 3.581A pdb=" N PHE H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 77 Processing helix chain 'I' and resid 82 through 95 removed outlier: 3.589A pdb=" N TYR I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 3.940A pdb=" N MET I 145 " --> pdb=" O CYS I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 158 through 176 removed outlier: 3.914A pdb=" N ARG I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 72 removed outlier: 3.681A pdb=" N ALA J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU J 58 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 135 through 140 removed outlier: 3.514A pdb=" N THR J 139 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 140' Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 152 through 170 Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 132 through 143 Processing helix chain 'K' and resid 148 through 167 removed outlier: 3.567A pdb=" N ALA K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 200 Processing helix chain 'L' and resid 57 through 77 removed outlier: 3.748A pdb=" N HIS L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 99 removed outlier: 3.784A pdb=" N ILE L 88 " --> pdb=" O THR L 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG L 99 " --> pdb=" O ILE L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 146 removed outlier: 3.523A pdb=" N GLN L 146 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 removed outlier: 3.524A pdb=" N ASN L 151 " --> pdb=" O PRO L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 186 removed outlier: 3.852A pdb=" N LYS L 176 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 76 removed outlier: 3.522A pdb=" N PHE M 60 " --> pdb=" O ASP M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 101 removed outlier: 3.663A pdb=" N ILE M 88 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS M 89 " --> pdb=" O PRO M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 157 removed outlier: 4.770A pdb=" N GLN M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Proline residue: M 148 - end of helix removed outlier: 3.668A pdb=" N VAL M 153 " --> pdb=" O LEU M 149 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU M 155 " --> pdb=" O ARG M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 180 Processing helix chain 'M' and resid 211 through 215 removed outlier: 3.754A pdb=" N MET M 214 " --> pdb=" O ILE M 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE M 215 " --> pdb=" O ALA M 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 215' Processing helix chain 'N' and resid 49 through 71 removed outlier: 3.896A pdb=" N GLN N 53 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA N 54 " --> pdb=" O ALA N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 89 removed outlier: 3.654A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 143 Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'O' and resid 18 through 30 removed outlier: 3.582A pdb=" N GLU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 101 removed outlier: 3.860A pdb=" N ARG O 83 " --> pdb=" O GLY O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 117 Processing helix chain 'O' and resid 118 through 122 Processing helix chain 'O' and resid 165 through 176 removed outlier: 3.618A pdb=" N GLY O 169 " --> pdb=" O ASN O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 195 Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 221 through 231 removed outlier: 3.583A pdb=" N VAL O 225 " --> pdb=" O THR O 221 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS O 226 " --> pdb=" O PRO O 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP O 227 " --> pdb=" O THR O 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.755A pdb=" N ALA P 24 " --> pdb=" O GLN P 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY P 29 " --> pdb=" O MET P 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 102 removed outlier: 3.866A pdb=" N ALA P 83 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN P 84 " --> pdb=" O THR P 80 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.890A pdb=" N LEU P 110 " --> pdb=" O PRO P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 Processing helix chain 'P' and resid 174 through 178 Processing helix chain 'P' and resid 185 through 200 removed outlier: 3.634A pdb=" N ALA P 189 " --> pdb=" O THR P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 237 removed outlier: 4.128A pdb=" N VAL P 233 " --> pdb=" O LYS P 229 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU P 234 " --> pdb=" O GLN P 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 15 removed outlier: 4.032A pdb=" N GLY Q 14 " --> pdb=" O SER Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 removed outlier: 3.525A pdb=" N GLU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 59 removed outlier: 3.758A pdb=" N VAL Q 59 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 98 removed outlier: 3.878A pdb=" N VAL Q 83 " --> pdb=" O ASP Q 79 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL Q 98 " --> pdb=" O HIS Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.518A pdb=" N ILE Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 175 Processing helix chain 'Q' and resid 184 through 197 Processing helix chain 'Q' and resid 221 through 236 removed outlier: 3.825A pdb=" N ILE Q 225 " --> pdb=" O ASN Q 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 29 removed outlier: 3.545A pdb=" N GLU R 25 " --> pdb=" O LEU R 21 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU R 29 " --> pdb=" O GLU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 104 Processing helix chain 'R' and resid 111 through 118 removed outlier: 3.563A pdb=" N ASN R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 183 removed outlier: 3.845A pdb=" N GLU R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 Processing helix chain 'R' and resid 230 through 240 removed outlier: 3.727A pdb=" N ASP R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 31 Processing helix chain 'S' and resid 78 through 98 Processing helix chain 'S' and resid 104 through 116 Processing helix chain 'S' and resid 117 through 122 Processing helix chain 'S' and resid 165 through 174 removed outlier: 4.098A pdb=" N ARG S 174 " --> pdb=" O THR S 170 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 196 removed outlier: 4.155A pdb=" N LYS S 189 " --> pdb=" O ASP S 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS S 190 " --> pdb=" O GLU S 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA S 194 " --> pdb=" O HIS S 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 32 removed outlier: 3.687A pdb=" N GLU T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA T 26 " --> pdb=" O GLN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 103 Processing helix chain 'T' and resid 107 through 122 Processing helix chain 'T' and resid 168 through 179 removed outlier: 4.731A pdb=" N THR T 174 " --> pdb=" O GLN T 170 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE T 176 " --> pdb=" O ALA T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 201 removed outlier: 3.852A pdb=" N ALA T 194 " --> pdb=" O VAL T 190 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 234 Processing helix chain 'T' and resid 235 through 239 Processing helix chain 'U' and resid 24 through 30 Processing helix chain 'U' and resid 83 through 105 removed outlier: 4.085A pdb=" N ARG U 88 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER U 89 " --> pdb=" O ALA U 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 126 removed outlier: 3.818A pdb=" N LEU U 114 " --> pdb=" O PRO U 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS U 115 " --> pdb=" O VAL U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 182 removed outlier: 3.720A pdb=" N SER U 175 " --> pdb=" O LYS U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 197 through 206 removed outlier: 4.277A pdb=" N LEU U 202 " --> pdb=" O ALA U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 231 through 241 Processing helix chain 'V' and resid 48 through 71 removed outlier: 3.999A pdb=" N ASP V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 89 removed outlier: 3.597A pdb=" N ARG V 89 " --> pdb=" O GLN V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 136 removed outlier: 4.513A pdb=" N ALA V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 139 No H-bonds generated for 'chain 'V' and resid 137 through 139' Processing helix chain 'V' and resid 147 through 164 removed outlier: 3.582A pdb=" N PHE V 164 " --> pdb=" O ALA V 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 77 Processing helix chain 'W' and resid 82 through 95 removed outlier: 3.589A pdb=" N TYR W 95 " --> pdb=" O ALA W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 146 removed outlier: 3.939A pdb=" N MET W 145 " --> pdb=" O CYS W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 153 Processing helix chain 'W' and resid 158 through 176 removed outlier: 3.914A pdb=" N ARG W 176 " --> pdb=" O ASN W 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 72 removed outlier: 3.681A pdb=" N ALA X 57 " --> pdb=" O THR X 53 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU X 58 " --> pdb=" O VAL X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 91 Processing helix chain 'X' and resid 135 through 140 removed outlier: 3.514A pdb=" N THR X 139 " --> pdb=" O GLY X 135 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU X 140 " --> pdb=" O ALA X 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 135 through 140' Processing helix chain 'X' and resid 141 through 146 Processing helix chain 'X' and resid 152 through 170 Processing helix chain 'Y' and resid 50 through 71 Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 148 through 167 removed outlier: 3.568A pdb=" N ALA Y 152 " --> pdb=" O GLU Y 148 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 192 through 200 Processing helix chain 'Z' and resid 57 through 77 removed outlier: 3.748A pdb=" N HIS Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 84 through 99 removed outlier: 3.785A pdb=" N ILE Z 88 " --> pdb=" O THR Z 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG Z 99 " --> pdb=" O ILE Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 146 removed outlier: 3.523A pdb=" N GLN Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 152 removed outlier: 3.525A pdb=" N ASN Z 151 " --> pdb=" O PRO Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 171 through 186 removed outlier: 3.852A pdb=" N LYS Z 176 " --> pdb=" O MET Z 172 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP Z 177 " --> pdb=" O ARG Z 173 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL Z 178 " --> pdb=" O LEU Z 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 76 removed outlier: 3.522A pdb=" N PHE a 60 " --> pdb=" O ASP a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 101 removed outlier: 3.664A pdb=" N ILE a 88 " --> pdb=" O SER a 84 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS a 89 " --> pdb=" O PRO a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 157 removed outlier: 4.769A pdb=" N GLN a 147 " --> pdb=" O ALA a 143 " (cutoff:3.500A) Proline residue: a 148 - end of helix removed outlier: 3.668A pdb=" N VAL a 153 " --> pdb=" O LEU a 149 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU a 155 " --> pdb=" O ARG a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 180 Processing helix chain 'a' and resid 211 through 215 removed outlier: 3.754A pdb=" N MET a 214 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE a 215 " --> pdb=" O ALA a 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 211 through 215' Processing helix chain 'b' and resid 49 through 71 removed outlier: 3.896A pdb=" N GLN b 53 " --> pdb=" O ALA b 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 89 removed outlier: 3.654A pdb=" N ALA b 79 " --> pdb=" O LEU b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 143 Processing helix chain 'b' and resid 148 through 167 Processing helix chain 'c' and resid 86 through 90 Processing helix chain 'c' and resid 158 through 162 removed outlier: 4.126A pdb=" N VAL c 161 " --> pdb=" O ASP c 158 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR c 162 " --> pdb=" O PRO c 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 158 through 162' Processing helix chain 'c' and resid 182 through 192 removed outlier: 3.515A pdb=" N LEU c 187 " --> pdb=" O GLN c 183 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL c 190 " --> pdb=" O LYS c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 204 Processing helix chain 'c' and resid 223 through 232 Processing helix chain 'c' and resid 251 through 266 removed outlier: 3.652A pdb=" N THR c 266 " --> pdb=" O GLU c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 277 through 280 Processing helix chain 'c' and resid 292 through 306 Processing helix chain 'c' and resid 347 through 359 removed outlier: 3.965A pdb=" N THR c 352 " --> pdb=" O LEU c 348 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS c 353 " --> pdb=" O GLU c 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 369 through 377 removed outlier: 3.608A pdb=" N LEU c 373 " --> pdb=" O ARG c 369 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS c 377 " --> pdb=" O LEU c 373 " (cutoff:3.500A) Processing helix chain 'c' and resid 384 through 399 removed outlier: 3.692A pdb=" N VAL c 388 " --> pdb=" O GLU c 384 " (cutoff:3.500A) Processing helix chain 'c' and resid 408 through 417 Processing helix chain 'c' and resid 428 through 433 removed outlier: 3.959A pdb=" N TYR c 432 " --> pdb=" O ARG c 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 93 removed outlier: 3.711A pdb=" N GLU d 93 " --> pdb=" O GLU d 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 90 through 93' Processing helix chain 'd' and resid 94 through 99 Processing helix chain 'd' and resid 191 through 207 Proline residue: d 204 - end of helix Processing helix chain 'd' and resid 210 through 215 Processing helix chain 'd' and resid 250 through 256 Processing helix chain 'd' and resid 269 through 278 removed outlier: 3.690A pdb=" N HIS d 277 " --> pdb=" O VAL d 273 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA d 278 " --> pdb=" O ALA d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 317 Processing helix chain 'd' and resid 357 through 369 removed outlier: 3.918A pdb=" N ILE d 367 " --> pdb=" O ARG d 363 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS d 368 " --> pdb=" O ILE d 364 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR d 369 " --> pdb=" O PHE d 365 " (cutoff:3.500A) Processing helix chain 'd' and resid 391 through 406 removed outlier: 3.591A pdb=" N ILE d 395 " --> pdb=" O SER d 391 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS d 396 " --> pdb=" O GLY d 392 " (cutoff:3.500A) Processing helix chain 'd' and resid 417 through 427 Processing helix chain 'e' and resid 57 through 74 removed outlier: 3.722A pdb=" N LYS e 62 " --> pdb=" O GLU e 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 82 removed outlier: 3.841A pdb=" N ARG e 81 " --> pdb=" O GLU e 78 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE e 82 " --> pdb=" O VAL e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 171 through 181 Processing helix chain 'e' and resid 182 through 187 Processing helix chain 'e' and resid 190 through 195 Processing helix chain 'e' and resid 242 through 256 Processing helix chain 'e' and resid 267 through 270 Processing helix chain 'e' and resid 287 through 296 removed outlier: 3.845A pdb=" N GLU e 291 " --> pdb=" O ARG e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 297 through 299 No H-bonds generated for 'chain 'e' and resid 297 through 299' Processing helix chain 'e' and resid 337 through 351 removed outlier: 3.651A pdb=" N ARG e 342 " --> pdb=" O ARG e 338 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU e 343 " --> pdb=" O ARG e 339 " (cutoff:3.500A) Processing helix chain 'e' and resid 360 through 365 Processing helix chain 'e' and resid 372 through 387 Processing helix chain 'e' and resid 396 through 407 Processing helix chain 'f' and resid 33 through 42 Processing helix chain 'f' and resid 44 through 51 removed outlier: 4.039A pdb=" N LYS f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 92 removed outlier: 3.701A pdb=" N LYS f 91 " --> pdb=" O ASP f 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 155 Proline residue: f 152 - end of helix Processing helix chain 'f' and resid 156 through 163 removed outlier: 4.309A pdb=" N GLN f 160 " --> pdb=" O PRO f 156 " (cutoff:3.500A) Processing helix chain 'f' and resid 182 through 189 Processing helix chain 'f' and resid 209 through 225 removed outlier: 3.618A pdb=" N ARG f 213 " --> pdb=" O GLY f 209 " (cutoff:3.500A) Processing helix chain 'f' and resid 255 through 265 Processing helix chain 'f' and resid 281 through 285 removed outlier: 3.714A pdb=" N THR f 284 " --> pdb=" O ARG f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 306 through 317 Processing helix chain 'f' and resid 327 through 335 removed outlier: 3.828A pdb=" N ILE f 331 " --> pdb=" O ASP f 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER f 335 " --> pdb=" O ILE f 331 " (cutoff:3.500A) Processing helix chain 'f' and resid 339 through 358 Processing helix chain 'f' and resid 363 through 375 removed outlier: 3.807A pdb=" N ARG f 372 " --> pdb=" O MET f 368 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS f 373 " --> pdb=" O LYS f 369 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 81 removed outlier: 3.528A pdb=" N ALA g 68 " --> pdb=" O HIS g 64 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET g 69 " --> pdb=" O GLU g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 174 removed outlier: 3.828A pdb=" N LYS g 173 " --> pdb=" O ASP g 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 191 through 203 Processing helix chain 'g' and resid 209 through 216 Processing helix chain 'g' and resid 232 through 241 Processing helix chain 'g' and resid 261 through 278 removed outlier: 4.427A pdb=" N ALA g 265 " --> pdb=" O ILE g 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL g 268 " --> pdb=" O GLY g 264 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG g 269 " --> pdb=" O ALA g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 289 through 293 removed outlier: 3.645A pdb=" N GLY g 292 " --> pdb=" O ASP g 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR g 293 " --> pdb=" O ALA g 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 289 through 293' Processing helix chain 'g' and resid 304 through 314 Processing helix chain 'g' and resid 339 through 344 removed outlier: 3.905A pdb=" N ARG g 344 " --> pdb=" O ALA g 341 " (cutoff:3.500A) Processing helix chain 'g' and resid 360 through 370 removed outlier: 3.641A pdb=" N SER g 370 " --> pdb=" O MET g 366 " (cutoff:3.500A) Processing helix chain 'g' and resid 380 through 388 removed outlier: 3.985A pdb=" N THR g 388 " --> pdb=" O LEU g 384 " (cutoff:3.500A) Processing helix chain 'g' and resid 393 through 411 removed outlier: 3.597A pdb=" N LYS g 397 " --> pdb=" O GLY g 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY g 411 " --> pdb=" O ALA g 407 " (cutoff:3.500A) Processing helix chain 'g' and resid 416 through 425 removed outlier: 3.717A pdb=" N TYR g 420 " --> pdb=" O THR g 416 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU g 425 " --> pdb=" O MET g 421 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 66 Processing helix chain 'h' and resid 101 through 104 removed outlier: 3.867A pdb=" N ASP h 104 " --> pdb=" O LYS h 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 101 through 104' Processing helix chain 'h' and resid 132 through 140 removed outlier: 3.703A pdb=" N SER h 136 " --> pdb=" O ASP h 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 164 Processing helix chain 'h' and resid 166 through 171 Processing helix chain 'h' and resid 198 through 206 removed outlier: 3.667A pdb=" N ALA h 204 " --> pdb=" O ALA h 200 " (cutoff:3.500A) Processing helix chain 'h' and resid 233 through 242 removed outlier: 3.750A pdb=" N MET h 237 " --> pdb=" O GLU h 233 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 279 removed outlier: 3.808A pdb=" N LEU h 276 " --> pdb=" O THR h 272 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN h 279 " --> pdb=" O GLU h 275 " (cutoff:3.500A) Processing helix chain 'h' and resid 321 through 334 Processing helix chain 'h' and resid 344 through 349 Processing helix chain 'h' and resid 356 through 372 removed outlier: 3.549A pdb=" N LYS h 360 " --> pdb=" O GLY h 356 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL h 362 " --> pdb=" O GLU h 358 " (cutoff:3.500A) Processing helix chain 'h' and resid 380 through 388 removed outlier: 3.654A pdb=" N GLU h 384 " --> pdb=" O GLN h 380 " (cutoff:3.500A) Processing helix chain 'i' and resid 476 through 481 Processing helix chain 'i' and resid 492 through 502 Processing helix chain 'i' and resid 506 through 521 removed outlier: 3.648A pdb=" N GLU i 510 " --> pdb=" O ALA i 506 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU i 521 " --> pdb=" O GLY i 517 " (cutoff:3.500A) Processing helix chain 'i' and resid 525 through 534 Processing helix chain 'i' and resid 542 through 559 removed outlier: 6.874A pdb=" N VAL i 550 " --> pdb=" O ARG i 546 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY i 551 " --> pdb=" O GLY i 547 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE i 552 " --> pdb=" O LEU i 548 " (cutoff:3.500A) Processing helix chain 'i' and resid 560 through 567 Processing helix chain 'i' and resid 567 through 573 Processing helix chain 'i' and resid 575 through 586 Processing helix chain 'i' and resid 595 through 606 Processing helix chain 'i' and resid 613 through 625 Processing helix chain 'i' and resid 632 through 642 removed outlier: 3.801A pdb=" N LEU i 639 " --> pdb=" O SER i 635 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU i 640 " --> pdb=" O VAL i 636 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU i 642 " --> pdb=" O SER i 638 " (cutoff:3.500A) Processing helix chain 'i' and resid 647 through 658 Processing helix chain 'i' and resid 659 through 661 No H-bonds generated for 'chain 'i' and resid 659 through 661' Processing helix chain 'i' and resid 680 through 693 removed outlier: 3.610A pdb=" N GLN i 685 " --> pdb=" O ASN i 681 " (cutoff:3.500A) Processing helix chain 'i' and resid 757 through 765 removed outlier: 4.022A pdb=" N VAL i 763 " --> pdb=" O SER i 759 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 164 Processing helix chain 'j' and resid 177 through 190 removed outlier: 4.056A pdb=" N LYS j 181 " --> pdb=" O GLN j 177 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 204 removed outlier: 3.751A pdb=" N SER j 203 " --> pdb=" O ARG j 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 209 through 221 Processing helix chain 'j' and resid 222 through 231 removed outlier: 4.296A pdb=" N GLN j 228 " --> pdb=" O ALA j 224 " (cutoff:3.500A) Processing helix chain 'j' and resid 247 through 254 removed outlier: 4.204A pdb=" N VAL j 253 " --> pdb=" O LEU j 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE j 254 " --> pdb=" O ARG j 250 " (cutoff:3.500A) Processing helix chain 'j' and resid 321 through 338 removed outlier: 3.910A pdb=" N ALA j 326 " --> pdb=" O GLU j 322 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE j 327 " --> pdb=" O PRO j 323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG j 330 " --> pdb=" O ALA j 326 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE j 331 " --> pdb=" O PHE j 327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER j 332 " --> pdb=" O HIS j 328 " (cutoff:3.500A) Processing helix chain 'j' and resid 339 through 344 Processing helix chain 'k' and resid 39 through 54 removed outlier: 4.102A pdb=" N VAL k 43 " --> pdb=" O ARG k 39 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS k 52 " --> pdb=" O LEU k 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN k 53 " --> pdb=" O SER k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 64 removed outlier: 3.918A pdb=" N SER k 64 " --> pdb=" O MET k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 73 Processing helix chain 'k' and resid 104 through 113 removed outlier: 4.430A pdb=" N TYR k 111 " --> pdb=" O GLN k 107 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU k 113 " --> pdb=" O CYS k 109 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 130 removed outlier: 3.633A pdb=" N MET k 130 " --> pdb=" O THR k 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 138 through 150 Processing helix chain 'k' and resid 152 through 156 removed outlier: 3.529A pdb=" N GLN k 155 " --> pdb=" O ILE k 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 162 through 166 removed outlier: 3.582A pdb=" N ILE k 165 " --> pdb=" O ALA k 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 183 through 195 removed outlier: 3.782A pdb=" N LEU k 192 " --> pdb=" O GLU k 188 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA k 195 " --> pdb=" O ARG k 191 " (cutoff:3.500A) Processing helix chain 'k' and resid 229 through 234 removed outlier: 3.873A pdb=" N ASP k 234 " --> pdb=" O MET k 230 " (cutoff:3.500A) Processing helix chain 'k' and resid 269 through 276 removed outlier: 4.154A pdb=" N LEU k 276 " --> pdb=" O LEU k 272 " (cutoff:3.500A) Processing helix chain 'k' and resid 280 through 289 removed outlier: 3.746A pdb=" N HIS k 288 " --> pdb=" O SER k 284 " (cutoff:3.500A) Processing helix chain 'k' and resid 293 through 298 removed outlier: 3.849A pdb=" N GLU k 298 " --> pdb=" O LYS k 294 " (cutoff:3.500A) Processing helix chain 'k' and resid 299 through 302 removed outlier: 3.620A pdb=" N TYR k 302 " --> pdb=" O ILE k 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 299 through 302' Processing helix chain 'k' and resid 303 through 310 Processing helix chain 'k' and resid 318 through 323 Processing helix chain 'k' and resid 346 through 370 removed outlier: 4.094A pdb=" N ARG k 350 " --> pdb=" O GLU k 346 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP k 351 " --> pdb=" O GLY k 347 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS k 361 " --> pdb=" O ARG k 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN k 362 " --> pdb=" O VAL k 358 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG k 364 " --> pdb=" O GLU k 360 " (cutoff:3.500A) Processing helix chain 'k' and resid 374 through 382 Processing helix chain 'k' and resid 386 through 399 removed outlier: 3.724A pdb=" N ASN k 399 " --> pdb=" O ASN k 395 " (cutoff:3.500A) Processing helix chain 'k' and resid 422 through 432 Processing helix chain 'l' and resid 10 through 15 removed outlier: 3.599A pdb=" N LEU l 15 " --> pdb=" O ARG l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 27 through 32 Processing helix chain 'l' and resid 42 through 61 Processing helix chain 'l' and resid 62 through 72 removed outlier: 3.644A pdb=" N LEU l 66 " --> pdb=" O GLN l 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 99 removed outlier: 3.756A pdb=" N MET l 99 " --> pdb=" O LEU l 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 120 removed outlier: 3.750A pdb=" N CYS l 113 " --> pdb=" O LEU l 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU l 120 " --> pdb=" O TRP l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 122 through 140 removed outlier: 3.664A pdb=" N ARG l 126 " --> pdb=" O ARG l 122 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN l 127 " --> pdb=" O THR l 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP l 139 " --> pdb=" O SER l 135 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR l 140 " --> pdb=" O LEU l 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 160 removed outlier: 3.946A pdb=" N ARG l 155 " --> pdb=" O SER l 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU l 156 " --> pdb=" O GLN l 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS l 159 " --> pdb=" O ARG l 155 " (cutoff:3.500A) Processing helix chain 'l' and resid 165 through 179 removed outlier: 4.132A pdb=" N HIS l 178 " --> pdb=" O SER l 174 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA l 179 " --> pdb=" O LYS l 175 " (cutoff:3.500A) Processing helix chain 'l' and resid 187 through 196 Processing helix chain 'l' and resid 203 through 218 Processing helix chain 'l' and resid 229 through 233 removed outlier: 3.531A pdb=" N TYR l 233 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'l' and resid 235 through 239 removed outlier: 3.537A pdb=" N TYR l 239 " --> pdb=" O PHE l 236 " (cutoff:3.500A) Processing helix chain 'l' and resid 243 through 259 removed outlier: 3.917A pdb=" N ALA l 247 " --> pdb=" O ASP l 243 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE l 259 " --> pdb=" O LEU l 255 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 272 removed outlier: 3.751A pdb=" N GLN l 268 " --> pdb=" O PRO l 264 " (cutoff:3.500A) Processing helix chain 'l' and resid 281 through 296 removed outlier: 4.025A pdb=" N GLU l 285 " --> pdb=" O GLY l 281 " (cutoff:3.500A) Processing helix chain 'l' and resid 299 through 304 Processing helix chain 'l' and resid 310 through 314 removed outlier: 3.780A pdb=" N LEU l 313 " --> pdb=" O ARG l 310 " (cutoff:3.500A) Processing helix chain 'l' and resid 321 through 340 removed outlier: 4.258A pdb=" N LYS l 325 " --> pdb=" O THR l 321 " (cutoff:3.500A) Processing helix chain 'l' and resid 346 through 353 removed outlier: 3.698A pdb=" N ILE l 350 " --> pdb=" O GLN l 346 " (cutoff:3.500A) Processing helix chain 'l' and resid 358 through 366 removed outlier: 3.608A pdb=" N GLU l 362 " --> pdb=" O LYS l 358 " (cutoff:3.500A) Processing helix chain 'l' and resid 395 through 418 removed outlier: 3.903A pdb=" N SER l 408 " --> pdb=" O ILE l 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS l 409 " --> pdb=" O GLN l 405 " (cutoff:3.500A) Processing helix chain 'm' and resid 18 through 28 removed outlier: 3.531A pdb=" N SER m 27 " --> pdb=" O ARG m 23 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 46 removed outlier: 3.551A pdb=" N LEU m 41 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA m 44 " --> pdb=" O GLU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 60 removed outlier: 3.667A pdb=" N TYR m 54 " --> pdb=" O MET m 50 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA m 56 " --> pdb=" O PRO m 52 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS m 58 " --> pdb=" O TYR m 54 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER m 60 " --> pdb=" O ALA m 56 " (cutoff:3.500A) Processing helix chain 'm' and resid 69 through 89 removed outlier: 4.001A pdb=" N ASP m 85 " --> pdb=" O LEU m 81 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU m 86 " --> pdb=" O LYS m 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU m 87 " --> pdb=" O ARG m 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU m 88 " --> pdb=" O LEU m 84 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 111 Processing helix chain 'm' and resid 120 through 125 removed outlier: 3.681A pdb=" N ARG m 125 " --> pdb=" O LEU m 121 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 152 removed outlier: 4.023A pdb=" N ILE m 147 " --> pdb=" O TYR m 143 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE m 150 " --> pdb=" O ARG m 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 153 through 163 Processing helix chain 'm' and resid 176 through 189 Processing helix chain 'm' and resid 193 through 203 removed outlier: 4.018A pdb=" N ALA m 198 " --> pdb=" O PHE m 194 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU m 199 " --> pdb=" O LYS m 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU m 200 " --> pdb=" O GLN m 196 " (cutoff:3.500A) Processing helix chain 'm' and resid 218 through 225 Processing helix chain 'm' and resid 226 through 231 removed outlier: 4.364A pdb=" N ALA m 230 " --> pdb=" O VAL m 226 " (cutoff:3.500A) Processing helix chain 'm' and resid 236 through 242 Processing helix chain 'm' and resid 253 through 261 Processing helix chain 'm' and resid 267 through 279 removed outlier: 3.639A pdb=" N PHE m 271 " --> pdb=" O ARG m 267 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN m 273 " --> pdb=" O SER m 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL m 278 " --> pdb=" O SER m 274 " (cutoff:3.500A) Processing helix chain 'm' and resid 288 through 309 removed outlier: 3.510A pdb=" N GLU m 309 " --> pdb=" O SER m 305 " (cutoff:3.500A) Processing helix chain 'm' and resid 316 through 321 Processing helix chain 'm' and resid 327 through 341 Processing helix chain 'm' and resid 361 through 384 removed outlier: 4.058A pdb=" N GLN m 365 " --> pdb=" O SER m 361 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR m 366 " --> pdb=" O LYS m 362 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS m 371 " --> pdb=" O GLN m 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 26 removed outlier: 3.880A pdb=" N LEU n 16 " --> pdb=" O HIS n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 82 Processing helix chain 'n' and resid 102 through 111 Processing helix chain 'n' and resid 169 through 174 Processing helix chain 'n' and resid 228 through 232 Processing helix chain 'n' and resid 243 through 264 Processing helix chain 'n' and resid 265 through 285 Processing helix chain 'o' and resid 92 through 101 removed outlier: 3.600A pdb=" N THR o 101 " --> pdb=" O CYS o 97 " (cutoff:3.500A) Processing helix chain 'o' and resid 112 through 119 removed outlier: 3.557A pdb=" N ALA o 117 " --> pdb=" O PHE o 113 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 137 removed outlier: 3.978A pdb=" N VAL o 131 " --> pdb=" O VAL o 127 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL o 137 " --> pdb=" O LYS o 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 35 removed outlier: 3.659A pdb=" N ILE p 35 " --> pdb=" O ASP p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 69 through 76 removed outlier: 3.619A pdb=" N LEU p 75 " --> pdb=" O ILE p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 85 through 99 removed outlier: 3.831A pdb=" N GLY p 89 " --> pdb=" O THR p 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 127 through 131 removed outlier: 4.408A pdb=" N LEU p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 127 through 131' Processing helix chain 'p' and resid 132 through 134 No H-bonds generated for 'chain 'p' and resid 132 through 134' Processing helix chain 'q' and resid 35 through 48 Processing helix chain 'q' and resid 83 through 87 Processing helix chain 'q' and resid 89 through 102 Processing helix chain 'q' and resid 122 through 130 removed outlier: 4.461A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN q 128 " --> pdb=" O GLY q 124 " (cutoff:3.500A) Processing helix chain 'q' and resid 132 through 137 removed outlier: 3.771A pdb=" N LEU q 136 " --> pdb=" O SER q 132 " (cutoff:3.500A) Processing helix chain 'q' and resid 190 through 201 removed outlier: 4.468A pdb=" N HIS q 199 " --> pdb=" O GLY q 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR q 201 " --> pdb=" O ASN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 210 through 218 Processing helix chain 'q' and resid 237 through 241 removed outlier: 3.580A pdb=" N HIS q 240 " --> pdb=" O HIS q 237 " (cutoff:3.500A) Processing helix chain 'q' and resid 243 through 262 removed outlier: 3.703A pdb=" N GLU q 247 " --> pdb=" O SER q 243 " (cutoff:3.500A) Processing helix chain 'q' and resid 267 through 274 removed outlier: 3.680A pdb=" N ALA q 271 " --> pdb=" O PRO q 267 " (cutoff:3.500A) Processing helix chain 'q' and resid 281 through 293 removed outlier: 3.648A pdb=" N LEU q 291 " --> pdb=" O HIS q 287 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET q 292 " --> pdb=" O VAL q 288 " (cutoff:3.500A) Processing helix chain 'q' and resid 296 through 303 Processing helix chain 's' and resid 50 through 63 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 37 removed outlier: 3.510A pdb=" N VAL C 41 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 209 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG C 212 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 167 through 169 removed outlier: 4.343A pdb=" N THR D 36 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.477A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 142 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU D 141 " --> pdb=" O MET D 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 removed outlier: 5.342A pdb=" N GLY E 216 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.994A pdb=" N SER E 73 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 164 through 165 removed outlier: 3.751A pdb=" N ILE F 165 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP F 215 " --> pdb=" O GLU F 225 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 225 " --> pdb=" O TRP F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 68 removed outlier: 3.562A pdb=" N PHE F 67 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AB5, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.636A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS G 154 " --> pdb=" O MET G 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 125 removed outlier: 3.969A pdb=" N CYS H 176 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE H 173 " --> pdb=" O TYR H 189 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU H 175 " --> pdb=" O ARG H 187 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG H 187 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL H 177 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE H 185 " --> pdb=" O VAL H 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 20 through 22 removed outlier: 3.522A pdb=" N ASP H 28 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 41 through 43 removed outlier: 4.589A pdb=" N LEU H 110 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 122 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 211 through 218 removed outlier: 4.073A pdb=" N THR H 213 " --> pdb=" O THR I 198 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AC2, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.534A pdb=" N ASP J 184 " --> pdb=" O GLY J 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 36 through 37 removed outlier: 3.663A pdb=" N LEU J 44 " --> pdb=" O PHE J 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL J 47 " --> pdb=" O ASN J 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 125 through 126 removed outlier: 4.037A pdb=" N LEU K 176 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.773A pdb=" N ALA K 20 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR K 25 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AC7, first strand: chain 'L' and resid 14 through 16 Processing sheet with id=AC8, first strand: chain 'L' and resid 29 through 31 removed outlier: 7.350A pdb=" N LEU L 29 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU L 31 " --> pdb=" O SER L 34 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 43 through 45 removed outlier: 3.992A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN L 131 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 136 through 137 removed outlier: 7.190A pdb=" N ILE M 189 " --> pdb=" O GLY M 201 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY M 201 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR M 191 " --> pdb=" O ILE M 199 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE M 199 " --> pdb=" O THR M 191 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR M 193 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL M 197 " --> pdb=" O THR M 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 43 through 44 Processing sheet with id=AD3, first strand: chain 'N' and resid 12 through 16 Processing sheet with id=AD4, first strand: chain 'N' and resid 20 through 21 removed outlier: 6.571A pdb=" N THR N 20 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 35 through 36 removed outlier: 4.218A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 174 through 178 removed outlier: 3.979A pdb=" N ILE N 174 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA N 178 " --> pdb=" O GLU N 185 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'O' and resid 73 through 74 removed outlier: 3.580A pdb=" N LEU O 133 " --> pdb=" O SER O 148 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 210 through 211 Processing sheet with id=AE1, first strand: chain 'P' and resid 35 through 37 Processing sheet with id=AE2, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AE3, first strand: chain 'Q' and resid 33 through 37 removed outlier: 3.510A pdb=" N VAL Q 41 " --> pdb=" O MET Q 211 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA Q 209 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG Q 212 " --> pdb=" O SER Q 216 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER Q 216 " --> pdb=" O ARG Q 212 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 167 through 169 removed outlier: 4.343A pdb=" N THR R 36 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 67 through 71 removed outlier: 6.477A pdb=" N ILE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 142 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU R 141 " --> pdb=" O MET R 156 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 159 through 161 removed outlier: 5.342A pdb=" N GLY S 216 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU S 220 " --> pdb=" O GLY S 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 63 through 64 removed outlier: 3.994A pdb=" N SER S 73 " --> pdb=" O LEU S 133 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 164 through 165 removed outlier: 3.753A pdb=" N ILE T 165 " --> pdb=" O ALA T 36 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP T 215 " --> pdb=" O GLU T 225 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU T 225 " --> pdb=" O TRP T 215 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 66 through 68 removed outlier: 3.562A pdb=" N PHE T 67 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 39 through 41 Processing sheet with id=AF2, first strand: chain 'U' and resid 39 through 41 Processing sheet with id=AF3, first strand: chain 'U' and resid 70 through 71 removed outlier: 3.637A pdb=" N GLY U 77 " --> pdb=" O ILE U 141 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS U 154 " --> pdb=" O MET U 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 124 through 125 removed outlier: 3.970A pdb=" N CYS V 176 " --> pdb=" O LEU V 14 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE V 173 " --> pdb=" O TYR V 189 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU V 175 " --> pdb=" O ARG V 187 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG V 187 " --> pdb=" O LEU V 175 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL V 177 " --> pdb=" O PHE V 185 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE V 185 " --> pdb=" O VAL V 177 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 20 through 22 removed outlier: 3.523A pdb=" N ASP V 28 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU V 22 " --> pdb=" O VAL V 26 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL V 26 " --> pdb=" O GLU V 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 41 through 43 removed outlier: 4.589A pdb=" N LEU V 110 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU V 122 " --> pdb=" O LEU V 110 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 211 through 215 removed outlier: 4.345A pdb=" N THR V 213 " --> pdb=" O THR W 198 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 41 through 43 Processing sheet with id=AF9, first strand: chain 'X' and resid 129 through 131 removed outlier: 3.534A pdb=" N ASP X 184 " --> pdb=" O GLY X 187 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 36 through 37 removed outlier: 3.663A pdb=" N LEU X 44 " --> pdb=" O PHE X 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL X 47 " --> pdb=" O ASN X 101 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 125 through 126 removed outlier: 4.036A pdb=" N LEU Y 176 " --> pdb=" O SER Y 188 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.772A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR Y 25 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 98 through 101 Processing sheet with id=AG5, first strand: chain 'Z' and resid 14 through 16 Processing sheet with id=AG6, first strand: chain 'Z' and resid 29 through 31 removed outlier: 7.350A pdb=" N LEU Z 29 " --> pdb=" O HIS Z 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Z 31 " --> pdb=" O SER Z 34 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 43 through 45 removed outlier: 3.992A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN Z 131 " --> pdb=" O SER Z 123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 136 through 137 Processing sheet with id=AG9, first strand: chain 'a' and resid 43 through 44 Processing sheet with id=AH1, first strand: chain 'b' and resid 12 through 13 Processing sheet with id=AH2, first strand: chain 'b' and resid 20 through 21 removed outlier: 6.571A pdb=" N THR b 20 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 35 through 36 removed outlier: 4.218A pdb=" N VAL b 111 " --> pdb=" O GLN b 123 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 174 through 178 removed outlier: 3.978A pdb=" N ILE b 174 " --> pdb=" O LEU b 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA b 178 " --> pdb=" O GLU b 185 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 93 through 97 removed outlier: 4.334A pdb=" N ARG c 139 " --> pdb=" O LEU c 153 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE c 151 " --> pdb=" O GLY c 141 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP c 143 " --> pdb=" O ILE c 149 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE c 149 " --> pdb=" O ASP c 143 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'c' and resid 111 through 112 Processing sheet with id=AH7, first strand: chain 'c' and resid 238 through 241 removed outlier: 6.205A pdb=" N ILE c 272 " --> pdb=" O LEU c 318 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA c 320 " --> pdb=" O ILE c 272 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE c 274 " --> pdb=" O ALA c 320 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU c 213 " --> pdb=" O ILE c 341 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 108 through 111 Processing sheet with id=AH9, first strand: chain 'd' and resid 120 through 124 Processing sheet with id=AI1, first strand: chain 'd' and resid 223 through 225 removed outlier: 3.875A pdb=" N THR d 331 " --> pdb=" O LEU d 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL d 282 " --> pdb=" O ILE d 328 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA d 330 " --> pdb=" O VAL d 282 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 139 through 142 removed outlier: 4.169A pdb=" N ASP e 141 " --> pdb=" O ALA e 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL e 130 " --> pdb=" O GLY e 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU e 87 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG f 78 " --> pdb=" O ILE e 89 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ARG f 97 " --> pdb=" O TYR f 110 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR f 110 " --> pdb=" O ARG f 97 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA f 99 " --> pdb=" O MET f 108 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 139 through 142 removed outlier: 4.169A pdb=" N ASP e 141 " --> pdb=" O ALA e 131 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL e 130 " --> pdb=" O GLY e 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU e 87 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG f 78 " --> pdb=" O ILE e 89 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL f 57 " --> pdb=" O THR g 131 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR g 131 " --> pdb=" O VAL f 57 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS g 121 " --> pdb=" O LEU g 96 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU g 96 " --> pdb=" O CYS g 121 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL g 123 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU g 150 " --> pdb=" O LEU g 164 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 100 through 101 removed outlier: 3.608A pdb=" N ALA e 101 " --> pdb=" O VAL e 113 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 226 through 231 removed outlier: 6.662A pdb=" N ALA e 226 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE e 263 " --> pdb=" O ALA e 226 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE e 228 " --> pdb=" O PHE e 263 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASP e 265 " --> pdb=" O ILE e 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL e 230 " --> pdb=" O ASP e 265 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA e 260 " --> pdb=" O LYS e 306 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE e 308 " --> pdb=" O ALA e 260 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE e 262 " --> pdb=" O ILE e 308 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA e 310 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE e 264 " --> pdb=" O ALA e 310 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL e 202 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR e 311 " --> pdb=" O VAL e 202 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET e 204 " --> pdb=" O THR e 311 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE e 331 " --> pdb=" O GLY e 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU e 203 " --> pdb=" O ILE e 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'f' and resid 195 through 199 removed outlier: 6.353A pdb=" N LEU f 196 " --> pdb=" O PHE f 231 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP f 233 " --> pdb=" O LEU f 196 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL f 198 " --> pdb=" O ASP f 233 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE f 230 " --> pdb=" O ILE f 276 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS f 170 " --> pdb=" O MET f 275 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE f 299 " --> pdb=" O TYR f 173 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'g' and resid 247 through 249 removed outlier: 6.644A pdb=" N THR g 247 " --> pdb=" O ILE g 282 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE g 284 " --> pdb=" O THR g 247 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU g 249 " --> pdb=" O PHE g 284 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP g 286 " --> pdb=" O LEU g 249 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER g 281 " --> pdb=" O LYS g 327 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE g 329 " --> pdb=" O SER g 281 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE g 283 " --> pdb=" O ILE g 329 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA g 331 " --> pdb=" O ILE g 283 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE g 285 " --> pdb=" O ALA g 331 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL g 223 " --> pdb=" O ALA g 330 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR g 332 " --> pdb=" O VAL g 223 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET g 225 " --> pdb=" O THR g 332 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR g 226 " --> pdb=" O ILE g 352 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 98 through 99 removed outlier: 7.441A pdb=" N ASP h 98 " --> pdb=" O LEU h 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'h' and resid 212 through 213 removed outlier: 7.007A pdb=" N SER h 244 " --> pdb=" O LYS h 290 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE h 292 " --> pdb=" O SER h 244 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE h 246 " --> pdb=" O ILE h 292 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA h 294 " --> pdb=" O ILE h 246 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'l' and resid 377 through 378 removed outlier: 3.708A pdb=" N ILE l 377 " --> pdb=" O ILE l 386 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'm' and resid 313 through 315 Processing sheet with id=AJ3, first strand: chain 'n' and resid 51 through 52 removed outlier: 4.283A pdb=" N GLY n 93 " --> pdb=" O LEU n 39 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY n 41 " --> pdb=" O ILE n 91 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE n 91 " --> pdb=" O GLY n 41 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'o' and resid 144 through 145 Processing sheet with id=AJ5, first strand: chain 'p' and resid 7 through 8 removed outlier: 5.983A pdb=" N MET p 7 " --> pdb=" O ILE p 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'q' and resid 67 through 73 removed outlier: 6.376A pdb=" N VAL q 69 " --> pdb=" O GLU q 60 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU q 60 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP q 71 " --> pdb=" O LEU q 58 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY q 55 " --> pdb=" O TRP q 111 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP q 111 " --> pdb=" O GLY q 55 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET q 57 " --> pdb=" O VAL q 109 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 143 through 146 removed outlier: 3.558A pdb=" N VAL q 144 " --> pdb=" O ASP q 158 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP q 158 " --> pdb=" O VAL q 144 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP q 146 " --> pdb=" O VAL q 156 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL q 156 " --> pdb=" O ASP q 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 3293 hydrogen bonds defined for protein. 9402 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: 34.81 Time building geometry restraints manager: 17.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.95: 1 0.95 - 1.27: 13149 1.27 - 1.59: 63421 1.59 - 1.91: 684 1.91 - 2.23: 2 Bond restraints: 77257 Sorted by residual: bond pdb=" C SER B 168 " pdb=" N VAL B 172 " ideal model delta sigma weight residual 1.332 2.148 -0.816 1.36e-02 5.41e+03 3.60e+03 bond pdb=" C THR N 201 " pdb=" N PRO N 202 " ideal model delta sigma weight residual 1.341 2.234 -0.893 1.60e-02 3.91e+03 3.12e+03 bond pdb=" C VAL Q 45 " pdb=" N GLU Q 46 " ideal model delta sigma weight residual 1.332 0.632 0.700 1.40e-02 5.10e+03 2.50e+03 bond pdb=" C CYS Q 63 " pdb=" N ALA Q 64 " ideal model delta sigma weight residual 1.331 1.550 -0.219 1.34e-02 5.57e+03 2.67e+02 bond pdb=" CA GLU S 237 " pdb=" C GLU S 237 " ideal model delta sigma weight residual 1.523 1.439 0.085 1.34e-02 5.57e+03 3.98e+01 ... (remaining 77252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.46: 104823 12.46 - 24.93: 61 24.93 - 37.39: 3 37.39 - 49.86: 0 49.86 - 62.32: 3 Bond angle restraints: 104890 Sorted by residual: angle pdb=" O CYS Q 63 " pdb=" C CYS Q 63 " pdb=" N ALA Q 64 " ideal model delta sigma weight residual 123.16 98.84 24.32 1.26e+00 6.30e-01 3.72e+02 angle pdb=" C ARG e 323 " pdb=" N PRO e 324 " pdb=" CD PRO e 324 " ideal model delta sigma weight residual 125.00 62.68 62.32 4.10e+00 5.95e-02 2.31e+02 angle pdb=" C GLU d 145 " pdb=" N PRO d 146 " pdb=" CD PRO d 146 " ideal model delta sigma weight residual 125.00 63.65 61.35 4.10e+00 5.95e-02 2.24e+02 angle pdb=" C PRO g 228 " pdb=" N PRO g 229 " pdb=" CD PRO g 229 " ideal model delta sigma weight residual 125.00 71.32 53.68 4.10e+00 5.95e-02 1.71e+02 angle pdb=" CA HIS P 240 " pdb=" C HIS P 240 " pdb=" N GLU P 241 " ideal model delta sigma weight residual 119.80 102.63 17.17 1.34e+00 5.57e-01 1.64e+02 ... (remaining 104885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 45977 35.12 - 70.24: 652 70.24 - 105.36: 50 105.36 - 140.49: 11 140.49 - 175.61: 6 Dihedral angle restraints: 46696 sinusoidal: 16352 harmonic: 30344 Sorted by residual: dihedral pdb=" CA LEU n 70 " pdb=" C LEU n 70 " pdb=" N ASP n 71 " pdb=" CA ASP n 71 " ideal model delta harmonic sigma weight residual 180.00 46.29 133.71 0 5.00e+00 4.00e-02 7.15e+02 dihedral pdb=" CA ALA i 661 " pdb=" C ALA i 661 " pdb=" N GLY i 662 " pdb=" CA GLY i 662 " ideal model delta harmonic sigma weight residual 180.00 60.98 119.02 0 5.00e+00 4.00e-02 5.67e+02 dihedral pdb=" CA ALA h 242 " pdb=" C ALA h 242 " pdb=" N PRO h 243 " pdb=" CA PRO h 243 " ideal model delta harmonic sigma weight residual 180.00 80.97 99.03 0 5.00e+00 4.00e-02 3.92e+02 ... (remaining 46693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 12030 0.198 - 0.397: 197 0.397 - 0.595: 10 0.595 - 0.794: 1 0.794 - 0.992: 1 Chirality restraints: 12239 Sorted by residual: chirality pdb=" CA GLU d 254 " pdb=" N GLU d 254 " pdb=" C GLU d 254 " pdb=" CB GLU d 254 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASN i 665 " pdb=" N ASN i 665 " pdb=" C ASN i 665 " pdb=" CB ASN i 665 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" CG LEU d 163 " pdb=" CB LEU d 163 " pdb=" CD1 LEU d 163 " pdb=" CD2 LEU d 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 12236 not shown) Planarity restraints: 13718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 168 " 0.098 2.00e-02 2.50e+03 1.75e-01 3.07e+02 pdb=" C SER B 168 " -0.300 2.00e-02 2.50e+03 pdb=" O SER B 168 " 0.139 2.00e-02 2.50e+03 pdb=" N VAL B 172 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER P 168 " 0.086 2.00e-02 2.50e+03 1.69e-01 2.86e+02 pdb=" C SER P 168 " -0.292 2.00e-02 2.50e+03 pdb=" O SER P 168 " 0.117 2.00e-02 2.50e+03 pdb=" N ALA P 169 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 236 " -0.072 2.00e-02 2.50e+03 1.57e-01 2.48e+02 pdb=" C LEU S 236 " 0.272 2.00e-02 2.50e+03 pdb=" O LEU S 236 " -0.113 2.00e-02 2.50e+03 pdb=" N GLU S 237 " -0.087 2.00e-02 2.50e+03 ... (remaining 13715 not shown) Histogram of nonbonded interaction distances: 0.19 - 1.13: 77 1.13 - 2.07: 399 2.07 - 3.01: 42403 3.01 - 3.96: 203862 3.96 - 4.90: 363653 Warning: very small nonbonded interaction distances. Nonbonded interactions: 610394 Sorted by model distance: nonbonded pdb=" CD1 LEU m 134 " pdb=" OE1 GLU m 169 " model vdw 0.185 3.460 nonbonded pdb=" NE ARG e 326 " pdb=" NZ LYS h 142 " model vdw 0.188 3.200 nonbonded pdb=" CZ ARG d 343 " pdb=" O3A ADP c 501 " model vdw 0.217 2.616 nonbonded pdb=" OE1 GLN c 165 " pdb=" CA PHE c 237 " model vdw 0.275 3.470 nonbonded pdb=" CZ ARG h 117 " pdb=" CE1 TYR h 121 " model vdw 0.310 3.570 ... (remaining 610389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 50 or (resid 51 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 163 or (r \ esid 164 and (name N or name CA or name C or name O or name CB )) or resid 165 t \ hrough 173 or (resid 174 through 175 and (name N or name CA or name C or name O \ or name CB )) or resid 176 or (resid 177 and (name N or name CA or name C or nam \ e O or name CB )) or resid 178 through 232)) selection = (chain 'O' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 51 or (resid 52 and (name N or name CA or name C or name O \ or name CB )) or resid 53 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 139 or (resid 140 and (name N or \ name CA or name C or name O or name CB )) or resid 141 through 148 or (resid 149 \ and (name N or name CA or name C or name O or name CB )) or resid 150 through 1 \ 98 or (resid 199 and (name N or name CA or name C or name O or name CB )) or res \ id 200 or (resid 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 232)) } ncs_group { reference = (chain 'B' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 through 231 or (resid 232 a \ nd (name N or name CA or name C or name O or name CB )) or resid 233 through 237 \ or (resid 238 through 243 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'P' and (resid 2 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 168 or resid 172 through 200 or res \ id 206 through 209 or (resid 210 and (name N or name CA or name C or name O or n \ ame CB )) or resid 211 through 243)) } ncs_group { reference = (chain 'C' and (resid 2 through 47 or (resid 49 through 52 and (name N or name C \ A or name C or name O or name CB )) or resid 53 through 181 or (resid 182 and (n \ ame N or name CA or name C or name O or name CB )) or resid 183 through 188 or ( \ resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ through 199 or resid 201 through 230 or (resid 231 through 235 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 2 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 165 or (resid 166 and (name N or na \ me CA or name C or name O or name CB )) or resid 167 through 169 or (resid 170 a \ nd (name N or name CA or name C or name O or name CB )) or resid 171 through 173 \ or (resid 174 and (name N or name CA or name C or name O or name CB )) or resid \ 175 through 198 or (resid 199 and (name N or name CA or name C or name O or nam \ e CB )) or resid 201 through 203 or (resid 204 and (name N or name CA or name C \ or name O or name CB )) or resid 205 or (resid 206 through 207 and (name N or na \ me CA or name C or name O or name CB )) or resid 208 through 214 or (resid 215 a \ nd (name N or name CA or name C or name O or name CB )) or resid 216 through 222 \ or (resid 223 through 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 235)) } ncs_group { reference = (chain 'D' and (resid 9 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 174 or (resid 175 an \ d (name N or name CA or name C or name O or name CB )) or resid 176 through 241) \ ) selection = (chain 'R' and (resid 9 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 171 or (resid 172 through 173 an \ d (name N or name CA or name C or name O or name CB )) or resid 174 through 186 \ or (resid 187 and (name N or name CA or name C or name O or name CB )) or resid \ 188 through 195 or (resid 196 and (name N or name CA or name C or name O or name \ CB )) or resid 197 through 208 or (resid 209 and (name N or name CA or name C o \ r name O or name CB )) or resid 210 through 240 or (resid 241 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)))) } ncs_group { reference = (chain 'E' and (resid 4 through 188 or (resid 189 and (name N or name CA or name \ C or name O or name CB )) or resid 190 through 216 or (resid 217 through 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 235 \ or (resid 236 through 237 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'S' and (resid 4 through 50 or (resid 51 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 201 or (resid 202 throug \ h 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thro \ ugh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) o \ r resid 209 through 237)) } ncs_group { reference = (chain 'F' and (resid 6 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 241)) selection = (chain 'T' and (resid 6 through 203 or resid 208 through 241)) } ncs_group { reference = (chain 'G' and (resid 8 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 144 or (resid 145 thro \ ugh 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 169 or (resid 170 through 171 and (name N or name CA or name C or name O o \ r name CB )) or resid 172 through 208 or (resid 209 and (name N or name CA or na \ me C or name O or name CB )) or resid 210 through 225 or (resid 226 and (name N \ or name CA or name C or name O or name CB )) or resid 227 through 242)) selection = (chain 'U' and (resid 8 through 187 or resid 192 through 195 or (resid 196 and ( \ name N or name CA or name C or name O or name CB )) or resid 197 through 242)) } ncs_group { reference = (chain 'H' and (resid 1 through 103 or resid 105 through 181 or (resid 182 and ( \ name N or name CA or name C or name O or name CB )) or resid 183 through 193 or \ (resid 194 through 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 or (resid 203 through 206 and (name N or name CA or \ name C or name O or name CB )) or resid 207 through 219 or (resid 220 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'V' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 103 or resid 105 through 220)) } ncs_group { reference = (chain 'I' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 204)) selection = (chain 'W' and (resid 1 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)))) } ncs_group { reference = (chain 'J' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 196)) selection = (chain 'X' and (resid 1 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 153 or (resid 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 196)) } ncs_group { reference = chain 'K' selection = (chain 'Y' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 105 or (resid 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 through 200)) } ncs_group { reference = (chain 'L' and (resid 1 through 2 or resid 4 through 160 or (resid 161 through 1 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 163 through \ 213)) selection = (chain 'Z' and (resid 1 through 2 or resid 4 through 172 or (resid 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB )) or resid 201 thr \ ough 213)) } ncs_group { reference = (chain 'M' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 205 or (resid 206 and (name N or \ name CA or name C or name O or name CB )) or resid 207 through 216)) selection = chain 'a' } ncs_group { reference = (chain 'N' and (resid 1 through 198 or (resid 199 through 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 202)) selection = (chain 'b' and (resid 1 through 201 or resid 203)) } ncs_group { reference = chain 't' selection = chain 'u' } 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=0.50 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.110 Check model and map are aligned: 0.440 Set scattering table: 0.520 Process input model: 144.170 Find NCS groups from input model: 4.680 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.893 77257 Z= 0.581 Angle : 1.467 62.323 104890 Z= 0.809 Chirality : 0.072 0.992 12239 Planarity : 0.011 0.261 13718 Dihedral : 13.187 175.607 27121 Min Nonbonded Distance : 0.185 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 1.71 % Allowed : 14.37 % Favored : 83.92 % Rotamer: Outliers : 3.10 % Allowed : 7.64 % Favored : 89.27 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.04 % Twisted Proline : 5.67 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.06), residues: 10342 helix: -3.45 (0.05), residues: 3900 sheet: -3.02 (0.11), residues: 1571 loop : -3.92 (0.07), residues: 4871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 138 HIS 0.023 0.003 HIS S 69 PHE 0.035 0.004 PHE N 8 TYR 0.054 0.003 TYR e 111 ARG 0.018 0.001 ARG f 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1482 time to evaluate : 6.665 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 TARDY: cannot create tardy model for: "TYR e 417 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.8764 (p0) cc_final: 0.8557 (p0) REVERT: B 108 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 235 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5769 (pt0) REVERT: D 122 GLN cc_start: 0.8525 (tt0) cc_final: 0.8304 (tt0) REVERT: E 68 ASN cc_start: 0.7534 (t160) cc_final: 0.7046 (t0) REVERT: E 115 LYS cc_start: 0.9445 (tmtm) cc_final: 0.8927 (tttm) REVERT: F 32 ASN cc_start: 0.7739 (p0) cc_final: 0.7235 (p0) REVERT: F 143 ASN cc_start: 0.8111 (p0) cc_final: 0.7837 (p0) REVERT: H 42 TYR cc_start: 0.8861 (m-10) cc_final: 0.8538 (m-10) REVERT: H 204 CYS cc_start: 0.5298 (t) cc_final: 0.4611 (t) REVERT: I 11 MET cc_start: 0.8207 (ptm) cc_final: 0.7956 (ptm) REVERT: I 64 GLN cc_start: 0.7970 (mt0) cc_final: 0.7699 (mt0) REVERT: J 35 MET cc_start: 0.8527 (mtm) cc_final: 0.8298 (mtm) REVERT: J 163 CYS cc_start: 0.8056 (m) cc_final: 0.7790 (m) REVERT: J 166 GLU cc_start: 0.7844 (tp30) cc_final: 0.7525 (tp30) REVERT: J 190 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8672 (p0) REVERT: K 56 GLU cc_start: 0.7417 (mp0) cc_final: 0.7143 (mp0) REVERT: M 50 MET cc_start: 0.7504 (mtp) cc_final: 0.7090 (ttp) REVERT: N 84 LYS cc_start: 0.8374 (ttpp) cc_final: 0.8007 (ttpt) REVERT: O 41 ASN cc_start: 0.8456 (p0) cc_final: 0.7981 (p0) REVERT: P 71 ASP cc_start: 0.7153 (p0) cc_final: 0.6563 (p0) REVERT: S 68 ASN cc_start: 0.7659 (t160) cc_final: 0.7254 (t0) REVERT: T 163 CYS cc_start: 0.6715 (p) cc_final: 0.6118 (p) REVERT: U 123 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8843 (tm-30) REVERT: V 29 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7941 (mtpp) REVERT: W 3 MET cc_start: 0.8551 (mmm) cc_final: 0.8106 (mmm) REVERT: W 77 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7643 (tm-30) REVERT: W 146 TYR cc_start: 0.7905 (m-80) cc_final: 0.7651 (m-80) REVERT: X 38 MET cc_start: 0.7562 (mmm) cc_final: 0.7319 (mmm) REVERT: Y 37 ILE cc_start: 0.9084 (pt) cc_final: 0.8604 (mt) REVERT: a 69 GLN cc_start: 0.8310 (tp40) cc_final: 0.7985 (tp40) REVERT: b 61 TYR cc_start: 0.8846 (t80) cc_final: 0.8593 (t80) REVERT: b 164 MET cc_start: 0.6655 (ptm) cc_final: 0.6262 (ppp) REVERT: b 192 ASP cc_start: 0.6596 (p0) cc_final: 0.5975 (p0) REVERT: c 164 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7020 (tmt) REVERT: c 167 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6129 (mt-10) REVERT: c 234 ASP cc_start: 0.6223 (t0) cc_final: 0.5892 (t0) REVERT: c 348 LEU cc_start: 0.8032 (tm) cc_final: 0.7709 (tp) REVERT: d 145 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: d 197 ILE cc_start: 0.9350 (tp) cc_final: 0.9055 (tp) REVERT: d 309 MET cc_start: 0.8083 (tmm) cc_final: 0.7576 (tmm) REVERT: d 327 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7659 (m) REVERT: d 387 LYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5704 (mmmm) REVERT: e 208 PRO cc_start: 0.6010 (Cg_endo) cc_final: 0.5716 (Cg_exo) REVERT: e 309 MET cc_start: 0.7396 (ptp) cc_final: 0.7159 (ptp) REVERT: e 411 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5768 (pm20) REVERT: e 412 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5389 (tp40) REVERT: f 225 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.7954 (m90) REVERT: f 289 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9001 (tt) REVERT: g 88 TYR cc_start: 0.7378 (t80) cc_final: 0.7056 (t80) REVERT: g 342 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8962 (tt) REVERT: g 437 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5933 (p90) REVERT: h 80 MET cc_start: 0.4886 (mpp) cc_final: 0.4516 (mmm) REVERT: h 137 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8665 (pp) REVERT: h 148 TYR cc_start: 0.5550 (m-80) cc_final: 0.5091 (m-80) REVERT: l 138 PHE cc_start: 0.8530 (t80) cc_final: 0.8145 (t80) outliers start: 219 outliers final: 109 residues processed: 1657 average time/residue: 0.7476 time to fit residues: 2074.4047 Evaluate side-chains 1004 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 881 time to evaluate : 6.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain D residue 20 ARG Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain J residue 190 ASN Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 224 GLU Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain U residue 166 THR Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 28 ASP Chi-restraints excluded: chain X residue 190 ASN Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain c residue 161 VAL Chi-restraints excluded: chain c residue 164 MET Chi-restraints excluded: chain c residue 165 GLN Chi-restraints excluded: chain c residue 167 GLU Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 222 LYS Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 333 ARG Chi-restraints excluded: chain d residue 142 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 235 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 265 LYS Chi-restraints excluded: chain d residue 266 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 276 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 327 VAL Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain d residue 387 LYS Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 390 LEU Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 323 ARG Chi-restraints excluded: chain e residue 326 ARG Chi-restraints excluded: chain e residue 398 ASP Chi-restraints excluded: chain e residue 399 PHE Chi-restraints excluded: chain e residue 407 ILE Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain e residue 411 GLU Chi-restraints excluded: chain e residue 412 GLN Chi-restraints excluded: chain e residue 415 GLU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain e residue 417 TYR Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 70 ILE Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 225 HIS Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain g residue 332 THR Chi-restraints excluded: chain g residue 342 LEU Chi-restraints excluded: chain g residue 343 LEU Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 396 CYS Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain g residue 425 LEU Chi-restraints excluded: chain g residue 430 LYS Chi-restraints excluded: chain g residue 431 LYS Chi-restraints excluded: chain g residue 432 LYS Chi-restraints excluded: chain g residue 436 GLN Chi-restraints excluded: chain g residue 437 TYR Chi-restraints excluded: chain h residue 69 GLN Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 114 VAL Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 135 VAL Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 140 VAL Chi-restraints excluded: chain h residue 142 LYS Chi-restraints excluded: chain h residue 145 ASP Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 196 LYS Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain h residue 271 ARG Chi-restraints excluded: chain h residue 349 GLU Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain l residue 157 LEU Chi-restraints excluded: chain l residue 160 MET Chi-restraints excluded: chain l residue 163 LYS Chi-restraints excluded: chain l residue 165 LEU Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 169 GLU Chi-restraints excluded: chain m residue 199 GLU Chi-restraints excluded: chain m residue 202 LEU Chi-restraints excluded: chain m residue 204 THR Chi-restraints excluded: chain m residue 207 THR Chi-restraints excluded: chain m residue 208 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 872 optimal weight: 20.0000 chunk 782 optimal weight: 0.8980 chunk 434 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 528 optimal weight: 2.9990 chunk 418 optimal weight: 5.9990 chunk 809 optimal weight: 0.0980 chunk 313 optimal weight: 0.8980 chunk 492 optimal weight: 0.9980 chunk 602 optimal weight: 1.9990 chunk 938 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 84 ASN B 198 ASN D 99 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS E 68 ASN E 190 HIS F 105 ASN F 201 HIS H 66 HIS I 161 HIS I 172 ASN J 71 ASN J 193 ASN L 8 ASN M 38 ASN M 104 ASN N 53 GLN O 62 HIS ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN O 188 HIS P 40 ASN P 84 ASN P 88 ASN P 95 GLN P 142 HIS P 198 ASN Q 122 ASN R 99 HIS R 186 HIS S 8 ASN ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 GLN T 97 ASN T 105 ASN T 110 HIS ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 HIS V 66 HIS X 71 ASN Y 62 GLN Z 8 ASN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 188 GLN b 53 GLN c 148 GLN ** c 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 433 ASN d 153 ASN d 154 HIS ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 133 HIS f 254 GLN f 262 ASN f 316 HIS f 339 ASN f 345 ASN g 436 GLN h 337 ASN ** m 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 178 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 77257 Z= 0.249 Angle : 0.917 33.017 104890 Z= 0.468 Chirality : 0.050 0.460 12239 Planarity : 0.008 0.170 13718 Dihedral : 10.806 175.997 11649 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.05 % Favored : 87.26 % Rotamer: Outliers : 3.99 % Allowed : 12.94 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 3.67 % Twisted General : 0.57 % 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: -4.20 (0.07), residues: 10345 helix: -1.95 (0.07), residues: 4072 sheet: -2.59 (0.12), residues: 1557 loop : -3.63 (0.08), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 91 HIS 0.017 0.001 HIS E 69 PHE 0.047 0.002 PHE W 163 TYR 0.047 0.002 TYR A 228 ARG 0.012 0.001 ARG d 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1076 time to evaluate : 6.611 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: B 33 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7650 (p) REVERT: B 108 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 21 TYR cc_start: 0.8978 (m-10) cc_final: 0.8407 (m-10) REVERT: C 52 LYS cc_start: 0.6830 (tptp) cc_final: 0.6471 (tptp) REVERT: C 235 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5969 (pt0) REVERT: D 22 PHE cc_start: 0.8383 (m-80) cc_final: 0.8166 (m-10) REVERT: D 157 ASP cc_start: 0.7559 (m-30) cc_final: 0.7357 (m-30) REVERT: E 66 VAL cc_start: 0.8008 (t) cc_final: 0.7791 (t) REVERT: E 68 ASN cc_start: 0.7419 (t0) cc_final: 0.7112 (t0) REVERT: E 115 LYS cc_start: 0.9411 (tmtm) cc_final: 0.9097 (tttm) REVERT: E 140 MET cc_start: 0.7740 (pmm) cc_final: 0.7158 (ptp) REVERT: F 32 ASN cc_start: 0.7573 (p0) cc_final: 0.7305 (p0) REVERT: F 152 ASP cc_start: 0.8286 (m-30) cc_final: 0.7958 (m-30) REVERT: F 170 GLN cc_start: 0.8468 (mm110) cc_final: 0.7968 (mm110) REVERT: F 181 MET cc_start: 0.8053 (tpp) cc_final: 0.7818 (tpp) REVERT: F 184 MET cc_start: 0.8101 (pmm) cc_final: 0.7564 (pmm) REVERT: G 21 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.7855 (ttm-80) REVERT: G 112 ASP cc_start: 0.8121 (p0) cc_final: 0.7549 (p0) REVERT: I 33 MET cc_start: 0.8581 (tmm) cc_final: 0.8319 (tmm) REVERT: I 167 SER cc_start: 0.8817 (p) cc_final: 0.8590 (p) REVERT: I 182 MET cc_start: 0.7750 (mtp) cc_final: 0.7504 (mtm) REVERT: J 166 GLU cc_start: 0.7824 (tp30) cc_final: 0.7612 (tp30) REVERT: L 213 ASP cc_start: 0.6732 (p0) cc_final: 0.6528 (p0) REVERT: N 119 MET cc_start: 0.8182 (ppp) cc_final: 0.7641 (ptt) REVERT: P 184 MET cc_start: 0.6721 (mmm) cc_final: 0.6301 (tpp) REVERT: T 185 THR cc_start: 0.8048 (p) cc_final: 0.7752 (t) REVERT: U 105 TYR cc_start: 0.8948 (m-80) cc_final: 0.8422 (m-80) REVERT: U 189 TRP cc_start: 0.4912 (t-100) cc_final: 0.4111 (t-100) REVERT: W 77 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7191 (tm-30) REVERT: X 37 LYS cc_start: 0.8170 (tptt) cc_final: 0.7755 (tptt) REVERT: X 38 MET cc_start: 0.7620 (mmm) cc_final: 0.7009 (mmm) REVERT: X 58 GLU cc_start: 0.7911 (pp20) cc_final: 0.7626 (pp20) REVERT: Z 130 TYR cc_start: 0.8218 (p90) cc_final: 0.8009 (p90) REVERT: a 69 GLN cc_start: 0.8322 (tp40) cc_final: 0.7990 (tp40) REVERT: a 86 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8238 (mmp80) REVERT: b 193 GLN cc_start: 0.8366 (mp10) cc_final: 0.8155 (mp10) REVERT: d 145 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: d 266 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (tt) REVERT: d 271 PHE cc_start: 0.8549 (m-10) cc_final: 0.8182 (m-10) REVERT: d 314 ASN cc_start: 0.7838 (t0) cc_final: 0.7493 (t0) REVERT: d 326 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5096 (mmmm) REVERT: d 365 PHE cc_start: 0.8204 (t80) cc_final: 0.7818 (t80) REVERT: e 208 PRO cc_start: 0.5886 (Cg_endo) cc_final: 0.5671 (Cg_exo) REVERT: e 267 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7409 (mt) REVERT: e 358 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6564 (m) REVERT: e 395 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6167 (pp) REVERT: e 412 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.6003 (tp-100) REVERT: f 64 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8178 (tp) REVERT: f 182 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (tt) REVERT: g 88 TYR cc_start: 0.7115 (t80) cc_final: 0.6915 (t80) REVERT: h 63 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7262 (pt) REVERT: h 69 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: h 139 MET cc_start: 0.7620 (tpt) cc_final: 0.7414 (tpt) REVERT: h 148 TYR cc_start: 0.5644 (m-80) cc_final: 0.4681 (m-80) REVERT: h 180 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8119 (mt) REVERT: h 205 HIS cc_start: 0.7799 (m90) cc_final: 0.7540 (m-70) REVERT: l 138 PHE cc_start: 0.8604 (t80) cc_final: 0.8084 (t80) REVERT: l 162 ASP cc_start: 0.2323 (OUTLIER) cc_final: 0.1927 (m-30) REVERT: l 163 LYS cc_start: 0.2387 (OUTLIER) cc_final: 0.1971 (mmmm) REVERT: l 212 MET cc_start: 0.7929 (tpt) cc_final: 0.7701 (tpt) REVERT: m 143 TYR cc_start: 0.7084 (t80) cc_final: 0.6866 (t80) REVERT: m 157 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8215 (mp) outliers start: 282 outliers final: 119 residues processed: 1289 average time/residue: 0.7304 time to fit residues: 1636.5984 Evaluate side-chains 993 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 855 time to evaluate : 6.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 85 CYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 148 CYS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain O residue 111 GLN Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 186 HIS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain T residue 227 VAL Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain W residue 4 SER Chi-restraints excluded: chain W residue 17 ASN Chi-restraints excluded: chain X residue 96 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 82 SER Chi-restraints excluded: chain a residue 86 ARG Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 220 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 164 MET Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 266 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 326 LYS Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 MET Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 324 PRO Chi-restraints excluded: chain e residue 358 VAL Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 411 GLU Chi-restraints excluded: chain e residue 412 GLN Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain f residue 321 THR Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 291 ILE Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 342 LEU Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 356 MET Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 396 CYS Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain g residue 431 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 GLN Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 126 ILE Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 178 LEU Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain h residue 271 ARG Chi-restraints excluded: chain h residue 349 GLU Chi-restraints excluded: chain h residue 350 LEU Chi-restraints excluded: chain l residue 157 LEU Chi-restraints excluded: chain l residue 162 ASP Chi-restraints excluded: chain l residue 163 LYS Chi-restraints excluded: chain l residue 165 LEU Chi-restraints excluded: chain l residue 223 LYS Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 251 LEU Chi-restraints excluded: chain l residue 256 LEU Chi-restraints excluded: chain l residue 259 ILE Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 521 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 chunk 780 optimal weight: 1.9990 chunk 638 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 939 optimal weight: 6.9990 chunk 1015 optimal weight: 8.9990 chunk 836 optimal weight: 3.9990 chunk 931 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 753 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN A 108 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN F 22 GLN F 143 ASN G 90 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 HIS L 36 HIS L 77 HIS ** O 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 HIS R 204 GLN S 8 ASN S 20 HIS S 152 ASN T 97 ASN T 110 HIS ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN U 92 GLN X 61 GLN Y 85 ASN Z 77 HIS ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN ** b 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 165 GLN d 154 HIS d 241 ASN d 242 GLN e 380 GLN ** e 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 218 GLN h 171 HIS ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 170 GLN l 207 GLN ** m 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 77257 Z= 0.328 Angle : 0.843 15.941 104890 Z= 0.435 Chirality : 0.049 0.293 12239 Planarity : 0.007 0.151 13718 Dihedral : 9.558 178.548 11488 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.42 % Favored : 87.08 % Rotamer: Outliers : 4.29 % Allowed : 14.93 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 3.11 % Twisted General : 0.39 % 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: -3.45 (0.08), residues: 10345 helix: -1.04 (0.08), residues: 4115 sheet: -2.38 (0.12), residues: 1598 loop : -3.46 (0.08), residues: 4632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP a 107 HIS 0.020 0.002 HIS R 186 PHE 0.046 0.002 PHE W 163 TYR 0.038 0.002 TYR e 403 ARG 0.025 0.001 ARG m 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 922 time to evaluate : 6.694 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9133 (ptpt) REVERT: A 88 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7796 (mtp180) REVERT: A 117 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: B 33 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7628 (p) REVERT: B 108 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7311 (tm-30) REVERT: B 184 MET cc_start: 0.7778 (tpt) cc_final: 0.7543 (tpt) REVERT: C 235 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5966 (pt0) REVERT: D 13 ASN cc_start: 0.8443 (m-40) cc_final: 0.8216 (m-40) REVERT: F 32 ASN cc_start: 0.7625 (p0) cc_final: 0.7401 (p0) REVERT: F 75 MET cc_start: 0.8436 (mmm) cc_final: 0.8009 (tpt) REVERT: F 135 PHE cc_start: 0.9009 (p90) cc_final: 0.8547 (p90) REVERT: F 150 MET cc_start: 0.8121 (tmm) cc_final: 0.7833 (tmm) REVERT: G 21 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.7863 (ttm-80) REVERT: G 46 ASP cc_start: 0.6539 (p0) cc_final: 0.6320 (p0) REVERT: G 112 ASP cc_start: 0.8236 (p0) cc_final: 0.7844 (p0) REVERT: H 127 MET cc_start: 0.8695 (mmt) cc_final: 0.8491 (mmt) REVERT: I 145 MET cc_start: 0.7902 (mtt) cc_final: 0.7678 (mtt) REVERT: J 167 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8879 (tm) REVERT: K 56 GLU cc_start: 0.7814 (mp0) cc_final: 0.7571 (mp0) REVERT: K 112 TYR cc_start: 0.8335 (m-80) cc_final: 0.8077 (m-80) REVERT: K 140 ASP cc_start: 0.7896 (t0) cc_final: 0.7204 (t0) REVERT: L 121 VAL cc_start: 0.9549 (OUTLIER) cc_final: 0.9348 (t) REVERT: L 184 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7473 (tt0) REVERT: L 213 ASP cc_start: 0.6783 (p0) cc_final: 0.6508 (p0) REVERT: N 120 MET cc_start: 0.7910 (ttp) cc_final: 0.7498 (ttp) REVERT: O 198 PHE cc_start: 0.6506 (t80) cc_final: 0.5958 (t80) REVERT: Q 47 LYS cc_start: 0.4115 (OUTLIER) cc_final: 0.3720 (ttmt) REVERT: R 98 ASN cc_start: 0.8883 (m-40) cc_final: 0.8678 (t0) REVERT: R 192 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7718 (mmtp) REVERT: S 84 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8987 (tp) REVERT: T 93 GLU cc_start: 0.7184 (mp0) cc_final: 0.6881 (mp0) REVERT: T 185 THR cc_start: 0.7983 (p) cc_final: 0.7686 (t) REVERT: U 189 TRP cc_start: 0.5267 (t-100) cc_final: 0.4418 (t-100) REVERT: W 11 MET cc_start: 0.7698 (ptm) cc_final: 0.7320 (ttm) REVERT: W 13 MET cc_start: 0.8501 (ptm) cc_final: 0.8089 (ttp) REVERT: W 77 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7449 (tm-30) REVERT: W 170 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8577 (mmm) REVERT: X 38 MET cc_start: 0.7739 (mmm) cc_final: 0.7061 (mmm) REVERT: X 49 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8331 (tm-30) REVERT: X 132 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.7237 (m170) REVERT: X 165 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: X 166 GLU cc_start: 0.8302 (tp30) cc_final: 0.7517 (tp30) REVERT: Y 56 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7094 (mt-10) REVERT: Z 33 PHE cc_start: 0.7181 (m-80) cc_final: 0.6950 (m-80) REVERT: Z 148 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8752 (tm) REVERT: a 69 GLN cc_start: 0.8399 (tp40) cc_final: 0.8113 (tp40) REVERT: a 86 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8467 (tpp80) REVERT: c 168 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: d 145 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5550 (mp0) REVERT: d 224 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9011 (pp) REVERT: d 266 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7841 (tt) REVERT: e 208 PRO cc_start: 0.6323 (Cg_endo) cc_final: 0.5996 (Cg_exo) REVERT: e 284 GLU cc_start: 0.8243 (pp20) cc_final: 0.7947 (tm-30) REVERT: e 324 PRO cc_start: 0.8559 (OUTLIER) cc_final: 0.8357 (Cg_endo) REVERT: e 412 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6344 (tp40) REVERT: f 64 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7681 (tp) REVERT: f 101 ASP cc_start: 0.8665 (t0) cc_final: 0.8271 (t70) REVERT: f 182 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (tt) REVERT: g 88 TYR cc_start: 0.7265 (t80) cc_final: 0.6964 (t80) REVERT: h 63 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7324 (pt) REVERT: h 69 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: h 148 TYR cc_start: 0.6022 (m-80) cc_final: 0.4951 (m-80) REVERT: h 180 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8274 (mt) REVERT: h 385 MET cc_start: 0.8407 (ptp) cc_final: 0.8070 (mtm) REVERT: i 634 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7345 (Cg_endo) REVERT: l 153 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8971 (tm) REVERT: l 162 ASP cc_start: 0.2695 (OUTLIER) cc_final: 0.2399 (m-30) REVERT: l 212 MET cc_start: 0.8127 (tpt) cc_final: 0.7881 (tpt) REVERT: m 143 TYR cc_start: 0.7290 (t80) cc_final: 0.7018 (t80) REVERT: m 157 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8270 (mp) REVERT: m 196 GLN cc_start: 0.8497 (mp10) cc_final: 0.8273 (mp10) outliers start: 303 outliers final: 159 residues processed: 1158 average time/residue: 0.7073 time to fit residues: 1424.5309 Evaluate side-chains 1003 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 816 time to evaluate : 6.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 85 CYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 32 HIS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 147 MET Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 206 MET Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 152 ASN Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain W residue 17 ASN Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain W residue 203 MET Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 86 ARG Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 230 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 241 ASN Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 266 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 282 VAL Chi-restraints excluded: chain d residue 284 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 111 TYR Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 179 GLU Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 296 MET Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 324 PRO Chi-restraints excluded: chain e residue 411 GLU Chi-restraints excluded: chain e residue 412 GLN Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 103 THR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain f residue 321 THR Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 259 MET Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 356 MET Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain g residue 431 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 GLN Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 134 LEU Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain h residue 271 ARG Chi-restraints excluded: chain h residue 349 GLU Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 153 LEU Chi-restraints excluded: chain l residue 157 LEU Chi-restraints excluded: chain l residue 162 ASP Chi-restraints excluded: chain l residue 163 LYS Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 251 LEU Chi-restraints excluded: chain l residue 256 LEU Chi-restraints excluded: chain l residue 259 ILE Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 928 optimal weight: 50.0000 chunk 706 optimal weight: 0.9980 chunk 487 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 448 optimal weight: 7.9990 chunk 631 optimal weight: 5.9990 chunk 943 optimal weight: 7.9990 chunk 998 optimal weight: 40.0000 chunk 492 optimal weight: 5.9990 chunk 893 optimal weight: 30.0000 chunk 269 optimal weight: 0.6980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 97 GLN F 143 ASN G 12 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN R 186 HIS S 43 HIS S 68 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 156 ASN Z 8 ASN Z 36 HIS ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 HIS ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 241 ASN ** e 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 86 GLN g 194 GLN ** g 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 160 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 77257 Z= 0.421 Angle : 0.869 16.281 104890 Z= 0.449 Chirality : 0.050 0.315 12239 Planarity : 0.007 0.179 13718 Dihedral : 9.217 171.149 11467 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.15 % Favored : 86.40 % Rotamer: Outliers : 5.11 % Allowed : 16.01 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.82 % Twisted General : 0.30 % 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: -3.08 (0.08), residues: 10345 helix: -0.58 (0.08), residues: 4142 sheet: -2.34 (0.12), residues: 1620 loop : -3.38 (0.08), residues: 4583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 157 HIS 0.010 0.002 HIS L 77 PHE 0.045 0.002 PHE W 163 TYR 0.033 0.002 TYR S 24 ARG 0.015 0.001 ARG d 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 861 time to evaluate : 6.639 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7520 (mp-120) REVERT: A 117 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8315 (mtm) REVERT: A 220 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8864 (mt) REVERT: B 3 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7939 (ptm160) REVERT: B 108 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 184 MET cc_start: 0.8106 (tpt) cc_final: 0.7782 (tpt) REVERT: B 240 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6015 (m-70) REVERT: C 235 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6263 (pt0) REVERT: E 59 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (m-70) REVERT: E 68 ASN cc_start: 0.7630 (t160) cc_final: 0.7054 (t0) REVERT: E 117 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8804 (tm-30) REVERT: E 220 GLU cc_start: 0.7169 (tp30) cc_final: 0.6918 (tp30) REVERT: F 32 ASN cc_start: 0.7603 (p0) cc_final: 0.7343 (p0) REVERT: G 21 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.7726 (ttm-80) REVERT: G 206 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8852 (pp) REVERT: H 85 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: I 145 MET cc_start: 0.8007 (mtt) cc_final: 0.7788 (mtt) REVERT: J 167 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8900 (tm) REVERT: L 213 ASP cc_start: 0.6912 (p0) cc_final: 0.6681 (p0) REVERT: O 111 GLN cc_start: 0.8456 (mt0) cc_final: 0.8066 (mt0) REVERT: O 155 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: O 198 PHE cc_start: 0.6434 (t80) cc_final: 0.6184 (t80) REVERT: R 147 ASP cc_start: 0.8243 (m-30) cc_final: 0.7987 (m-30) REVERT: R 192 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7790 (mmtp) REVERT: S 84 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.8895 (tp) REVERT: S 88 MET cc_start: 0.8479 (ttp) cc_final: 0.8261 (ttp) REVERT: S 152 ASN cc_start: 0.8818 (m-40) cc_final: 0.8402 (m-40) REVERT: T 117 MET cc_start: 0.7826 (tpt) cc_final: 0.7360 (tpp) REVERT: T 122 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7394 (t80) REVERT: T 185 THR cc_start: 0.7977 (p) cc_final: 0.7540 (t) REVERT: V 157 GLU cc_start: 0.8012 (tp30) cc_final: 0.7756 (tp30) REVERT: W 77 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7412 (tm-30) REVERT: W 84 TYR cc_start: 0.7966 (t80) cc_final: 0.7725 (t80) REVERT: W 170 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8485 (mmm) REVERT: X 132 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.7191 (m170) REVERT: Y 45 MET cc_start: 0.8107 (mpp) cc_final: 0.7870 (mpp) REVERT: Z 43 CYS cc_start: 0.4905 (p) cc_final: 0.4667 (p) REVERT: Z 83 MET cc_start: 0.7874 (tpt) cc_final: 0.7319 (mmm) REVERT: Z 148 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8832 (tm) REVERT: Z 213 ASP cc_start: 0.6002 (p0) cc_final: 0.5753 (p0) REVERT: b 193 GLN cc_start: 0.8674 (mp10) cc_final: 0.8457 (mp10) REVERT: b 196 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (ptpp) REVERT: c 232 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7617 (ppp80) REVERT: d 145 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: d 187 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8491 (tp) REVERT: d 224 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9059 (pp) REVERT: d 419 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7484 (t80) REVERT: e 267 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8311 (mt) REVERT: e 284 GLU cc_start: 0.8509 (pp20) cc_final: 0.8261 (tm-30) REVERT: f 64 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7313 (tp) REVERT: f 101 ASP cc_start: 0.8677 (t0) cc_final: 0.8024 (t70) REVERT: f 110 TYR cc_start: 0.7581 (p90) cc_final: 0.7314 (p90) REVERT: g 88 TYR cc_start: 0.7415 (t80) cc_final: 0.7102 (t80) REVERT: g 132 TYR cc_start: 0.8361 (m-10) cc_final: 0.8055 (m-10) REVERT: g 175 MET cc_start: 0.8443 (mpp) cc_final: 0.8152 (mpp) REVERT: g 291 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8487 (pp) REVERT: h 63 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7321 (pt) REVERT: h 80 MET cc_start: 0.4948 (mpp) cc_final: 0.4444 (mpp) REVERT: h 148 TYR cc_start: 0.6186 (m-80) cc_final: 0.5198 (m-80) REVERT: h 180 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8474 (mt) REVERT: l 129 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8849 (mm) REVERT: l 148 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8207 (t70) REVERT: l 153 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9053 (tm) REVERT: l 212 MET cc_start: 0.8182 (tpt) cc_final: 0.7909 (tpt) REVERT: m 86 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: m 143 TYR cc_start: 0.7428 (t80) cc_final: 0.7152 (t80) REVERT: m 157 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8390 (mp) outliers start: 361 outliers final: 196 residues processed: 1157 average time/residue: 0.6891 time to fit residues: 1393.6477 Evaluate side-chains 1015 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 786 time to evaluate : 6.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 32 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 88 ASN Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 90 ILE Chi-restraints excluded: chain T residue 122 TYR Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 227 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain W residue 4 SER Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 119 PHE Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 203 MET Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 118 MET Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 139 VAL Chi-restraints excluded: chain b residue 196 LYS Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 232 ARG Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 CYS Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 216 ILE Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain d residue 419 PHE Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain e residue 111 TYR Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 179 GLU Chi-restraints excluded: chain e residue 204 MET Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 296 MET Chi-restraints excluded: chain e residue 307 VAL Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 411 GLU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 103 THR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 248 SER Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain f residue 321 THR Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 225 MET Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 291 ILE Chi-restraints excluded: chain g residue 332 THR Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain g residue 431 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 145 ASP Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 153 LEU Chi-restraints excluded: chain l residue 163 LYS Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 256 LEU Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 831 optimal weight: 20.0000 chunk 566 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 743 optimal weight: 0.7980 chunk 411 optimal weight: 2.9990 chunk 852 optimal weight: 0.4980 chunk 690 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 509 optimal weight: 1.9990 chunk 896 optimal weight: 30.0000 chunk 251 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 GLN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 241 ASN e 137 ASN h 129 ASN ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 77257 Z= 0.214 Angle : 0.772 19.172 104890 Z= 0.394 Chirality : 0.047 0.299 12239 Planarity : 0.006 0.164 13718 Dihedral : 8.644 165.714 11444 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.71 % Favored : 87.90 % Rotamer: Outliers : 4.07 % Allowed : 17.82 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.27 % 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: -2.65 (0.08), residues: 10345 helix: -0.09 (0.08), residues: 4117 sheet: -2.07 (0.12), residues: 1585 loop : -3.27 (0.08), residues: 4643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 157 HIS 0.006 0.001 HIS d 120 PHE 0.036 0.002 PHE W 163 TYR 0.042 0.002 TYR A 228 ARG 0.010 0.000 ARG U 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 910 time to evaluate : 6.731 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. REVERT: A 88 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7421 (mtp180) REVERT: A 117 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: A 157 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7208 (p90) REVERT: A 220 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8835 (mt) REVERT: B 108 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 184 MET cc_start: 0.8056 (tpt) cc_final: 0.7685 (tpt) REVERT: B 240 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6012 (m-70) REVERT: E 122 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (ttm110) REVERT: F 75 MET cc_start: 0.8234 (mmm) cc_final: 0.7753 (tpp) REVERT: F 150 MET cc_start: 0.8105 (tmm) cc_final: 0.7819 (tmm) REVERT: G 21 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.7526 (ttm-80) REVERT: G 206 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (pp) REVERT: H 85 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: I 119 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7165 (p90) REVERT: I 145 MET cc_start: 0.7857 (mtt) cc_final: 0.7632 (mtt) REVERT: J 167 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8955 (tm) REVERT: K 100 MET cc_start: 0.8739 (mmm) cc_final: 0.8454 (mpp) REVERT: L 213 ASP cc_start: 0.6742 (p0) cc_final: 0.6481 (p0) REVERT: O 111 GLN cc_start: 0.8497 (mt0) cc_final: 0.8197 (mt0) REVERT: O 155 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: O 198 PHE cc_start: 0.6281 (t80) cc_final: 0.6006 (t80) REVERT: R 81 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8919 (tm) REVERT: R 192 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7772 (mmtp) REVERT: T 117 MET cc_start: 0.7829 (tpt) cc_final: 0.7123 (tpp) REVERT: T 185 THR cc_start: 0.7797 (p) cc_final: 0.7446 (t) REVERT: U 117 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7571 (tpp80) REVERT: W 77 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7418 (tm-30) REVERT: W 84 TYR cc_start: 0.7921 (t80) cc_final: 0.7639 (t80) REVERT: W 95 TYR cc_start: 0.7680 (t80) cc_final: 0.7412 (t80) REVERT: W 170 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8594 (mmm) REVERT: X 132 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.7133 (m170) REVERT: X 165 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: Z 33 PHE cc_start: 0.6911 (m-80) cc_final: 0.6615 (m-80) REVERT: Z 130 TYR cc_start: 0.8042 (p90) cc_final: 0.7804 (p90) REVERT: Z 148 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8585 (tm) REVERT: Z 149 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8903 (pp) REVERT: b 32 ASP cc_start: 0.6543 (p0) cc_final: 0.5959 (p0) REVERT: b 164 MET cc_start: 0.6474 (tmm) cc_final: 0.6268 (tmm) REVERT: b 193 GLN cc_start: 0.8649 (mp10) cc_final: 0.8394 (mp10) REVERT: c 376 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8580 (mt) REVERT: d 145 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: d 224 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8924 (pp) REVERT: d 257 GLN cc_start: 0.6441 (mt0) cc_final: 0.6218 (pm20) REVERT: e 89 ILE cc_start: 0.9381 (pp) cc_final: 0.9121 (pt) REVERT: e 267 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8301 (mt) REVERT: e 284 GLU cc_start: 0.8375 (pp20) cc_final: 0.8175 (tm-30) REVERT: f 64 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7312 (tp) REVERT: f 101 ASP cc_start: 0.8600 (t0) cc_final: 0.8349 (t70) REVERT: f 110 TYR cc_start: 0.7405 (p90) cc_final: 0.7131 (p90) REVERT: f 182 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8644 (tt) REVERT: g 88 TYR cc_start: 0.7471 (t80) cc_final: 0.7181 (t80) REVERT: g 132 TYR cc_start: 0.8193 (m-10) cc_final: 0.7832 (m-10) REVERT: g 281 SER cc_start: 0.8673 (t) cc_final: 0.8311 (m) REVERT: g 348 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8057 (mm) REVERT: h 80 MET cc_start: 0.5111 (mpp) cc_final: 0.4632 (mpp) REVERT: h 148 TYR cc_start: 0.5933 (m-80) cc_final: 0.3867 (m-80) REVERT: h 180 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8454 (mt) REVERT: h 205 HIS cc_start: 0.8073 (m90) cc_final: 0.7803 (m-70) REVERT: l 129 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8767 (mm) REVERT: l 167 VAL cc_start: 0.8869 (m) cc_final: 0.8629 (m) REVERT: l 194 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8210 (mtm-85) REVERT: l 212 MET cc_start: 0.8205 (tpt) cc_final: 0.7763 (tpt) REVERT: l 231 TYR cc_start: 0.8023 (m-10) cc_final: 0.7325 (m-80) REVERT: m 86 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: m 137 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (mmm-85) REVERT: m 138 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8849 (pt) REVERT: m 143 TYR cc_start: 0.7258 (t80) cc_final: 0.6971 (t80) REVERT: m 157 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8333 (mp) outliers start: 288 outliers final: 154 residues processed: 1145 average time/residue: 0.7458 time to fit residues: 1497.8550 Evaluate side-chains 997 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 813 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 119 PHE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 157 ARG Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain W residue 203 MET Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 306 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 376 LEU Chi-restraints excluded: chain c residue 377 CYS Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 241 ASN Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain d residue 419 PHE Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 135 HIS Chi-restraints excluded: chain e residue 179 GLU Chi-restraints excluded: chain e residue 204 MET Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 296 MET Chi-restraints excluded: chain e residue 307 VAL Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain f residue 321 THR Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 342 LEU Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 134 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 251 LEU Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 137 ARG Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 201 PHE Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 335 optimal weight: 0.9980 chunk 899 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 586 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 chunk 999 optimal weight: 5.9990 chunk 829 optimal weight: 30.0000 chunk 462 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 524 optimal weight: 5.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 143 HIS T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 GLN d 241 ASN ** d 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 129 ASN ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 77257 Z= 0.261 Angle : 0.777 12.080 104890 Z= 0.397 Chirality : 0.047 0.514 12239 Planarity : 0.006 0.139 13718 Dihedral : 8.361 156.711 11422 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.40 % Favored : 87.21 % Rotamer: Outliers : 4.55 % Allowed : 18.34 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.28 % 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: -2.48 (0.08), residues: 10345 helix: 0.10 (0.08), residues: 4150 sheet: -2.01 (0.12), residues: 1595 loop : -3.25 (0.08), residues: 4600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP K 184 HIS 0.007 0.001 HIS T 72 PHE 0.038 0.002 PHE W 163 TYR 0.033 0.002 TYR d 225 ARG 0.010 0.001 ARG d 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 838 time to evaluate : 7.233 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. REVERT: A 117 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8346 (mtm) REVERT: A 157 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.7274 (p90) REVERT: B 108 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 184 MET cc_start: 0.8100 (tpt) cc_final: 0.7763 (tpt) REVERT: B 240 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.5896 (m-70) REVERT: E 108 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8908 (tt) REVERT: E 117 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8719 (tm-30) REVERT: E 122 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (ttm110) REVERT: F 150 MET cc_start: 0.8215 (tmm) cc_final: 0.7983 (tmm) REVERT: G 21 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.7681 (ttm-80) REVERT: G 112 ASP cc_start: 0.8519 (p0) cc_final: 0.8296 (p0) REVERT: G 113 MET cc_start: 0.7342 (pmm) cc_final: 0.7053 (pmm) REVERT: G 206 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8779 (pp) REVERT: H 57 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7579 (mm-40) REVERT: H 85 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: H 127 MET cc_start: 0.8658 (mmt) cc_final: 0.8088 (mmt) REVERT: I 119 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7117 (p90) REVERT: J 111 GLU cc_start: 0.6765 (pp20) cc_final: 0.6345 (pp20) REVERT: J 167 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8994 (tm) REVERT: K 100 MET cc_start: 0.8674 (mmm) cc_final: 0.8458 (mpp) REVERT: K 136 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8156 (t80) REVERT: L 213 ASP cc_start: 0.6799 (p0) cc_final: 0.6563 (p0) REVERT: N 120 MET cc_start: 0.7891 (ttp) cc_final: 0.7449 (ttp) REVERT: O 111 GLN cc_start: 0.8515 (mt0) cc_final: 0.8175 (mt0) REVERT: O 155 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: O 188 HIS cc_start: 0.8237 (t-90) cc_final: 0.8037 (t70) REVERT: O 198 PHE cc_start: 0.6289 (t80) cc_final: 0.6008 (t80) REVERT: P 71 ASP cc_start: 0.7392 (p0) cc_final: 0.7030 (p0) REVERT: P 163 CYS cc_start: 0.8236 (t) cc_final: 0.7992 (t) REVERT: R 81 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8952 (tm) REVERT: R 192 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7777 (mmtp) REVERT: T 122 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7216 (t80) REVERT: T 185 THR cc_start: 0.7737 (p) cc_final: 0.7411 (t) REVERT: U 138 MET cc_start: 0.7731 (mmp) cc_final: 0.7261 (mmp) REVERT: W 77 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7610 (tm-30) REVERT: W 84 TYR cc_start: 0.7877 (t80) cc_final: 0.7661 (t80) REVERT: W 170 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: X 40 GLU cc_start: 0.6736 (tp30) cc_final: 0.6197 (tp30) REVERT: X 132 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.7207 (m170) REVERT: X 165 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: Y 45 MET cc_start: 0.8492 (mpp) cc_final: 0.7747 (mpp) REVERT: Z 83 MET cc_start: 0.7742 (mmm) cc_final: 0.7512 (mmm) REVERT: Z 148 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8629 (tm) REVERT: Z 149 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8954 (pp) REVERT: Z 213 ASP cc_start: 0.6093 (p0) cc_final: 0.5745 (p0) REVERT: b 193 GLN cc_start: 0.8629 (mp10) cc_final: 0.8386 (mp10) REVERT: d 145 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: d 224 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8998 (pp) REVERT: d 315 GLN cc_start: 0.8104 (tp40) cc_final: 0.7862 (tp40) REVERT: e 89 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9168 (pt) REVERT: e 267 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8298 (mt) REVERT: e 393 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8427 (mm) REVERT: f 64 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7325 (tp) REVERT: f 101 ASP cc_start: 0.8567 (t0) cc_final: 0.8249 (t70) REVERT: f 110 TYR cc_start: 0.7449 (p90) cc_final: 0.7162 (p90) REVERT: f 182 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8701 (tt) REVERT: g 86 LEU cc_start: 0.6223 (tt) cc_final: 0.5783 (mt) REVERT: g 88 TYR cc_start: 0.7540 (t80) cc_final: 0.7288 (t80) REVERT: g 132 TYR cc_start: 0.8197 (m-10) cc_final: 0.7850 (m-10) REVERT: g 348 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7937 (mm) REVERT: g 368 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8889 (mm) REVERT: h 80 MET cc_start: 0.5016 (mpp) cc_final: 0.4758 (mpp) REVERT: h 113 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7983 (tmm-80) REVERT: h 180 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8422 (mt) REVERT: l 129 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8747 (mm) REVERT: m 86 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6698 (pm20) REVERT: m 137 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (mmm-85) REVERT: m 138 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8847 (pt) REVERT: m 143 TYR cc_start: 0.7428 (t80) cc_final: 0.7121 (t80) REVERT: m 157 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8362 (mp) REVERT: m 233 ARG cc_start: 0.7097 (tmt170) cc_final: 0.6704 (tpt90) outliers start: 322 outliers final: 198 residues processed: 1106 average time/residue: 0.6779 time to fit residues: 1316.6425 Evaluate side-chains 1025 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 792 time to evaluate : 6.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 119 PHE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 69 MET Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 5 MET Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 157 ARG Chi-restraints excluded: chain T residue 122 TYR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain Z residue 195 ILE Chi-restraints excluded: chain Z residue 203 ILE Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 151 ILE Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 306 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 377 CYS Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 216 ILE Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 275 GLU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 284 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 179 GLU Chi-restraints excluded: chain e residue 204 MET Chi-restraints excluded: chain e residue 230 VAL Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 246 MET Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 296 MET Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 63 GLN Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 103 THR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain f residue 321 THR Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 168 TYR Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 259 MET Chi-restraints excluded: chain g residue 342 LEU Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 368 ILE Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 134 LEU Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 235 PHE Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 157 LEU Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 137 ARG Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 141 VAL Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 963 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 chunk 569 optimal weight: 6.9990 chunk 729 optimal weight: 0.6980 chunk 565 optimal weight: 6.9990 chunk 841 optimal weight: 20.0000 chunk 558 optimal weight: 0.7980 chunk 995 optimal weight: 0.1980 chunk 623 optimal weight: 4.9990 chunk 607 optimal weight: 0.9990 chunk 459 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 84 ASN C 175 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 118 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 201 GLN T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 GLN d 241 ASN d 332 ASN ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 77257 Z= 0.207 Angle : 0.757 12.862 104890 Z= 0.384 Chirality : 0.046 0.416 12239 Planarity : 0.005 0.110 13718 Dihedral : 8.164 164.540 11422 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.36 % Favored : 88.27 % Rotamer: Outliers : 4.30 % Allowed : 19.15 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.25 % 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: -2.27 (0.08), residues: 10345 helix: 0.35 (0.08), residues: 4156 sheet: -1.92 (0.12), residues: 1611 loop : -3.21 (0.08), residues: 4578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 184 HIS 0.008 0.001 HIS h 205 PHE 0.032 0.001 PHE W 163 TYR 0.047 0.001 TYR A 228 ARG 0.015 0.000 ARG l 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 876 time to evaluate : 6.787 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. REVERT: A 88 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7420 (mtp180) REVERT: A 157 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7398 (p90) REVERT: A 220 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 108 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 184 MET cc_start: 0.8090 (tpt) cc_final: 0.7707 (tpt) REVERT: B 240 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.5815 (m-70) REVERT: C 115 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8760 (mtpt) REVERT: E 8 ASN cc_start: 0.5802 (OUTLIER) cc_final: 0.5068 (p0) REVERT: E 108 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8840 (tt) REVERT: E 122 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (ttm110) REVERT: F 75 MET cc_start: 0.8203 (tpp) cc_final: 0.7907 (tpp) REVERT: F 150 MET cc_start: 0.8122 (tmm) cc_final: 0.7889 (tmm) REVERT: G 21 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.7585 (ttm-80) REVERT: G 113 MET cc_start: 0.7238 (pmm) cc_final: 0.7023 (pmm) REVERT: G 206 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (pp) REVERT: H 85 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: I 96 GLU cc_start: 0.8315 (pp20) cc_final: 0.8091 (pp20) REVERT: I 119 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6876 (p90) REVERT: J 111 GLU cc_start: 0.6566 (pp20) cc_final: 0.6317 (pp20) REVERT: J 167 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8991 (tm) REVERT: K 136 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8283 (t80) REVERT: L 213 ASP cc_start: 0.6945 (p0) cc_final: 0.6719 (p0) REVERT: M 110 MET cc_start: 0.7908 (ptp) cc_final: 0.7627 (ptp) REVERT: O 155 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: O 198 PHE cc_start: 0.6210 (t80) cc_final: 0.5985 (t80) REVERT: P 71 ASP cc_start: 0.7572 (p0) cc_final: 0.7346 (p0) REVERT: R 81 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8905 (tm) REVERT: R 192 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7811 (mmtp) REVERT: R 206 MET cc_start: 0.6512 (mpp) cc_final: 0.6098 (pmm) REVERT: S 68 ASN cc_start: 0.6491 (t0) cc_final: 0.6029 (t0) REVERT: T 117 MET cc_start: 0.7739 (tpt) cc_final: 0.7048 (tpp) REVERT: T 122 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7211 (t80) REVERT: T 185 THR cc_start: 0.7853 (p) cc_final: 0.7464 (t) REVERT: U 117 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7536 (tpp80) REVERT: V 24 MET cc_start: 0.7342 (mmm) cc_final: 0.7065 (mmm) REVERT: V 157 GLU cc_start: 0.8039 (tp30) cc_final: 0.7791 (tp30) REVERT: W 77 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7588 (tm-30) REVERT: W 84 TYR cc_start: 0.7905 (t80) cc_final: 0.7672 (t80) REVERT: X 132 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7176 (m170) REVERT: X 141 SER cc_start: 0.7558 (OUTLIER) cc_final: 0.7291 (t) REVERT: X 165 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: X 166 GLU cc_start: 0.7865 (tp30) cc_final: 0.7648 (tp30) REVERT: Y 45 MET cc_start: 0.8431 (mpp) cc_final: 0.7918 (mpp) REVERT: Z 83 MET cc_start: 0.7686 (mmm) cc_final: 0.7263 (tpp) REVERT: Z 131 GLN cc_start: 0.7578 (mp10) cc_final: 0.7367 (mm110) REVERT: Z 148 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8564 (tm) REVERT: Z 149 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8770 (pp) REVERT: Z 213 ASP cc_start: 0.6377 (p0) cc_final: 0.6080 (p0) REVERT: b 193 GLN cc_start: 0.8567 (mp10) cc_final: 0.8303 (mp10) REVERT: d 145 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: d 224 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8793 (pp) REVERT: d 315 GLN cc_start: 0.8069 (tp40) cc_final: 0.7823 (tp40) REVERT: e 267 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8316 (mt) REVERT: e 393 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8419 (mm) REVERT: f 61 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8646 (mt) REVERT: f 64 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7268 (tp) REVERT: f 101 ASP cc_start: 0.8494 (t0) cc_final: 0.8260 (t70) REVERT: f 110 TYR cc_start: 0.7375 (p90) cc_final: 0.7109 (p90) REVERT: f 182 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8702 (tt) REVERT: g 88 TYR cc_start: 0.7337 (t80) cc_final: 0.7026 (t80) REVERT: g 132 TYR cc_start: 0.8131 (m-10) cc_final: 0.7889 (m-10) REVERT: g 177 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6776 (p) REVERT: g 281 SER cc_start: 0.8162 (m) cc_final: 0.7875 (m) REVERT: g 348 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7866 (mm) REVERT: h 80 MET cc_start: 0.5860 (mpp) cc_final: 0.5328 (mpp) REVERT: h 113 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7916 (tmm-80) REVERT: h 180 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8393 (mt) REVERT: h 234 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8563 (pp) REVERT: l 129 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (mm) REVERT: l 148 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8113 (t70) REVERT: m 86 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: m 87 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: m 138 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8836 (pt) REVERT: m 157 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8317 (mp) REVERT: m 233 ARG cc_start: 0.7091 (tmt170) cc_final: 0.6568 (tpt90) outliers start: 304 outliers final: 188 residues processed: 1122 average time/residue: 0.6896 time to fit residues: 1354.2896 Evaluate side-chains 1040 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 813 time to evaluate : 6.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 119 PHE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 157 ARG Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 122 TYR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 168 GLN Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain Z residue 195 ILE Chi-restraints excluded: chain Z residue 203 ILE Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 138 MET Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 306 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 385 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 164 MET Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 216 ILE Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 281 ILE Chi-restraints excluded: chain d residue 284 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 111 TYR Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 179 GLU Chi-restraints excluded: chain e residue 204 MET Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 296 MET Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 411 GLU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 75 ASN Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain g residue 168 TYR Chi-restraints excluded: chain g residue 177 VAL Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 259 MET Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 134 LEU Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 180 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 234 LEU Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 157 LEU Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 87 GLU Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 201 PHE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 615 optimal weight: 0.4980 chunk 397 optimal weight: 0.1980 chunk 594 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 632 optimal weight: 0.8980 chunk 678 optimal weight: 20.0000 chunk 492 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 782 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 84 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN G 92 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 201 GLN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 168 GLN ** Y 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 379 ASN d 332 ASN e 83 GLN ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 258 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 77257 Z= 0.193 Angle : 0.753 12.687 104890 Z= 0.381 Chirality : 0.046 0.384 12239 Planarity : 0.005 0.109 13718 Dihedral : 7.947 179.889 11414 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.42 % Favored : 88.23 % Rotamer: Outliers : 3.86 % Allowed : 20.05 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.24 % 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: -2.11 (0.08), residues: 10345 helix: 0.51 (0.08), residues: 4158 sheet: -1.82 (0.13), residues: 1566 loop : -3.15 (0.08), residues: 4621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 184 HIS 0.008 0.001 HIS m 136 PHE 0.036 0.001 PHE W 163 TYR 0.039 0.001 TYR A 228 ARG 0.010 0.000 ARG W 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 875 time to evaluate : 6.691 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. REVERT: A 88 ARG cc_start: 0.7676 (mmm160) cc_final: 0.7430 (mtp180) REVERT: A 157 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.7378 (p90) REVERT: B 108 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 184 MET cc_start: 0.8102 (tpt) cc_final: 0.7759 (tpt) REVERT: B 240 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.5863 (m-70) REVERT: C 115 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8743 (mtpt) REVERT: E 8 ASN cc_start: 0.5694 (OUTLIER) cc_final: 0.5012 (p0) REVERT: E 108 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 117 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8672 (tm-30) REVERT: E 122 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: F 75 MET cc_start: 0.8262 (tpp) cc_final: 0.7982 (tpp) REVERT: F 150 MET cc_start: 0.8096 (tmm) cc_final: 0.7890 (tmm) REVERT: G 21 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7561 (ttm-80) REVERT: G 206 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8695 (pp) REVERT: H 63 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9098 (tp) REVERT: H 85 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: J 167 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8977 (tm) REVERT: K 40 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: K 136 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8227 (t80) REVERT: L 213 ASP cc_start: 0.6953 (p0) cc_final: 0.6734 (p0) REVERT: M 110 MET cc_start: 0.7918 (ptp) cc_final: 0.7666 (ptp) REVERT: O 111 GLN cc_start: 0.8439 (mt0) cc_final: 0.8008 (mt0) REVERT: R 109 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8951 (t) REVERT: R 147 ASP cc_start: 0.8173 (m-30) cc_final: 0.7588 (t70) REVERT: R 189 MET cc_start: 0.6453 (tpp) cc_final: 0.6159 (tpp) REVERT: R 192 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7879 (mmtp) REVERT: R 206 MET cc_start: 0.6663 (mpp) cc_final: 0.5996 (pmm) REVERT: T 101 ASN cc_start: 0.8674 (t0) cc_final: 0.8430 (m-40) REVERT: T 117 MET cc_start: 0.7757 (tpt) cc_final: 0.7016 (tpp) REVERT: T 185 THR cc_start: 0.7665 (p) cc_final: 0.7382 (t) REVERT: U 117 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7535 (tpp80) REVERT: U 138 MET cc_start: 0.7519 (mmp) cc_final: 0.7009 (mmp) REVERT: V 24 MET cc_start: 0.7264 (mmm) cc_final: 0.7032 (mmm) REVERT: V 54 MET cc_start: 0.7283 (ttt) cc_final: 0.6787 (tmm) REVERT: V 157 GLU cc_start: 0.7971 (tp30) cc_final: 0.7742 (tp30) REVERT: W 77 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7479 (tm-30) REVERT: W 84 TYR cc_start: 0.7865 (t80) cc_final: 0.7564 (t80) REVERT: X 132 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.7114 (m170) REVERT: X 141 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7234 (t) REVERT: X 165 GLU cc_start: 0.7733 (pp20) cc_final: 0.7530 (pp20) REVERT: Y 45 MET cc_start: 0.8297 (mpp) cc_final: 0.7853 (mpp) REVERT: Z 83 MET cc_start: 0.7662 (mmm) cc_final: 0.7220 (tpp) REVERT: Z 131 GLN cc_start: 0.7555 (mp10) cc_final: 0.7349 (mm110) REVERT: Z 148 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8528 (tm) REVERT: Z 149 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8632 (pp) REVERT: Z 213 ASP cc_start: 0.6380 (p0) cc_final: 0.6047 (p0) REVERT: b 193 GLN cc_start: 0.8563 (mp10) cc_final: 0.8277 (mp10) REVERT: d 145 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: d 315 GLN cc_start: 0.8036 (tp40) cc_final: 0.7812 (tp40) REVERT: d 366 GLN cc_start: 0.8838 (pp30) cc_final: 0.8323 (pp30) REVERT: d 389 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6104 (t0) REVERT: e 120 ASP cc_start: 0.8265 (p0) cc_final: 0.7613 (p0) REVERT: e 267 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8288 (mt) REVERT: e 284 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7609 (tm-30) REVERT: e 393 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8403 (mm) REVERT: f 64 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7175 (tp) REVERT: f 101 ASP cc_start: 0.8486 (t0) cc_final: 0.8238 (t70) REVERT: f 110 TYR cc_start: 0.7285 (p90) cc_final: 0.7012 (p90) REVERT: f 182 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (tt) REVERT: g 88 TYR cc_start: 0.7417 (t80) cc_final: 0.7014 (t80) REVERT: g 132 TYR cc_start: 0.8074 (m-10) cc_final: 0.7811 (m-10) REVERT: g 281 SER cc_start: 0.8165 (m) cc_final: 0.7864 (m) REVERT: g 348 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7829 (mm) REVERT: g 368 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8892 (mm) REVERT: h 80 MET cc_start: 0.6157 (mpp) cc_final: 0.5623 (mpp) REVERT: h 113 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7894 (tmm-80) REVERT: h 189 TYR cc_start: 0.8542 (p90) cc_final: 0.8315 (p90) REVERT: h 248 MET cc_start: 0.9126 (mmt) cc_final: 0.8920 (mmm) REVERT: l 148 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7972 (t70) REVERT: m 86 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6761 (pm20) REVERT: m 87 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: m 104 MET cc_start: 0.7654 (mtp) cc_final: 0.7014 (mtm) REVERT: m 138 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8765 (pt) REVERT: m 157 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8324 (mp) outliers start: 273 outliers final: 178 residues processed: 1103 average time/residue: 0.6743 time to fit residues: 1300.2508 Evaluate side-chains 1016 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 806 time to evaluate : 6.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 40 TYR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 205 ASP Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain S residue 20 HIS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 152 LEU Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 136 TYR Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain Z residue 195 ILE Chi-restraints excluded: chain Z residue 203 ILE Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 138 MET Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 306 LEU Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 148 CYS Chi-restraints excluded: chain d residue 164 MET Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 241 ASN Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 284 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 389 ASP Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 204 MET Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 75 ASN Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 168 TYR Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 368 ILE Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 251 ILE Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 251 LEU Chi-restraints excluded: chain l residue 261 LEU Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 87 GLU Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 201 PHE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 905 optimal weight: 9.9990 chunk 953 optimal weight: 4.9990 chunk 870 optimal weight: 30.0000 chunk 927 optimal weight: 20.0000 chunk 558 optimal weight: 0.9990 chunk 404 optimal weight: 1.9990 chunk 728 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 838 optimal weight: 10.0000 chunk 877 optimal weight: 30.0000 chunk 924 optimal weight: 0.0070 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN G 92 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 77257 Z= 0.248 Angle : 0.771 11.783 104890 Z= 0.390 Chirality : 0.047 0.369 12239 Planarity : 0.005 0.111 13718 Dihedral : 7.831 168.073 11402 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.81 % Favored : 87.92 % Rotamer: Outliers : 3.79 % Allowed : 20.34 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.21 % 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: -2.03 (0.08), residues: 10345 helix: 0.58 (0.08), residues: 4160 sheet: -1.80 (0.13), residues: 1578 loop : -3.12 (0.08), residues: 4607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 184 HIS 0.010 0.001 HIS m 136 PHE 0.047 0.002 PHE W 163 TYR 0.033 0.002 TYR d 225 ARG 0.015 0.001 ARG U 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 836 time to evaluate : 7.115 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7428 (mtp180) REVERT: A 157 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 220 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8705 (mt) REVERT: B 108 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 184 MET cc_start: 0.8042 (tpt) cc_final: 0.7686 (tpt) REVERT: B 240 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.5882 (m-70) REVERT: C 115 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8723 (mtpt) REVERT: E 8 ASN cc_start: 0.5828 (OUTLIER) cc_final: 0.5132 (p0) REVERT: E 108 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8952 (tt) REVERT: E 117 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8657 (tm-30) REVERT: E 122 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8304 (ttm110) REVERT: F 75 MET cc_start: 0.8291 (tpp) cc_final: 0.7995 (tpp) REVERT: G 21 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.7593 (ttm-80) REVERT: G 113 MET cc_start: 0.7308 (pmm) cc_final: 0.6832 (pmm) REVERT: G 206 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8573 (pp) REVERT: H 63 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9034 (tp) REVERT: H 85 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: I 119 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6985 (p90) REVERT: J 167 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8930 (tm) REVERT: L 158 MET cc_start: 0.7808 (mmm) cc_final: 0.7510 (tpp) REVERT: L 184 GLU cc_start: 0.7707 (tt0) cc_final: 0.7360 (tt0) REVERT: M 110 MET cc_start: 0.8100 (ptp) cc_final: 0.7856 (ptp) REVERT: O 111 GLN cc_start: 0.8462 (mt0) cc_final: 0.8072 (mt0) REVERT: O 198 PHE cc_start: 0.6256 (t80) cc_final: 0.5988 (t80) REVERT: R 109 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8945 (m) REVERT: R 147 ASP cc_start: 0.8276 (m-30) cc_final: 0.8043 (m-30) REVERT: R 189 MET cc_start: 0.6439 (tpp) cc_final: 0.6206 (tpp) REVERT: R 192 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7892 (mmtp) REVERT: R 206 MET cc_start: 0.6564 (mpp) cc_final: 0.6055 (pmm) REVERT: T 75 MET cc_start: 0.7383 (tpp) cc_final: 0.7020 (tpp) REVERT: T 101 ASN cc_start: 0.8688 (t0) cc_final: 0.8444 (m-40) REVERT: T 117 MET cc_start: 0.7685 (tpt) cc_final: 0.7030 (tpp) REVERT: T 122 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7184 (t80) REVERT: T 185 THR cc_start: 0.7695 (p) cc_final: 0.7457 (t) REVERT: U 117 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7615 (tpp80) REVERT: V 24 MET cc_start: 0.7377 (mmm) cc_final: 0.7071 (tpp) REVERT: V 54 MET cc_start: 0.7468 (ttt) cc_final: 0.7173 (ppp) REVERT: W 84 TYR cc_start: 0.7862 (t80) cc_final: 0.7570 (t80) REVERT: W 170 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8504 (mmm) REVERT: X 37 LYS cc_start: 0.8442 (tptp) cc_final: 0.8230 (tppt) REVERT: X 132 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.7219 (m170) REVERT: X 141 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7420 (t) REVERT: X 166 GLU cc_start: 0.8131 (tp30) cc_final: 0.7898 (tp30) REVERT: X 185 LYS cc_start: 0.8780 (tppt) cc_final: 0.8531 (tppt) REVERT: Y 45 MET cc_start: 0.8395 (mpp) cc_final: 0.7860 (mpp) REVERT: Z 83 MET cc_start: 0.7689 (mmm) cc_final: 0.7249 (tpp) REVERT: Z 148 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8600 (tm) REVERT: Z 149 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8733 (pp) REVERT: Z 213 ASP cc_start: 0.6331 (p0) cc_final: 0.5958 (p0) REVERT: b 193 GLN cc_start: 0.8605 (mp10) cc_final: 0.8296 (mp10) REVERT: c 144 ARG cc_start: 0.7233 (ptt-90) cc_final: 0.6991 (ptt-90) REVERT: d 107 MET cc_start: 0.7708 (pmm) cc_final: 0.7277 (pmm) REVERT: d 241 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7216 (t0) REVERT: d 366 GLN cc_start: 0.8841 (pp30) cc_final: 0.8403 (pp30) REVERT: e 267 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8377 (mt) REVERT: e 284 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7742 (tm-30) REVERT: e 393 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8425 (mm) REVERT: e 399 PHE cc_start: 0.8080 (t80) cc_final: 0.7419 (t80) REVERT: e 412 GLN cc_start: 0.7168 (tp-100) cc_final: 0.6753 (pt0) REVERT: f 64 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7481 (tp) REVERT: f 101 ASP cc_start: 0.8515 (t0) cc_final: 0.8254 (t70) REVERT: f 110 TYR cc_start: 0.7327 (p90) cc_final: 0.7072 (p90) REVERT: f 182 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8766 (tt) REVERT: g 88 TYR cc_start: 0.7325 (t80) cc_final: 0.6938 (t80) REVERT: g 132 TYR cc_start: 0.8023 (m-10) cc_final: 0.7817 (m-10) REVERT: g 177 VAL cc_start: 0.7010 (OUTLIER) cc_final: 0.6669 (p) REVERT: g 281 SER cc_start: 0.8176 (m) cc_final: 0.7882 (m) REVERT: g 368 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8907 (mm) REVERT: h 113 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7836 (tmm-80) REVERT: h 189 TYR cc_start: 0.8567 (p90) cc_final: 0.8349 (p90) REVERT: l 129 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8753 (mm) REVERT: l 148 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.7998 (t70) REVERT: m 86 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: m 87 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: m 138 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8812 (pt) REVERT: m 157 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8356 (mp) outliers start: 268 outliers final: 193 residues processed: 1058 average time/residue: 0.6845 time to fit residues: 1274.7143 Evaluate side-chains 1028 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 801 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 119 PHE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain P residue 22 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain S residue 20 HIS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 122 TYR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 152 LEU Chi-restraints excluded: chain W residue 170 MET Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 63 CYS Chi-restraints excluded: chain Y residue 136 TYR Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain Z residue 195 ILE Chi-restraints excluded: chain Z residue 203 ILE Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain c residue 132 THR Chi-restraints excluded: chain c residue 138 MET Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 306 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 PHE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 148 CYS Chi-restraints excluded: chain d residue 164 MET Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 216 ILE Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 241 ASN Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 284 ILE Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 316 LEU Chi-restraints excluded: chain d residue 351 ILE Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 278 GLN Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 75 ASN Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 177 VAL Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 310 MET Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 368 ILE Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 99 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 251 ILE Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 240 ASP Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 251 LEU Chi-restraints excluded: chain l residue 261 LEU Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 87 GLU Chi-restraints excluded: chain m residue 128 TYR Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 201 PHE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 609 optimal weight: 0.5980 chunk 981 optimal weight: 30.0000 chunk 598 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 682 optimal weight: 2.9990 chunk 1029 optimal weight: 5.9990 chunk 947 optimal weight: 8.9990 chunk 819 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 633 optimal weight: 7.9990 chunk 502 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 167 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 GLN S 68 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 193 ASN ** Y 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 GLN a 188 GLN ** c 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 302 ASN ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 278 ASN ** m 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 77257 Z= 0.386 Angle : 0.844 11.952 104890 Z= 0.431 Chirality : 0.049 0.373 12239 Planarity : 0.006 0.114 13718 Dihedral : 7.992 166.250 11395 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.04 % Favored : 86.67 % Rotamer: Outliers : 3.63 % Allowed : 20.62 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.21 % 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: -2.14 (0.08), residues: 10345 helix: 0.46 (0.08), residues: 4158 sheet: -1.84 (0.12), residues: 1646 loop : -3.16 (0.08), residues: 4541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP K 184 HIS 0.014 0.002 HIS X 32 PHE 0.035 0.002 PHE I 163 TYR 0.047 0.002 TYR W 95 ARG 0.019 0.001 ARG W 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 804 time to evaluate : 6.713 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 157 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7467 (p90) REVERT: A 220 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8806 (mt) REVERT: B 108 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 184 MET cc_start: 0.8193 (tpt) cc_final: 0.7866 (tpt) REVERT: B 240 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.5918 (m-70) REVERT: E 8 ASN cc_start: 0.5863 (OUTLIER) cc_final: 0.5428 (p0) REVERT: E 68 ASN cc_start: 0.7751 (t0) cc_final: 0.7239 (t0) REVERT: E 108 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9002 (tt) REVERT: E 117 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8684 (tm-30) REVERT: E 122 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (ttm110) REVERT: F 75 MET cc_start: 0.8475 (tpp) cc_final: 0.8041 (tpp) REVERT: G 21 ARG cc_start: 0.8535 (mtp-110) cc_final: 0.7708 (ttm-80) REVERT: G 113 MET cc_start: 0.7591 (pmm) cc_final: 0.7270 (pmm) REVERT: H 85 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: I 102 TYR cc_start: 0.8880 (m-80) cc_final: 0.8658 (m-80) REVERT: I 119 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7691 (p90) REVERT: J 167 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9054 (tm) REVERT: K 45 MET cc_start: 0.8189 (mpp) cc_final: 0.7959 (mpp) REVERT: K 100 MET cc_start: 0.8337 (mpp) cc_final: 0.7893 (mpp) REVERT: R 189 MET cc_start: 0.6378 (tpp) cc_final: 0.6166 (tpp) REVERT: R 192 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7929 (mmtp) REVERT: R 206 MET cc_start: 0.6668 (mpp) cc_final: 0.6425 (pmm) REVERT: S 68 ASN cc_start: 0.7284 (t0) cc_final: 0.7004 (t0) REVERT: T 117 MET cc_start: 0.7790 (tpt) cc_final: 0.7230 (tpp) REVERT: T 122 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7249 (t80) REVERT: T 185 THR cc_start: 0.7871 (p) cc_final: 0.7556 (t) REVERT: U 117 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7736 (tpp80) REVERT: W 11 MET cc_start: 0.7035 (ttt) cc_final: 0.6834 (ttt) REVERT: W 77 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7883 (tm-30) REVERT: W 84 TYR cc_start: 0.7932 (t80) cc_final: 0.7690 (t80) REVERT: X 37 LYS cc_start: 0.8535 (tptp) cc_final: 0.8280 (tppp) REVERT: X 132 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.7193 (m170) REVERT: X 141 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7820 (t) REVERT: X 185 LYS cc_start: 0.8765 (tppt) cc_final: 0.8496 (tppt) REVERT: Y 45 MET cc_start: 0.8422 (mpp) cc_final: 0.7722 (mpp) REVERT: Z 43 CYS cc_start: 0.4638 (p) cc_final: 0.4378 (p) REVERT: Z 148 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8774 (tm) REVERT: c 148 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: d 241 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7974 (t0) REVERT: d 366 GLN cc_start: 0.8825 (pp30) cc_final: 0.8464 (pp30) REVERT: e 267 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8667 (mt) REVERT: e 284 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7946 (tm-30) REVERT: e 393 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8518 (mm) REVERT: e 399 PHE cc_start: 0.8265 (t80) cc_final: 0.7589 (t80) REVERT: f 64 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7741 (tp) REVERT: f 101 ASP cc_start: 0.8503 (t0) cc_final: 0.8239 (t70) REVERT: f 110 TYR cc_start: 0.7778 (p90) cc_final: 0.7494 (p90) REVERT: f 182 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (tt) REVERT: g 88 TYR cc_start: 0.7367 (t80) cc_final: 0.7045 (t80) REVERT: g 132 TYR cc_start: 0.8153 (m-10) cc_final: 0.7904 (m-10) REVERT: g 168 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5507 (p90) REVERT: g 177 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7141 (p) REVERT: g 281 SER cc_start: 0.8170 (m) cc_final: 0.7925 (m) REVERT: g 368 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8949 (mm) REVERT: h 113 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8102 (tmm-80) REVERT: l 148 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8213 (t70) REVERT: l 161 ASP cc_start: 0.5641 (p0) cc_final: 0.5377 (p0) REVERT: m 86 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6672 (pm20) REVERT: m 87 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: m 138 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8858 (pt) REVERT: m 157 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8415 (mp) REVERT: m 184 GLN cc_start: 0.8991 (tp40) cc_final: 0.8781 (tp40) outliers start: 257 outliers final: 187 residues processed: 1024 average time/residue: 0.6993 time to fit residues: 1264.8364 Evaluate side-chains 995 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 779 time to evaluate : 6.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 24 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain I residue 119 PHE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 214 MET Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 184 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 151 ASP Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 42 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain R residue 47 CYS Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 182 GLN Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain S residue 20 HIS Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain T residue 122 TYR Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 80 MET Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 190 THR Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain U residue 210 PHE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 55 THR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain W residue 13 MET Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 152 LEU Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 44 LEU Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 132 HIS Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 150 THR Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 174 VAL Chi-restraints excluded: chain Y residue 188 SER Chi-restraints excluded: chain Z residue 106 VAL Chi-restraints excluded: chain Z residue 135 PHE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 149 LEU Chi-restraints excluded: chain Z residue 174 LEU Chi-restraints excluded: chain Z residue 195 ILE Chi-restraints excluded: chain Z residue 203 ILE Chi-restraints excluded: chain a residue 5 MET Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 MET Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain c residue 138 MET Chi-restraints excluded: chain c residue 148 GLN Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 PHE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 148 CYS Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 201 VAL Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain d residue 241 ASN Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 351 ILE Chi-restraints excluded: chain d residue 412 MET Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 100 THR Chi-restraints excluded: chain e residue 236 VAL Chi-restraints excluded: chain e residue 246 MET Chi-restraints excluded: chain e residue 267 ILE Chi-restraints excluded: chain e residue 278 GLN Chi-restraints excluded: chain e residue 311 THR Chi-restraints excluded: chain e residue 322 LEU Chi-restraints excluded: chain e residue 328 ASP Chi-restraints excluded: chain e residue 360 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain e residue 416 PHE Chi-restraints excluded: chain f residue 50 LEU Chi-restraints excluded: chain f residue 64 LEU Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 71 VAL Chi-restraints excluded: chain f residue 75 ASN Chi-restraints excluded: chain f residue 79 TYR Chi-restraints excluded: chain f residue 178 THR Chi-restraints excluded: chain f residue 182 LEU Chi-restraints excluded: chain f residue 320 ILE Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain g residue 168 TYR Chi-restraints excluded: chain g residue 177 VAL Chi-restraints excluded: chain g residue 182 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 348 LEU Chi-restraints excluded: chain g residue 368 ILE Chi-restraints excluded: chain g residue 390 ASP Chi-restraints excluded: chain g residue 397 LYS Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 118 ASN Chi-restraints excluded: chain h residue 137 LEU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain h residue 219 LEU Chi-restraints excluded: chain h residue 251 ILE Chi-restraints excluded: chain l residue 126 ARG Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain l residue 261 LEU Chi-restraints excluded: chain m residue 86 GLU Chi-restraints excluded: chain m residue 87 GLU Chi-restraints excluded: chain m residue 138 LEU Chi-restraints excluded: chain m residue 157 ILE Chi-restraints excluded: chain m residue 201 PHE Chi-restraints excluded: chain m residue 211 TYR Chi-restraints excluded: chain m residue 249 VAL Chi-restraints excluded: chain m residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 650 optimal weight: 10.0000 chunk 872 optimal weight: 0.0030 chunk 251 optimal weight: 0.9990 chunk 755 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 820 optimal weight: 40.0000 chunk 343 optimal weight: 0.5980 chunk 842 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 379 ASN ** d 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074001 restraints weight = 244080.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075849 restraints weight = 136534.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077280 restraints weight = 83287.090| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 77257 Z= 0.201 Angle : 0.782 12.293 104890 Z= 0.395 Chirality : 0.047 0.338 12239 Planarity : 0.005 0.111 13718 Dihedral : 7.745 163.666 11393 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.94 % Favored : 88.79 % Rotamer: Outliers : 3.05 % Allowed : 21.31 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.08), residues: 10345 helix: 0.67 (0.08), residues: 4145 sheet: -1.69 (0.13), residues: 1551 loop : -3.09 (0.08), residues: 4649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Q 156 HIS 0.009 0.001 HIS m 136 PHE 0.037 0.002 PHE A 198 TYR 0.028 0.001 TYR d 225 ARG 0.012 0.001 ARG J 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20809.16 seconds wall clock time: 358 minutes 46.12 seconds (21526.12 seconds total)